Nickel in PDB 1ztc: Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
Protein crystallography data
The structure of Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution, PDB code: 1ztc
was solved by
Joint Center For Structural Genomics (Jcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.60 /
2.10
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.783,
127.343,
152.224,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.7 /
17.8
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
(pdb code 1ztc). 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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution, PDB code: 1ztc:
Jump to Nickel binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Nickel binding site 1 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 1 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni301
b:65.1
occ:1.00
|
OD2
|
A:ASP162
|
2.2
|
51.5
|
1.0
|
NE2
|
A:HIS199
|
2.2
|
43.7
|
1.0
|
NE2
|
A:HIS74
|
2.2
|
46.5
|
1.0
|
O
|
A:HOH425
|
2.5
|
40.5
|
1.0
|
O
|
A:HOH387
|
2.6
|
50.0
|
1.0
|
OD1
|
A:ASP162
|
2.8
|
60.3
|
1.0
|
OD2
|
A:ASP73
|
2.9
|
56.0
|
1.0
|
CG
|
A:ASP162
|
2.9
|
49.7
|
1.0
|
CD2
|
A:HIS74
|
3.0
|
43.3
|
1.0
|
CE1
|
A:HIS199
|
3.2
|
43.5
|
1.0
|
CD2
|
A:HIS199
|
3.2
|
47.5
|
1.0
|
CE1
|
A:HIS74
|
3.4
|
47.5
|
1.0
|
NI
|
A:NI302
|
3.6
|
59.9
|
1.0
|
O
|
A:HOH402
|
3.7
|
62.6
|
1.0
|
O
|
A:HOH306
|
3.8
|
43.0
|
1.0
|
CG
|
A:ASP73
|
3.8
|
51.8
|
1.0
|
OD1
|
A:ASP73
|
4.0
|
52.2
|
1.0
|
CG
|
A:HIS74
|
4.2
|
45.9
|
1.0
|
ND1
|
A:HIS199
|
4.3
|
48.7
|
1.0
|
CE1
|
A:HIS69
|
4.3
|
46.3
|
1.0
|
CG
|
A:HIS199
|
4.3
|
44.4
|
1.0
|
CB
|
A:ASP162
|
4.3
|
45.3
|
1.0
|
O
|
A:HOH435
|
4.4
|
62.2
|
1.0
|
ND1
|
A:HIS74
|
4.4
|
46.6
|
1.0
|
NE2
|
A:HIS69
|
4.4
|
46.3
|
1.0
|
CB
|
A:PRO198
|
4.8
|
44.4
|
1.0
|
CG
|
A:PRO198
|
5.0
|
43.3
|
1.0
|
|
Nickel binding site 2 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 2 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni302
b:59.9
occ:1.00
|
NE2
|
A:HIS69
|
2.2
|
46.3
|
1.0
|
O
|
A:HOH425
|
2.2
|
40.5
|
1.0
|
ND1
|
A:HIS71
|
2.2
|
57.8
|
1.0
|
NE2
|
A:HIS140
|
2.3
|
52.3
|
1.0
|
OD2
|
A:ASP162
|
2.3
|
51.5
|
1.0
|
O
|
A:HOH306
|
2.4
|
43.0
|
1.0
|
CE1
|
A:HIS71
|
3.0
|
61.5
|
1.0
|
CE1
|
A:HIS69
|
3.1
|
46.3
|
1.0
|
CD2
|
A:HIS69
|
3.1
|
43.8
|
1.0
|
CD2
|
A:HIS140
|
3.2
|
48.5
|
1.0
|
CE1
|
A:HIS140
|
3.2
|
48.5
|
1.0
|
CG
|
A:HIS71
|
3.2
|
59.0
|
1.0
|
CG
|
A:ASP162
|
3.4
|
49.7
|
1.0
|
NI
|
A:NI301
|
3.6
|
65.1
|
1.0
|
CB
|
