Nickel in PDB 4z42: Crystal Structure of Urease From Yersinia Enterocolitica
Enzymatic activity of Crystal Structure of Urease From Yersinia Enterocolitica
All present enzymatic activity of Crystal Structure of Urease From Yersinia Enterocolitica:
3.5.1.5;
Protein crystallography data
The structure of Crystal Structure of Urease From Yersinia Enterocolitica, PDB code: 4z42
was solved by
G.Studer,
R.P.Jakob,
M.A.Mahi,
U.Wiesand,
T.Schwede,
T.Maier,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.71 /
3.01
|
|
Space group
|
H 3 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
157.200,
157.200,
774.620,
90.00,
90.00,
120.00
|
|
R / Rfree (%)
|
27.7 /
29.8
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of Urease From Yersinia Enterocolitica
(pdb code 4z42). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the
Crystal Structure of Urease From Yersinia Enterocolitica, PDB code: 4z42:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Nickel binding site 1 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 1 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 1 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni601
b:81.5
occ:1.00
|
HE1
|
C:HIS251
|
1.9
|
0.6
|
1.0
|
|
NI
|
C:NI602
|
2.0
|
82.8
|
1.0
|
|
CE1
|
C:HIS251
|
2.4
|
0.6
|
1.0
|
|
ND1
|
C:HIS251
|
2.5
|
0.7
|
1.0
|
|
HE2
|
C:HIS224
|
2.9
|
0.4
|
1.0
|
|
HE1
|
C:HIS139
|
2.9
|
87.8
|
1.0
|
|
HE2
|
C:HIS277
|
3.0
|
0.6
|
1.0
|
|
OD2
|
C:ASP365
|
3.0
|
0.7
|
1.0
|
|
HE2
|
C:HIS141
|
3.4
|
92.6
|
1.0
|
|
HE2
|
C:HIS325
|
3.4
|
0.5
|
1.0
|
|
CE1
|
C:HIS139
|
3.5
|
87.8
|
1.0
|
|
NE2
|
C:HIS139
|
3.5
|
87.2
|
1.0
|
|
NE2
|
C:HIS277
|
3.6
|
0.6
|
1.0
|
|
NE2
|
C:HIS224
|
3.6
|
0.4
|
1.0
|
|
CG
|
C:ASP365
|
3.8
|
0.9
|
1.0
|
|
NE2
|
C:HIS251
|
3.8
|
0.9
|
1.0
|
|
OD1
|
C:ASP365
|
3.8
|
0.2
|
1.0
|
|
O
|
C:GLY172
|
3.8
|
92.7
|
1.0
|
|
HD2
|
C:HIS277
|
3.9
|
0.5
|
1.0
|
|
CG
|
C:HIS251
|
3.9
|
0.1
|
1.0
|
|
CD2
|
C:HIS277
|
4.1
|
0.5
|
1.0
|
|
HE1
|
C:HIS141
|
4.1
|
92.1
|
1.0
|
|
NE2
|
C:HIS141
|
4.1
|
92.6
|
1.0
|
|
NE2
|
C:HIS325
|
4.2
|
0.5
|
1.0
|
|
HE1
|
C:HIS325
|
4.2
|
0.9
|
1.0
|
|
HE2
|
C:HIS251
