Nickel in PDB 1ysj: Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
Enzymatic activity of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
All present enzymatic activity of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family:
3.5.1.14;
Protein crystallography data
The structure of Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family, PDB code: 1ysj
was solved by
G.Minasov,
L.Shuvalova,
J.S.Brunzelle,
F.R.Collart,
W.F.Anderson,
Midwestcenter For Structural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.40
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
233.854,
42.157,
75.449,
90.00,
106.71,
90.00
|
R / Rfree (%)
|
18.2 /
24.7
|
Nickel Binding Sites:
The binding sites of Nickel atom in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
(pdb code 1ysj). This binding sites where shown within
5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the
Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family, PDB code: 1ysj:
Jump to Nickel binding site number:
1;
2;
3;
4;
Nickel binding site 1 out
of 4 in 1ysj
Go back to
Nickel Binding Sites List in 1ysj
Nickel binding site 1 out
of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni381
b:35.1
occ:1.00
|
O
|
A:HOH383
|
1.9
|
39.7
|
1.0
|
NE2
|
A:HIS100
|
2.0
|
38.8
|
1.0
|
NE2
|
A:HIS158
|
2.2
|
46.2
|
1.0
|
O
|
A:HOH489
|
2.3
|
29.5
|
0.5
|
SG
|
A:CYS98
|
2.5
|
47.0
|
1.0
|
CD2
|
A:HIS100
|
3.0
|
39.6
|
1.0
|
CE1
|
A:HIS100
|
3.1
|
43.1
|
1.0
|
CD2
|
A:HIS158
|
3.1
|
42.8
|
1.0
|
CE1
|
A:HIS158
|
3.2
|
44.1
|
1.0
|
NI
|
A:NI382
|
3.3
|
42.6
|
1.0
|
CB
|
A:CYS98
|
3.5
|
43.3
|
1.0
|
OE1
|
A:GLU133
|
3.6
|
53.9
|
1.0
|
OE2
|
A:GLU134
|
3.6
|
49.7
|
1.0
|
O
|
A:CYS98
|
3.9
|
42.9
|
1.0
|
OD2
|
A:ASP73
|
4.1
|
59.4
|
1.0
|
ND1
|
A:HIS100
|
4.2
|
45.0
|
1.0
|
CG
|
A:HIS100
|
4.2
|
42.8
|
1.0
|
O
|
A:HOH385
|
4.2
|
49.4
|
1.0
|
ND1
|
A:HIS158
|
4.3
|
43.0
|
1.0
|
CG
|
A:HIS158
|
4.3
|
46.4
|
1.0
|
CD
|
A:GLU133
|
4.3
|
58.9
|
1.0
|
O
|
A:HOH518
|
4.5
|
47.5
|
0.5
|
CD
|
A:GLU134
|
4.5
|
46.9
|
1.0
|
CE1
|
A:HIS103
|
4.6
|
42.9
|
1.0
|
C
|
A:CYS98
|
4.6
|
43.6
|
1.0
|
CA
|
A:CYS98
|
4.6
|
44.4
|
1.0
|
OE2
|
A:GLU133
|
4.8
|
61.0
|
1.0
|
OE1
|
A:GLU134
|
4.9
|
43.0
|
1.0
|
OE1
|
A:GLU325
|
4.9
|
59.4
|
1.0
|
CG
|
A:ASP73
|
4.9
|
53.2
|
1.0
|
|
Nickel binding site 2 out
of 4 in 1ysj
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Nickel Binding Sites List in 1ysj
Nickel binding site 2 out
of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ni382
b:42.6
occ:1.00
|
NE2
|
A:HIS350
|
2.3
|
50.8
|
1.0
|
O
|
A:HOH385
|
2.3
|
49.4
|
1.0
|
OE2
|
A:GLU134
|
2.4
|
49.7
|
1.0
|
OE1
|
A:GLU134
|
2.4
|
43.0
|
1.0
|
O
|
A:HOH383
|
2.5
|
39.7
|
1.0
|
SG
|
A:CYS98
|
2.6
|
47.0
|
1.0
|
CD
|
A:GLU134
|
2.8
|
46.9
|
1.0
|
CD2
|
A:HIS350
|
3.2
|
49.2
|
1.0
|
CE1
|
A:HIS350
|
3.3
|
50.1
|
1.0
|
NI
|
A:NI381
|
3.3
|
35.1
|
1.0
|
CB
|
A:CYS98
|
3.4
|
43.3
|
1.0
|
O
|
A:HOH384
|
3.5
|
46.0
|
1.0
|
O
|
A:HOH518
|
4.1
|
47.5
|
0.5
|
OE1
|
A:GLU133
|
4.1
|
53.9
|
1.0
|
CG
|
A:GLU134
|
4.3
|
45.4
|
1.0
|
NE2
|
A:HIS100
|
4.3
|
38.8