A:HIS71
|
3.7
|
49.0
|
1.0
|
CB
|
A:ASP162
|
3.8
|
45.3
|
1.0
|
O
|
A:HOH387
|
3.9
|
50.0
|
1.0
|
NE2
|
A:HIS71
|
4.1
|
66.2
|
1.0
|
ND1
|
A:HIS69
|
4.2
|
44.9
|
1.0
|
CG
|
A:HIS69
|
4.3
|
44.7
|
1.0
|
CD2
|
A:HIS71
|
4.3
|
66.9
|
1.0
|
O
|
A:HOH402
|
4.3
|
62.6
|
1.0
|
ND1
|
A:HIS140
|
4.3
|
51.9
|
1.0
|
CG
|
A:HIS140
|
4.4
|
47.5
|
1.0
|
NE2
|
A:HIS74
|
4.4
|
46.5
|
1.0
|
OD1
|
A:ASP162
|
4.5
|
60.3
|
1.0
|
CD2
|
A:HIS74
|
4.5
|
43.3
|
1.0
|
OD1
|
A:ASP73
|
4.8
|
52.2
|
1.0
|
|
Nickel binding site 3 out
of 8 in 1ztc
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Nickel Binding Sites List in 1ztc
Nickel binding site 3 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni301
b:65.7
occ:1.00
|
NE2
|
B:HIS199
|
2.2
|
49.7
|
1.0
|
OD2
|
B:ASP162
|
2.2
|
52.9
|
1.0
|
NE2
|
B:HIS74
|
2.2
|
45.7
|
1.0
|
O
|
B:HOH402
|
2.5
|
51.6
|
1.0
|
OD1
|
B:ASP162
|
2.7
|
55.0
|
1.0
|
O
|
B:HOH336
|
2.8
|
67.5
|
1.0
|
CG
|
B:ASP162
|
2.9
|
48.1
|
1.0
|
OD2
|
B:ASP73
|
2.9
|
52.5
|
1.0
|
CD2
|
B:HIS74
|
3.1
|
46.7
|
1.0
|
CD2
|
B:HIS199
|
3.1
|
47.6
|
1.0
|
CE1
|
B:HIS199
|
3.2
|
44.0
|
1.0
|
CE1
|
B:HIS74
|
3.3
|
47.9
|
1.0
|
O
|
B:HOH403
|
3.3
|
67.6
|
1.0
|
NI
|
B:NI302
|
3.5
|
59.3
|
1.0
|
CG
|
B:ASP73
|
3.8
|
51.6
|
1.0
|
O
|
B:HOH305
|
3.8
|
42.8
|
1.0
|
OD1
|
B:ASP73
|
4.0
|
51.3
|
1.0
|
CG
|
B:HIS74
|
4.3
|
46.0
|
1.0
|
CG
|
B:HIS199
|
4.3
|
48.2
|
1.0
|
ND1
|
B:HIS199
|
4.3
|
48.8
|
1.0
|
CB
|
B:ASP162
|
4.4
|
46.6
|
1.0
|
ND1
|
B:HIS74
|
4.4
|
46.0
|
1.0
|
CE1
|
B:HIS69
|
4.4
|
45.6
|
1.0
|
NE2
|
B:HIS69
|
4.4
|
44.2
|
1.0
|
CB
|
B:PRO198
|
4.8
|
44.7
|
1.0
|
|
Nickel binding site 4 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 4 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni302
b:59.3
occ:1.00
|
ND1
|
B:HIS71
|
2.2
|
57.7
|
1.0
|
NE2
|
B:HIS69
|
2.2
|
44.2
|
1.0
|
OD2
|
B:ASP162
|
2.2
|
52.9
|
1.0
|
NE2
|
B:HIS140
|
2.3
|
51.7
|
1.0
|
O
|
B:HOH402
|
2.3
|
51.6
|
1.0
|
O
|
B:HOH305
|
2.6
|
42.8
|
1.0
|
CE1
|
B:HIS71
|
3.0
|
63.2
|
1.0
|
CD2
|
B:HIS69
|
3.1
|
41.7
|
1.0
|
CE1
|
B:HIS69
|
3.2
|
45.6
|
1.0
|
CD2
|
B:HIS140
|
3.2
|
48.3
|
1.0
|
CG
|
B:HIS71
|
3.2
|
56.0
|
1.0
|
CE1
|
B:HIS140
|
3.3
|
45.7
|
1.0
|
CG
|
B:ASP162
|
3.3
|
48.1
|
1.0
|
NI
|
B:NI301
|
3.5
|
65.7
|
1.0
|
CB
|
B:HIS71
|
3.7
|
46.8
|
1.0
|
CB
|
B:ASP162
|
3.8
|
46.6
|
1.0
|
NE2
|
B:HIS71
|
4.1
|
68.4
|
1.0
|
O
|
B:HOH336
|
4.1
|
67.5
|
1.0
|
CG
|
B:HIS69
|
4.2
|
45.1
|
1.0
|
CD2
|
B:HIS71
|
4.2
|
66.5
|
1.0
|
ND1
|
B:HIS69
|
4.3
|
48.4
|
1.0
|
NE2