|
4.3
|
0.9
|
1.0
|
|
O
|
C:GLY282
|
4.3
|
0.2
|
1.0
|
|
HD2
|
C:HIS224
|
4.4
|
0.1
|
1.0
|
|
CD2
|
C:HIS224
|
4.4
|
0.1
|
1.0
|
|
CD2
|
C:HIS251
|
4.5
|
1.0
|
1.0
|
|
CE1
|
C:HIS141
|
4.5
|
92.1
|
1.0
|
|
HZ1
|
C:LYS222
|
4.5
|
0.3
|
1.0
|
|
HB2
|
C:HIS251
|
4.5
|
0.6
|
1.0
|
|
CE1
|
C:HIS325
|
4.6
|
0.9
|
1.0
|
|
CE1
|
C:HIS224
|
4.6
|
0.3
|
1.0
|
|
HE1
|
C:HIS224
|
4.7
|
0.3
|
1.0
|
|
ND1
|
C:HIS139
|
4.7
|
87.6
|
1.0
|
|
CE1
|
C:HIS277
|
4.7
|
0.8
|
1.0
|
|
HA3
|
C:GLY282
|
4.7
|
0.2
|
1.0
|
|
CB
|
C:HIS251
|
4.8
|
0.6
|
1.0
|
|
CD2
|
C:HIS139
|
4.8
|
85.9
|
1.0
|
|
C
|
C:GLY282
|
4.8
|
0.6
|
1.0
|
|
O
|
C:ALA368
|
4.9
|
0.6
|
1.0
|
|
HA
|
C:THR173
|
5.0
|
86.6
|
1.0
|
|
Nickel binding site 2 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 2 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 2 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni602
b:82.8
occ:1.00
|
HE2
|
C:HIS141
|
1.7
|
92.6
|
1.0
|
|
NI
|
C:NI601
|
2.0
|
81.5
|
1.0
|
|
NE2
|
C:HIS139
|
2.1
|
87.2
|
1.0
|
|
OD1
|
C:ASP365
|
2.2
|
0.2
|
1.0
|
|
OD2
|
C:ASP365
|
2.3
|
0.7
|
1.0
|
|
CG
|
C:ASP365
|
2.4
|
0.9
|
1.0
|
|
CE1
|
C:HIS139
|
2.5
|
87.8
|
1.0
|
|
NE2
|
C:HIS141
|
2.5
|
92.6
|
1.0
|
|
HE1
|
C:HIS139
|
2.6
|
87.8
|
1.0
|
|
CD2
|
C:HIS139
|
3.2
|
85.9
|
1.0
|
|
HE1
|
C:HIS141
|
3.3
|
92.1
|
1.0
|
|
CE1
|
C:HIS141
|
3.3
|
92.1
|
1.0
|
|
HD2
|
C:HIS139
|
3.6
|
85.9
|
1.0
|
|
ND1
|
C:HIS139
|
3.7
|
87.6
|
1.0
|
|
CD2
|
C:HIS141
|
3.7
|
91.6
|
1.0
|
|
CB
|
C:ASP365
|
3.8
|
0.1
|
1.0
|
|
HE1
|
C:HIS251
|
3.9
|
0.6
|
1.0
|
|
HD2
|
C:HIS141
|
3.9
|
91.6
|
1.0
|
|
HB2
|
C:ASP365
|
3.9
|
0.1
|
1.0
|
|
CG
|
C:HIS139
|
4.0
|
84.3
|
1.0
|
|
HA
|
C:ASP365
|
4.0
|
0.4
|
1.0
|
|
HE2
|
C:HIS277
|
4.1
|
0.6
|
1.0
|
|
HG23
|
C:THR174
|
4.1
|
87.3
|
1.0
|
|
ND1
|
C:HIS251
|
4.2
|
0.7
|
1.0
|
|
HD2
|
C:HIS277
|
4.2
|
0.5
|
1.0
|
|
HB3
|
C:ALA368
|
4.2
|
0.7
|
1.0
|
|
HE2
|
C:HIS224
|
4.2
|
0.4
|
1.0
|
|
O
|
C:GLY172
|
4.2
|
92.7
|
1.0
|
|
O
|
C:ALA368
|
4.3
|
0.6
|
1.0
|
|
HD1
|
C:HIS139
|
4.3
|
87.6
|
1.0
|
|
CE1
|
C:HIS251
|
4.4
|
0.6
|
1.0
|
|
HB1
|
C:ALA368
|
4.4
|
0.7
|
1.0
|
|
HB3
|
C:ASP365
|
4.4
|
0.1
|