|
1.0
|
CD1
|
A:LEU77
|
4.4
|
46.1
|
1.0
|
CG
|
A:HIS350
|
4.4
|
46.3
|
1.0
|
ND1
|
A:HIS350
|
4.4
|
50.8
|
1.0
|
CE1
|
A:HIS100
|
4.6
|
43.1
|
1.0
|
O
|
A:HOH452
|
4.8
|
29.4
|
1.0
|
CA
|
A:CYS98
|
4.8
|
44.4
|
1.0
|
O
|
A:HOH386
|
4.9
|
42.7
|
1.0
|
NE2
|
A:HIS158
|
4.9
|
46.2
|
1.0
|
O
|
A:HOH489
|
5.0
|
29.5
|
0.5
|
|
Nickel binding site 3 out
of 4 in 1ysj
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Nickel Binding Sites List in 1ysj
Nickel binding site 3 out
of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni381
b:36.2
occ:1.00
|
O
|
B:HOH383
|
2.1
|
31.1
|
1.0
|
NE2
|
B:HIS158
|
2.1
|
49.5
|
1.0
|
NE2
|
B:HIS100
|
2.3
|
42.6
|
1.0
|
SG
|
B:CYS98
|
2.4
|
45.0
|
1.0
|
O
|
B:HOH493
|
2.4
|
21.3
|
0.5
|
CE1
|
B:HIS158
|
3.1
|
45.8
|
1.0
|
CD2
|
B:HIS100
|
3.1
|
40.9
|
1.0
|
CD2
|
B:HIS158
|
3.1
|
44.2
|
1.0
|
NI
|
B:NI382
|
3.3
|
39.7
|
1.0
|
CE1
|
B:HIS100
|
3.4
|
44.2
|
1.0
|
CB
|
B:CYS98
|
3.5
|
43.3
|
1.0
|
O
|
B:HOH535
|
3.5
|
32.0
|
0.5
|
OE1
|
B:GLU133
|
3.6
|
56.0
|
1.0
|
OE1
|
B:GLU134
|
3.7
|
50.8
|
1.0
|
O
|
B:CYS98
|
3.8
|
42.9
|
1.0
|
OD2
|
B:ASP73
|
4.0
|
49.8
|
1.0
|
O
|
B:HOH386
|
4.1
|
44.5
|
1.0
|
ND1
|
B:HIS158
|
4.2
|
44.0
|
1.0
|
CG
|
B:HIS158
|
4.3
|
43.6
|
1.0
|
CG
|
B:HIS100
|
4.3
|
44.3
|
1.0
|
ND1
|
B:HIS100
|
4.4
|
44.8
|
1.0
|
CD
|
B:GLU133
|
4.4
|
58.3
|
1.0
|
CE1
|
B:HIS103
|
4.5
|
44.4
|
1.0
|
C
|
B:CYS98
|
4.5
|
43.7
|
1.0
|
CA
|
B:CYS98
|
4.6
|
43.4
|
1.0
|
CD
|
B:GLU134
|
4.6
|
52.2
|
1.0
|
CG
|
B:ASP73
|
4.9
|
48.1
|
1.0
|
|
Nickel binding site 4 out
of 4 in 1ysj
Go back to
Nickel Binding Sites List in 1ysj
Nickel binding site 4 out
of 4 in the Crystal Structure of Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family
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 Bacillus Subtilis Yxep Protein (APC1829), A Dinuclear Metal Binding Peptidase From M20 Family within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ni382
b:39.7
occ:1.00
|
O
|
B:HOH386
|
2.2
|
44.5
|
1.0
|
NE2
|
B:HIS350
|
2.3
|
44.4
|
1.0
|
SG
|
B:CYS98
|
2.4
|
45.0
|
1.0
|
OE1
|
B:GLU134
|
2.4
|
50.8
|
1.0
|
OE2
|
B:GLU134
|
2.5
|
55.3
|
1.0
|
O
|
B:HOH383
|
2.6
|
31.1
|
1.0
|
CD
|
B:GLU134
|
2.8
|
52.2
|
1.0
|
CD2
|
B:HIS350
|
3.2
|
47.3
|
1.0
|
NI
|
B:NI381
|
3.3
|
36.2
|
1.0
|
CE1
|
B:HIS350
|
3.3
|
41.0
|
1.0
|
CB
|
B:CYS98
|
3.3
|
43.3
|
1.0
|
O
|
B:HOH384
|
3.7
|
55.8
|
1.0
|
OE1
|
B:GLU133
|
4.1
|
56.0
|
1.0
|
O
|
B:HOH535
|
4.2
|
32.0
|
0.5
|
NE2
|
B:HIS100
|
4.3
|
42.6
|
1.0
|
CG
|
B:GLU134
|
4.3
|
47.1
|
1.0
|
CG
|
B:HIS350
|
4.3
|
47.3
|
1.0
|
ND1
|
B:HIS350
|
4.4
|
45.3
|
1.0
|
CD1
|
B:LEU77
|
4.4
|
49.0
|
1.0
|
CA
|
B:CYS98
|
4.7
|
43.4
|
1.0
|
O
|
B:HOH460
|
4.8
|
38.6
|
1.0
|
NE2
|
B:HIS158
|
4.8
|
49.5
|
1.0
|
CE1
|
B:HIS100
|
4.8
|
44.2
|
1.0
|
O
|
B:HOH385
|
4.9
|
46.8
|
1.0
|
O
|
B:HOH493
|
4.9
|
21.3
|
0.5
|
|
Reference:
G.Minasov,
L.Shuvalova,
J.S.Brunzelle,
F.R.Collart,
W.F.Anderson.
Structure of Bacillus Subtilis Yxep Protein, A Dinuclear Metal Binding Peptidase From M20 Family To Be Published.
Page generated: Wed Oct 9 16:33:32 2024
|