|
B:HIS74
|
4.3
|
45.7
|
1.0
|
O
|
B:HOH403
|
4.3
|
67.6
|
1.0
|
OD1
|
B:ASP162
|
4.3
|
55.0
|
1.0
|
CG
|
B:HIS140
|
4.3
|
47.5
|
1.0
|
ND1
|
B:HIS140
|
4.3
|
48.5
|
1.0
|
CD2
|
B:HIS74
|
4.5
|
46.7
|
1.0
|
OD1
|
B:ASP73
|
4.8
|
51.3
|
1.0
|
|
Nickel binding site 5 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 5 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni301
b:65.0
occ:1.00
|
OD2
|
C:ASP162
|
2.2
|
51.6
|
1.0
|
NE2
|
C:HIS199
|
2.3
|
48.6
|
1.0
|
NE2
|
C:HIS74
|
2.3
|
41.5
|
1.0
|
O
|
C:HOH393
|
2.4
|
47.7
|
1.0
|
OD1
|
C:ASP162
|
2.8
|
56.3
|
1.0
|
CG
|
C:ASP162
|
2.8
|
49.1
|
1.0
|
O
|
C:HOH361
|
2.9
|
64.9
|
1.0
|
OD2
|
C:ASP73
|
2.9
|
50.5
|
1.0
|
CD2
|
C:HIS74
|
3.1
|
48.3
|
1.0
|
CD2
|
C:HIS199
|
3.2
|
46.6
|
1.0
|
CE1
|
C:HIS199
|
3.2
|
44.3
|
1.0
|
CE1
|
C:HIS74
|
3.4
|
44.1
|
1.0
|
NI
|
C:NI302
|
3.5
|
59.7
|
1.0
|
CG
|
C:ASP73
|
3.9
|
51.5
|
1.0
|
O
|
C:HOH305
|
3.9
|
45.0
|
1.0
|
OD1
|
C:ASP73
|
4.0
|
49.2
|
1.0
|
CE1
|
C:HIS69
|
4.3
|
48.1
|
1.0
|
CB
|
C:ASP162
|
4.3
|
47.1
|
1.0
|
ND1
|
C:HIS199
|
4.3
|
49.6
|
1.0
|
NE2
|
C:HIS69
|
4.3
|
44.1
|
1.0
|
CG
|
C:HIS199
|
4.4
|
45.6
|
1.0
|
CG
|
C:HIS74
|
4.4
|
41.6
|
1.0
|
ND1
|
C:HIS74
|
4.5
|
45.0
|
1.0
|
CB
|
C:PRO198
|
4.8
|
44.0
|
1.0
|
CG
|
C:PRO198
|
5.0
|
43.3
|
1.0
|
|
Nickel binding site 6 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 6 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ni302
b:59.7
occ:1.00
|
NE2
|
C:HIS69
|
2.1
|
44.1
|
1.0
|
ND1
|
C:HIS71
|
2.2
|
57.6
|
1.0
|
OD2
|
C:ASP162
|
2.3
|
51.6
|
1.0
|
NE2
|
C:HIS140
|
2.3
|
48.9
|
1.0
|
O
|
C:HOH393
|
2.4
|
47.7
|
1.0
|
O
|
C:HOH305
|
2.5
|
45.0
|
1.0
|
CE1
|
C:HIS71
|
3.0
|
62.3
|
1.0
|
CD2
|
C:HIS69
|
3.1
|
43.7
|
1.0
|
CE1
|
C:HIS69
|
3.2
|
48.1
|
1.0
|
CD2
|
C:HIS140
|
3.2
|
49.0
|
1.0
|
CG
|
C:HIS71
|
3.3
|
56.5
|
1.0
|
CE1
|
C:HIS140
|
3.3
|
43.3
|
1.0
|
CG
|
C:ASP162
|
3.3
|
49.1
|
1.0
|
NI
|
C:NI301
|
3.5
|
65.0
|
1.0
|
CB
|
C:HIS71
|
3.7
|
48.0
|
1.0
|
CB
|
C:ASP162
|
3.8
|
47.1
|
1.0
|
NE2
|
C:HIS71
|
4.1
|
66.3
|
1.0
|
O
|
C:HOH361
|
4.2
|
64.9
|
1.0
|
CG
|
C:HIS69
|
4.2
|
44.0
|
1.0
|
ND1
|
C:HIS69
|
4.2
|
48.7
|
1.0
|
CD2
|
C:HIS71
|
4.3
|
66.3
|
1.0
|
NE2
|
C:HIS74
|
4.3
|
41.5
|
1.0
|
ND1
|
C:HIS140
|
4.4
|
48.8
|
1.0
|
CG
|
C:HIS140
|
4.4
|
47.5
|
1.0
|
OD1
|
C:ASP162
|
4.4
|
56.3
|
1.0
|
CD2
|
C:HIS74
|
4.6
|
48.3
|
1.0
|
OD1
|
C:ASP73
|
4.8
|
49.2
|
1.0
|
|
Nickel binding site 7 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 7 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni301