1.0
|
|
CA
|
C:ASP365
|
4.5
|
0.4
|
1.0
|
|
ND1
|
C:HIS141
|
4.6
|
91.4
|
1.0
|
|
NE2
|
C:HIS277
|
4.7
|
0.6
|
1.0
|
|
CG
|
C:HIS141
|
4.7
|
88.8
|
1.0
|
|
CD2
|
C:HIS277
|
4.7
|
0.5
|
1.0
|
|
CB
|
C:ALA368
|
4.8
|
0.7
|
1.0
|
|
NE2
|
C:HIS224
|
5.0
|
0.4
|
1.0
|
|
HA
|
C:THR173
|
5.0
|
86.6
|
1.0
|
|
CG2
|
C:THR174
|
5.0
|
87.3
|
1.0
|
|
HE2
|
C:HIS325
|
5.0
|
0.5
|
1.0
|
|
Nickel binding site 3 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 3 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 3 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni601
b:53.2
occ:1.00
|
HE1
|
F:HIS251
|
2.0
|
77.3
|
1.0
|
|
NI
|
F:NI602
|
2.1
|
45.8
|
1.0
|
|
ND1
|
F:HIS251
|
2.3
|
75.8
|
1.0
|
|
CE1
|
F:HIS251
|
2.4
|
77.3
|
1.0
|
|
HE2
|
F:HIS277
|
2.4
|
80.1
|
1.0
|
|
HE1
|
F:HIS139
|
2.5
|
64.7
|
1.0
|
|
OD2
|
F:ASP365
|
2.9
|
85.3
|
1.0
|
|
HE2
|
F:HIS139
|
3.0
|
64.0
|
1.0
|
|
NE2
|
F:HIS277
|
3.1
|
80.1
|
1.0
|
|
CE1
|
F:HIS139
|
3.1
|
64.7
|
1.0
|
|
HE2
|
F:HIS224
|
3.3
|
90.0
|
1.0
|
|
HD2
|
F:HIS277
|
3.4
|
80.3
|
1.0
|
|
NE2
|
F:HIS139
|
3.4
|
64.0
|
1.0
|
|
CD2
|
F:HIS277
|
3.5
|
80.3
|
1.0
|
|
CG
|
F:HIS251
|
3.6
|
75.1
|
1.0
|
|
NE2
|
F:HIS251
|
3.7
|
79.8
|
1.0
|
|
CG
|
F:ASP365
|
3.8
|
79.2
|
1.0
|
|
HE2
|
F:HIS141
|
3.8
|
65.2
|
1.0
|
|
HE2
|
F:HIS325
|
3.9
|
0.9
|
1.0
|
|
NE2
|
F:HIS224
|
3.9
|
90.0
|
1.0
|
|
OD1
|
F:ASP365
|
4.0
|
79.4
|
1.0
|
|
HB2
|
F:HIS251
|
4.2
|
70.2
|
1.0
|
|
O
|
F:GLY282
|
4.2
|
94.7
|
1.0
|
|
CE1
|
F:HIS277
|
4.2
|
81.5
|
1.0
|
|
HE2
|
F:HIS251
|
4.3
|
79.8
|
1.0
|
|
CD2
|
F:HIS251
|
4.3
|
79.3
|
1.0
|
|
O
|
F:GLY172
|
4.3
|
68.1
|
1.0
|
|
ND1
|
F:HIS139
|
4.4
|
64.3
|
1.0
|
|
HZ1
|
F:LYS222
|
4.4
|
0.1
|
1.0
|
|
HA3
|
F:GLY282
|
4.5
|
90.0
|
1.0
|
|
HD2
|
F:HIS224
|
4.5
|
88.3
|
1.0
|
|
CB
|
F:HIS251
|
4.5
|
70.2
|
1.0
|
|
HE1
|
F:HIS325
|
4.5
|
0.9
|
1.0
|
|
NE2
|
F:HIS141
|
4.5
|
65.2
|
1.0
|
|
HE1
|
F:HIS141
|
4.5
|
65.0
|
1.0
|
|
CD2
|
F:HIS224
|
4.6
|
88.3
|
1.0
|
|
HE1
|
F:HIS277
|
4.6
|
81.5
|
1.0
|
|
NE2
|
F:HIS325
|
4.6
|
0.9
|
1.0
|
|
C
|
F:GLY282
|
4.7
|
95.3
|
1.0
|
|
CD2
|
F:HIS139
|
4.7
|
62.3
|
1.0
|
|
HB3
|
F:PHE276
|
4.8