b:65.3
occ:1.00
|
OD2
|
D:ASP162
|
2.2
|
50.0
|
1.0
|
NE2
|
D:HIS199
|
2.2
|
45.8
|
1.0
|
NE2
|
D:HIS74
|
2.3
|
45.2
|
1.0
|
O
|
D:HOH399
|
2.4
|
49.1
|
1.0
|
O
|
D:HOH409
|
2.5
|
55.8
|
1.0
|
OD1
|
D:ASP162
|
2.7
|
56.2
|
1.0
|
CG
|
D:ASP162
|
2.8
|
48.8
|
1.0
|
OD2
|
D:ASP73
|
2.9
|
54.0
|
1.0
|
CD2
|
D:HIS74
|
3.1
|
43.9
|
1.0
|
CD2
|
D:HIS199
|
3.1
|
48.1
|
1.0
|
CE1
|
D:HIS199
|
3.2
|
44.3
|
1.0
|
CE1
|
D:HIS74
|
3.3
|
47.3
|
1.0
|
NI
|
D:NI302
|
3.5
|
58.6
|
1.0
|
O
|
D:HOH306
|
3.8
|
45.9
|
1.0
|
CG
|
D:ASP73
|
3.9
|
52.1
|
1.0
|
OD1
|
D:ASP73
|
4.1
|
52.6
|
1.0
|
CG
|
D:HIS74
|
4.3
|
44.0
|
1.0
|
CG
|
D:HIS199
|
4.3
|
45.5
|
1.0
|
CB
|
D:ASP162
|
4.3
|
45.6
|
1.0
|
ND1
|
D:HIS199
|
4.3
|
46.9
|
1.0
|
CE1
|
D:HIS69
|
4.3
|
47.8
|
1.0
|
ND1
|
D:HIS74
|
4.4
|
44.3
|
1.0
|
NE2
|
D:HIS69
|
4.4
|
41.5
|
1.0
|
O
|
D:HOH382
|
4.6
|
61.2
|
1.0
|
CB
|
D:PRO198
|
4.7
|
44.6
|
1.0
|
CG
|
D:PRO198
|
5.0
|
42.3
|
1.0
|
|
Nickel binding site 8 out
of 8 in 1ztc
Go back to
Nickel Binding Sites List in 1ztc
Nickel binding site 8 out
of 8 in the Crystal Structure of A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution
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 A Putative Metallo-Beta-Lactamase (TM0894) From Thermotoga Maritima at 2.10 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ni302
b:58.6
occ:1.00
|
ND1
|
D:HIS71
|
2.2
|
56.1
|
1.0
|
NE2
|
D:HIS69
|
2.2
|
41.5
|
1.0
|
OD2
|
D:ASP162
|
2.3
|
50.0
|
1.0
|
NE2
|
D:HIS140
|
2.3
|
51.5
|
1.0
|
O
|
D:HOH399
|
2.4
|
49.1
|
1.0
|
O
|
D:HOH306
|
2.5
|
45.9
|
1.0
|
CE1
|
D:HIS71
|
3.0
|
61.5
|
1.0
|
CE1
|
D:HIS69
|
3.1
|
47.8
|
1.0
|
CD2
|
D:HIS69
|
3.1
|
44.7
|
1.0
|
CE1
|
D:HIS140
|
3.2
|
47.6
|
1.0
|
CD2
|
D:HIS140
|
3.3
|
50.3
|
1.0
|
CG
|
D:HIS71
|
3.3
|
57.6
|
1.0
|
CG
|
D:ASP162
|
3.3
|
48.8
|
1.0
|
NI
|
D:NI301
|
3.5
|
65.3
|
1.0
|
CB
|
D:HIS71
|
3.7
|
47.0
|
1.0
|
CB
|
D:ASP162
|
3.8
|
45.6
|
1.0
|
O
|
D:HOH409
|
3.9
|
55.8
|
1.0
|
NE2
|
D:HIS71
|
4.2
|
65.7
|
1.0
|
ND1
|
D:HIS69
|
4.3
|
47.7
|
1.0
|
CG
|
D:HIS69
|
4.3
|
44.3
|
1.0
|
NE2
|
D:HIS74
|
4.3
|
45.2
|
1.0
|
ND1
|
D:HIS140
|
4.3
|
49.1
|
1.0
|
CD2
|
D:HIS71
|
4.3
|
65.6
|
1.0
|
CG
|
D:HIS140
|
4.4
|
46.9
|
1.0
|
OD1
|
D:ASP162
|
4.4
|
56.2
|
1.0
|
CD2
|
D:HIS74
|
4.5
|
43.9
|
1.0
|
OD1
|
D:ASP73
|
4.8
|
52.6
|
1.0
|
|
Reference:
Joint Center For Structural Genomics (Jcsg),
Joint Center For Structural Genomics (Jcsg).
N/A N/A.
Page generated: Wed Oct 9 16:35:17 2024
|