|
70.0
|
1.0
|
|
CG
|
F:HIS277
|
4.8
|
80.2
|
1.0
|
|
CE1
|
F:HIS224
|
4.9
|
92.1
|
1.0
|
|
HA2
|
F:GLY282
|
4.9
|
90.0
|
1.0
|
|
CE1
|
F:HIS141
|
4.9
|
65.0
|
1.0
|
|
CA
|
F:GLY282
|
5.0
|
90.0
|
1.0
|
|
CE1
|
F:HIS325
|
5.0
|
0.9
|
1.0
|
|
HB3
|
F:HIS251
|
5.0
|
70.2
|
1.0
|
|
HB2
|
F:PHE276
|
5.0
|
70.0
|
1.0
|
|
HE1
|
F:HIS224
|
5.0
|
92.1
|
1.0
|
|
Nickel binding site 4 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 4 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 4 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ni602
b:45.8
occ:1.00
|
HE2
|
F:HIS139
|
1.6
|
64.0
|
1.0
|
|
HE2
|
F:HIS141
|
1.8
|
65.2
|
1.0
|
|
NE2
|
F:HIS139
|
2.1
|
64.0
|
1.0
|
|
NI
|
F:NI601
|
2.1
|
53.2
|
1.0
|
|
OD1
|
F:ASP365
|
2.2
|
79.4
|
1.0
|
|
OD2
|
F:ASP365
|
2.3
|
85.3
|
1.0
|
|
CG
|
F:ASP365
|
2.4
|
79.2
|
1.0
|
|
CE1
|
F:HIS139
|
2.5
|
64.7
|
1.0
|
|
HE1
|
F:HIS139
|
2.5
|
64.7
|
1.0
|
|
NE2
|
F:HIS141
|
2.7
|
65.2
|
1.0
|
|
CD2
|
F:HIS139
|
3.2
|
62.3
|
1.0
|
|
HE1
|
F:HIS141
|
3.3
|
65.0
|
1.0
|
|
CE1
|
F:HIS141
|
3.4
|
65.0
|
1.0
|
|
HD2
|
F:HIS139
|
3.6
|
62.3
|
1.0
|
|
ND1
|
F:HIS139
|
3.7
|
64.3
|
1.0
|
|
CB
|
F:ASP365
|
3.8
|
69.8
|
1.0
|
|
CD2
|
F:HIS141
|
3.8
|
64.4
|
1.0
|
|
HE1
|
F:HIS251
|
3.9
|
77.3
|
1.0
|
|
HB2
|
F:ASP365
|
3.9
|
69.8
|
1.0
|
|
CG
|
F:HIS139
|
4.0
|
60.6
|
1.0
|
|
HA
|
F:ASP365
|
4.0
|
65.9
|
1.0
|
|
HD2
|
F:HIS141
|
4.1
|
64.4
|
1.0
|
|
HG23
|
F:THR174
|
4.1
|
68.0
|
1.0
|
|
HE2
|
F:HIS277
|
4.1
|
80.1
|
1.0
|
|
ND1
|
F:HIS251
|
4.2
|
75.8
|
1.0
|
|
HD2
|
F:HIS277
|
4.2
|
80.3
|
1.0
|
|
HB3
|
F:ALA368
|
4.2
|
72.4
|
1.0
|
|
HE2
|
F:HIS224
|
4.2
|
90.0
|
1.0
|
|
O
|
F:GLY172
|
4.2
|
68.1
|
1.0
|
|
O
|
F:ALA368
|
4.3
|
79.9
|
1.0
|
|
CE1
|
F:HIS251
|
4.4
|
77.3
|
1.0
|
|
HB3
|
F:ASP365
|
4.4
|
69.8
|
1.0
|
|
HB1
|
F:ALA368
|
4.4
|
72.4
|
1.0
|
|
CA
|
F:ASP365
|
4.5
|
65.9
|
1.0
|
|
ND1
|
F:HIS141
|
4.6
|
64.7
|
1.0
|
|
NE2
|
F:HIS277
|
4.7
|
80.1
|
1.0
|
|
CD2
|
F:HIS277
|
4.7
|
80.3
|
1.0
|
|
CB
|
F:ALA368
|
4.8
|
72.4
|
1.0
|
|
CG
|
F:HIS141
|
4.8
|
62.0
|
1.0
|
|
HA
|
F:THR173
|
4.9
|
63.8
|
1.0
|
|
CG2
|
F:THR174
|
4.9
|
68.0
|
1.0
|
|
HG21
|
F:THR174
|
4.9
|
68.0
|
1.0
|
|
NE2
|
F:HIS224
|
5.0
|
90.0
|
1.0
|
|
HE2
|
F:HIS325
|
5.0
|
0.9
|
1.0
|
|
Nickel binding site 5 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 5 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 5 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ni601
b:41.7
occ:1.00
|
NI
|
I:NI602
|
1.5
|
40.9
|
1.0
|
|
HE1
|
I:HIS251
|
2.5
|
69.0
|
1.0
|
|
HE1
|
I:HIS139
|
2.5
|
62.0
|
1.0
|
|
ND1
|
I:HIS251
|
2.7
|
68.2
|
1.0
|
|
CE1
|
I:HIS251
|
2.9
|
69.0
|
1.0
|
|
OD2
|
I:ASP365
|
2.9
|
90.4
|
1.0
|
|
NE2
|
I:HIS139
|
2.9
|
61.1
|
1.0
|
|
CE1
|
I:HIS139
|
3.0
|
62.0
|
1.0
|
|
HE2
|
I:HIS141
|
3.0
|
69.4
|
1.0
|
|
HE2
|
I:HIS277
|
3.0
|
84.5
|
1.0
|
|
HE2
|
I:HIS224
|
3.1
|
66.5
|
1.0
|
|
CG
|
I:ASP365
|
3.6
|
84.5
|
1.0
|
|
OD1
|
I:ASP365
|
3.6
|
84.3
|
1.0
|
|
HE1
|
I:HIS141
|
3.7
|
68.6
|
1.0
|
|
NE2
|
I:HIS141
|
3.7
|
69.4
|
1.0
|
|
NE2
|
I:HIS277
|
3.7
|
84.5
|
1.0
|
|
NE2
|
I:HIS224
|
3.8
|
66.5
|
1.0
|
|
HD2
|
I:HIS277
|
3.9
|
84.9
|
1.0
|
|
O
|
I:GLY172
|
3.9
|
59.8
|
1.0
|
|
HE2
|
I:HIS325
|
3.9
|
0.6
|
1.0
|
|
CG
|
I:HIS251
|
4.0
|
67.2
|
1.0
|
|
CE1
|
I:HIS141
|
4.1
|
68.6
|
1.0
|
|
CD2
|
I:HIS277
|
4.1
|
84.9
|
1.0
|
|
HD2
|
I:HIS224
|
4.2
|
65.0
|
1.0
|
|
NE2
|
I:HIS251
|
4.2
|
70.9
|
1.0
|
|
HZ1
|
I:LYS222
|
4.2
|
0.4
|
1.0
|
|
CD2
|
I:HIS139
|
4.3
|
60.2
|
1.0
|
|
ND1
|
I:HIS139
|
4.3
|
62.2
|
1.0
|
|
CD2
|
I:HIS224
|
4.4
|
65.0
|
1.0
|
|
HB2
|
I:HIS251
|
4.4
|
62.5
|
1.0
|
|
NE2
|
I:HIS325
|
4.7
|
0.6
|
1.0
|
|
HA
|
I:THR173
|
4.7
|
51.2
|
1.0
|
|
HE2
|
I:HIS251
|
4.8
|
70.9
|
1.0
|
|
HE1
|
I:HIS325
|
4.8
|
0.6
|
1.0
|
|
CD2
|
I:HIS251
|
4.8
|
70.6
|
1.0
|
|
HD1
|
I:HIS139
|
4.8
|
62.2
|
1.0
|
|
HE2
|
I:LYS222
|
4.8
|
98.6
|
1.0
|
|
CB
|
I:HIS251
|
4.8
|
62.5
|
1.0
|
|
HD2
|
I:HIS139
|
4.8
|
60.2
|
1.0
|
|
CE1
|
I:HIS224
|
4.9
|
68.0
|
1.0
|
|
O
|
I:GLY282
|
4.9
|
80.5
|
1.0
|
|
CE1
|
I:HIS277
|
4.9
|
85.5
|
1.0
|
|
CB
|
I:ASP365
|
4.9
|
75.4
|
1.0
|
|
CG
|
I:HIS139
|
4.9
|
58.8
|
1.0
|
|
HG23
|
I:THR174
|
4.9
|
56.0
|
1.0
|
|
HB2
|
I:ASP365
|
5.0
|
75.4
|
1.0
|
|
C
|
I:GLY172
|
5.0
|
58.8
|
1.0
|
|
HE3
|
I:LYS222
|
5.0
|
98.6
|
1.0
|
|
CD2
|
I:HIS141
|
5.0
|
68.9
|
1.0
|
|
Nickel binding site 6 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 6 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 6 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
I:Ni602
b:40.9
occ:1.00
|
NI
|
I:NI601
|
1.5
|
41.7
|
1.0
|
|
HE2
|
I:HIS141
|
1.7
|
69.4
|
1.0
|
|
NE2
|
I:HIS139
|
2.1
|
61.1
|
1.0
|
|
OD1
|
I:ASP365
|
2.2
|
84.3
|
1.0
|
|
OD2
|
I:ASP365
|
2.3
|
90.4
|
1.0
|
|
CG
|
I:ASP365
|
2.4
|
84.5
|
1.0
|
|
NE2
|
I:HIS141
|
2.5
|
69.4
|
1.0
|
|
CE1
|
I:HIS139
|
2.5
|
62.0
|
1.0
|
|
HE1
|
I:HIS139
|
2.6
|
62.0
|
1.0
|
|
CD2
|
I:HIS139
|
3.2
|
60.2
|
1.0
|
|
HE1
|
I:HIS141
|
3.2
|
68.6
|
1.0
|
|
CE1
|
I:HIS141
|
3.3
|
68.6
|
1.0
|
|
HD2
|
I:HIS139
|
3.6
|
60.2
|
1.0
|
|
CD2
|
I:HIS141
|
3.7
|
68.9
|
1.0
|
|
ND1
|
I:HIS139
|
3.7
|
62.2
|
1.0
|
|
CB
|
I:ASP365
|
3.8
|
75.4
|
1.0
|
|
HE1
|
I:HIS251
|
3.9
|
69.0
|
1.0
|
|
HD2
|
I:HIS141
|
3.9
|
68.9
|
1.0
|
|
HB2
|
I:ASP365
|
3.9
|
75.4
|
1.0
|
|
CG
|
I:HIS139
|
4.0
|
58.8
|
1.0
|
|
HA
|
I:ASP365
|
4.0
|
72.1
|
1.0
|
|
HE2
|
I:HIS277
|
4.1
|
84.5
|
1.0
|
|
HG23
|
I:THR174
|
4.1
|
56.0
|
1.0
|
|
ND1
|
I:HIS251
|
4.1
|
68.2
|
1.0
|
|
HD2
|
I:HIS277
|
4.2
|
84.9
|
1.0
|
|
HB3
|
I:ALA368
|
4.2
|
80.2
|
1.0
|
|
HE2
|
I:HIS224
|
4.2
|
66.5
|
1.0
|
|
O
|
I:GLY172
|
4.2
|
59.8
|
1.0
|
|
O
|
I:ALA368
|
4.3
|
87.0
|
1.0
|
|
HD1
|
I:HIS139
|
4.3
|
62.2
|
1.0
|
|
CE1
|
I:HIS251
|
4.4
|
69.0
|
1.0
|
|
HB1
|
I:ALA368
|
4.4
|
80.2
|
1.0
|
|
HB3
|
I:ASP365
|
4.4
|
75.4
|
1.0
|
|
ND1
|
I:HIS141
|
4.5
|
68.2
|
1.0
|
|
CA
|
I:ASP365
|
4.5
|
72.1
|
1.0
|
|
CG
|
I:HIS141
|
4.7
|
66.2
|
1.0
|
|
NE2
|
I:HIS277
|
4.7
|
84.5
|
1.0
|
|
CD2
|
I:HIS277
|
4.7
|
84.9
|
1.0
|
|
CB
|
I:ALA368
|
4.8
|
80.2
|
1.0
|
|
NE2
|
I:HIS224
|
5.0
|
66.5
|
1.0
|
|
HA
|
I:THR173
|
5.0
|
51.2
|
1.0
|
|
CG2
|
I:THR174
|
5.0
|
56.0
|
1.0
|
|
HE2
|
I:HIS325
|
5.0
|
0.6
|
1.0
|
|
Nickel binding site 7 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 7 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 7 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni601
b:52.8
occ:1.00
|
HE1
|
L:HIS251
|
1.9
|
72.3
|
1.0
|
|
HE2
|
L:HIS277
|
2.0
|
77.5
|
1.0
|
|
ND1
|
L:HIS251
|
2.0
|
70.5
|
1.0
|
|
CE1
|
L:HIS251
|
2.2
|
72.3
|
1.0
|
|
HE1
|
L:HIS139
|
2.4
|
61.4
|
1.0
|
|
NI
|
L:NI602
|
2.4
|
43.5
|
1.0
|
|
NE2
|
L:HIS277
|
2.6
|
77.5
|
1.0
|
|
OD2
|
L:ASP365
|
3.0
|
0.5
|
1.0
|
|
HD2
|
L:HIS277
|
3.1
|
77.9
|
1.0
|
|
CE1
|
L:HIS139
|
3.2
|
61.4
|
1.0
|
|
CD2
|
L:HIS277
|
3.2
|
77.9
|
1.0
|
|
CG
|
L:HIS251
|
3.4
|
69.8
|
1.0
|
|
HE2
|
L:HIS224
|
3.5
|
68.6
|
1.0
|
|
NE2
|
L:HIS251
|
3.5
|
74.6
|
1.0
|
|
NE2
|
L:HIS139
|
3.5
|
60.8
|
1.0
|
|
CE1
|
L:HIS277
|
3.8
|
78.8
|
1.0
|
|
HB2
|
L:HIS251
|
3.9
|
65.5
|
1.0
|
|
CG
|
L:ASP365
|
3.9
|
0.4
|
1.0
|
|
O
|
L:GLY282
|
4.0
|
85.3
|
1.0
|
|
HE2
|
L:HIS325
|
4.0
|
0.3
|
1.0
|
|
HE2
|
L:HIS141
|
4.0
|
66.1
|
1.0
|
|
CD2
|
L:HIS251
|
4.1
|
73.7
|
1.0
|
|
NE2
|
L:HIS224
|
4.1
|
68.6
|
1.0
|
|
HE2
|
L:HIS251
|
4.1
|
74.6
|
1.0
|
|
HE1
|
L:HIS277
|
4.1
|
78.8
|
1.0
|
|
HA3
|
L:GLY282
|
4.2
|
83.1
|
1.0
|
|
CB
|
L:HIS251
|
4.3
|
65.5
|
1.0
|
|
OD1
|
L:ASP365
|
4.3
|
0.2
|
1.0
|
|
ND1
|
L:HIS139
|
4.3
|
61.0
|
1.0
|
|
HZ1
|
L:LYS222
|
4.4
|
99.7
|
1.0
|
|
C
|
L:GLY282
|
4.4
|
85.8
|
1.0
|
|
CG
|
L:HIS277
|
4.4
|
78.2
|
1.0
|
|
HB3
|
L:PHE276
|
4.5
|
69.0
|
1.0
|
|
HE1
|
L:HIS325
|
4.6
|
0.6
|
1.0
|
|
HD1
|
L:HIS139
|
4.7
|
61.0
|
1.0
|
|
HD2
|
L:HIS224
|
4.7
|
66.3
|
1.0
|
|
HB2
|
L:PHE276
|
4.7
|
69.0
|
1.0
|
|
CD2
|
L:HIS224
|
4.7
|
66.3
|
1.0
|
|
CA
|
L:GLY282
|
4.7
|
83.1
|
1.0
|
|
O
|
L:GLY172
|
4.7
|
60.2
|
1.0
|
|
ND1
|
L:HIS277
|
4.7
|
80.0
|
1.0
|
|
NE2
|
L:HIS325
|
4.7
|
0.3
|
1.0
|
|
HA2
|
L:GLY282
|
4.8
|
83.1
|
1.0
|
|
NE2
|
L:HIS141
|
4.8
|
66.1
|
1.0
|
|
HB3
|
L:HIS251
|
4.8
|
65.5
|
1.0
|
|
HE1
|
L:HIS141
|
4.8
|
65.6
|
1.0
|
|
HA3
|
L:GLY283
|
4.9
|
84.2
|
1.0
|
|
CD2
|
L:HIS139
|
4.9
|
59.3
|
1.0
|
|
HD2
|
L:PHE276
|
4.9
|
68.2
|
1.0
|
|
CE1
|
L:HIS224
|
4.9
|
70.6
|
1.0
|
|
HD2
|
L:HIS251
|
5.0
|
73.7
|
1.0
|
|
Nickel binding site 8 out
of 8 in 4z42
Go back to
Nickel Binding Sites List in 4z42
Nickel binding site 8 out
of 8 in the Crystal Structure of Urease From Yersinia Enterocolitica
 Mono view
 Stereo pair view
|
|
A full contact list of Nickel with other atoms in the Ni binding
site number 8 of Crystal Structure of Urease From Yersinia Enterocolitica within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Ni602
b:43.5
occ:1.00
|
HE2
|
L:HIS141
|
1.7
|
66.1
|
1.0
|
|
NE2
|
L:HIS139
|
2.1
|
60.8
|
1.0
|
|
OD1
|
L:ASP365
|
2.2
|
0.2
|
1.0
|
|
OD2
|
L:ASP365
|
2.3
|
0.5
|
1.0
|
|
CG
|
L:ASP365
|
2.4
|
0.4
|
1.0
|
|
NI
|
L:NI601
|
2.4
|
52.8
|
1.0
|
|
NE2
|
L:HIS141
|
2.5
|
66.1
|
1.0
|
|
CE1
|
L:HIS139
|
2.5
|
61.4
|
1.0
|
|
HE1
|
L:HIS139
|
2.6
|
61.4
|
1.0
|
|
CD2
|
L:HIS139
|
3.2
|
59.3
|
1.0
|
|
HE1
|
L:HIS141
|
3.3
|
65.6
|
1.0
|
|
CE1
|
L:HIS141
|
3.3
|
65.6
|
1.0
|
|
HD2
|
L:HIS139
|
3.6
|
59.3
|
1.0
|
|
ND1
|
L:HIS139
|
3.7
|
61.0
|
1.0
|
|
CD2
|
L:HIS141
|
3.7
|
65.4
|
1.0
|
|
CB
|
L:ASP365
|
3.8
|
95.6
|
1.0
|
|
HE1
|
L:HIS251
|
3.9
|
72.3
|
1.0
|
|
HD2
|
L:HIS141
|
3.9
|
65.4
|
1.0
|
|
HB2
|
L:ASP365
|
3.9
|
95.6
|
1.0
|
|
CG
|
L:HIS139
|
4.0
|
58.1
|
1.0
|
|
HA
|
L:ASP365
|
4.0
|
91.7
|
1.0
|
|
HG23
|
L:THR174
|
4.1
|
49.4
|
1.0
|
|
HE2
|
L:HIS277
|
4.1
|
77.5
|
1.0
|
|
ND1
|
L:HIS251
|
4.2
|
70.5
|
1.0
|
|
HD2
|
L:HIS277
|
4.2
|
77.9
|
1.0
|
|
HB3
|
L:ALA368
|
4.2
|
90.2
|
1.0
|
|
HE2
|
L:HIS224
|
4.2
|
68.6
|
1.0
|
|
O
|
L:GLY172
|
4.2
|
60.2
|
1.0
|
|
O
|
L:ALA368
|
4.3
|
96.2
|
1.0
|
|
HD1
|
L:HIS139
|
4.3
|
61.0
|
1.0
|
|
CE1
|
L:HIS251
|
4.4
|
72.3
|
1.0
|
|
HB1
|
L:ALA368
|
4.4
|
90.2
|
1.0
|
|
HB3
|
L:ASP365
|
4.4
|
95.6
|
1.0
|
|
CA
|
L:ASP365
|
4.5
|
91.7
|
1.0
|
|
ND1
|
L:HIS141
|
4.5
|
64.9
|
1.0
|
|
CG
|
L:HIS141
|
4.7
|
63.2
|
1.0
|
|
NE2
|
L:HIS277
|
4.7
|
77.5
|
1.0
|
|
CD2
|
L:HIS277
|
4.7
|
77.9
|
1.0
|
|
CB
|
L:ALA368
|
4.8
|
90.2
|
1.0
|
|
CG2
|
L:THR174
|
4.9
|
49.4
|
1.0
|
|
NE2
|
L:HIS224
|
5.0
|
68.6
|
1.0
|
|
HA
|
L:THR173
|
5.0
|
53.4
|
1.0
|
|
HG21
|
L:THR174
|
5.0
|
49.4
|
1.0
|
|
HE2
|
L:HIS325
|
5.0
|
0.3
|
1.0
|
|
Reference:
G.Studer,
R.P.Jakob,
M.A.Mahi,
U.Wiesand,
T.Schwede,
T.Maier.
Crystal Structure of Urease From Yersinia Enterocolitica To Be Published.
Page generated: Wed Oct 9 19:24:16 2024
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