Zinc in PDB 6kua: Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Enzymatic activity of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
All present enzymatic activity of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus:
3.5.1.19;
Protein crystallography data
The structure of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus, PDB code: 6kua
was solved by
F.Shang,
J.Lan,
W.Liu,
Y.Xu,
Y.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.40 /
2.10
|
Space group
|
P 41
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.019,
89.019,
210.694,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
22.7
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
(pdb code 6kua). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the
Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus, PDB code: 6kua:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
Zinc binding site 1 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 1 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn201
b:0.8
occ:1.00
|
NE2
|
A:HIS56
|
2.3
|
66.4
|
1.0
|
CD2
|
A:HIS56
|
3.0
|
61.3
|
1.0
|
OD2
|
A:ASP54
|
3.1
|
61.1
|
1.0
|
CG
|
A:ASP54
|
3.4
|
58.3
|
1.0
|
CE1
|
A:HIS56
|
3.4
|
62.1
|
1.0
|
OD1
|
A:ASP54
|
3.7
|
57.7
|
1.0
|
CB
|
A:ASP54
|
4.1
|
47.9
|
1.0
|
CG
|
A:HIS56
|
4.2
|
64.8
|
1.0
|
ND1
|
A:HIS56
|
4.4
|
62.5
|
1.0
|
CZ
|
A:PHE15
|
4.7
|
61.2
|
1.0
|
|
Zinc binding site 2 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 2 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn201
b:1.0
occ:1.00
|
CE1
|
C:HIS56
|
2.1
|
63.6
|
1.0
|
NE2
|
C:HIS56
|
2.6
|
70.2
|
1.0
|
ND1
|
C:HIS56
|
3.2
|
61.6
|
1.0
|
CD2
|
C:HIS56
|
3.8
|
66.0
|
1.0
|
CG
|
C:HIS56
|
4.1
|
64.7
|
1.0
|
OD2
|
C:ASP54
|
4.6
|
49.9
|
1.0
|
O
|
C:HOH324
|
4.6
|
51.4
|
1.0
|
CG
|
C:ASP54
|
4.6
|
48.9
|
1.0
|
OD1
|
C:ASP54
|
4.8
|
51.2
|
1.0
|
CZ
|
C:PHE15
|
4.9
|
52.5
|
1.0
|
CE1
|
C:TYR107
|
5.0
|
25.9
|
1.0
|
|
Zinc binding site 3 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 3 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn201
b:99.6
occ:1.00
|
NE2
|
D:HIS56
|
2.5
|
73.2
|
1.0
|
OD1
|
D:ASP54
|
3.0
|
51.3
|
1.0
|
CE1
|
D:HIS56
|
3.0
|
69.0
|
1.0
|
O
|
C:HOH319
|
3.5
|
28.4
|
1.0
|
O
|
D:THR105
|
3.6
|
31.5
|
1.0
|
CD2
|
D:HIS56
|
3.6
|
63.7
|
1.0
|
CG
|
D:ASP54
|
3.7
|
51.8
|
1.0
|
OD2
|
D:ASP54
|
4.0
|
53.0
|
1.0
|
CA
|
D:ARG106
|
4.2
|
24.0
|
1.0
|
C
|
D:THR105
|
4.2
|
28.3
|
1.0
|
ND1
|
D:HIS56
|
4.2
|
69.3
|
1.0
|
C
|
D:ARG106
|
4.2
|
25.5
|
1.0
|
N
|
D:TYR107
|
4.4
|
25.4
|
1.0
|
CD1
|
D:TYR107
|
4.4
|
23.7
|
1.0
|
CE1
|
D:TYR107
|
4.5
|
26.6
|
1.0
|
CG
|
D:HIS56
|
4.5
|
66.0
|
1.0
|
N
|
D:ARG106
|
4.5
|
26.4
|
1.0
|
O
|
D:ARG106
|
4.6
|
25.5
|
1.0
|
CB
|
D:ASP54
|
4.7
|
43.3
|
1.0
|
|
Zinc binding site 4 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 4 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn201
b:0.1
occ:1.00
|
NE2
|
E:HIS56
|
2.4
|
63.2
|
1.0
|
CE1
|
E:HIS56
|
3.0
|
65.3
|
1.0
|
CD2
|
E:HIS56
|
3.4
|
63.1
|
1.0
|
ND1
|
E:HIS56
|
4.0
|
67.6
|
1.0
|
CG
|
E:HIS56
|
4.2
|
67.1
|
1.0
|
OD1
|
E:ASP54
|
4.6
|
47.0
|
1.0
|
CG
|
E:ASP54
|
4.7
|
51.2
|
1.0
|
CE1
|
E:TYR107
|
4.7
|
21.4
|
1.0
|
OD2
|
E:ASP54
|
4.8
|
52.9
|
1.0
|
O
|
F:HOH344
|
4.9
|
21.9
|
1.0
|
|
Zinc binding site 5 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 5 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn201
b:88.3
occ:1.00
|
CE1
|
F:HIS56
|
2.8
|
67.8
|
1.0
|
NE2
|
F:HIS56
|
3.1
|
70.7
|
1.0
|
ND1
|
F:HIS56
|
3.2
|
64.3
|
1.0
|
O
|
F:HOH365
|
3.2
|
46.5
|
1.0
|
CD2
|
F:HIS56
|
3.6
|
65.5
|
1.0
|
CG
|
F:HIS56
|
3.6
|
62.5
|
1.0
|
CG
|
F:ASP54
|
3.7
|
51.1
|
1.0
|
OD2
|
F:ASP54
|
3.9
|
51.9
|
1.0
|
CB
|
F:ASP54
|
3.9
|
44.0
|
1.0
|
OD1
|
F:ASP54
|
4.0
|
47.9
|
1.0
|
CB
|
F:HIS56
|
4.6
|
62.2
|
1.0
|
CZ
|
F:PHE15
|
4.8
|
52.1
|
1.0
|
|
Zinc binding site 6 out
of 7 in 6kua
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Zinc Binding Sites List in 6kua
Zinc binding site 6 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Zn201
b:1.0
occ:1.00
|
OD2
|
G:ASP54
|
2.8
|
57.0
|
1.0
|
CD2
|
G:HIS56
|
2.8
|
74.9
|
1.0
|
NE2
|
G:HIS56
|
3.4
|
77.7
|
1.0
|
CG
|
G:HIS56
|
3.4
|
76.4
|
1.0
|
O
|
G:THR105
|
3.6
|
32.6
|
1.0
|
N
|
G:HIS56
|
3.8
|
69.3
|
1.0
|
C
|
G:LEU55
|
3.8
|
64.9
|
1.0
|
CB
|
G:LEU55
|
3.8
|
54.5
|
1.0
|
CA
|
G:THR105
|
3.9
|
29.5
|
1.0
|
N
|
G:LEU55
|
3.9
|
48.9
|
1.0
|
CG
|
G:ASP54
|
4.0
|
55.6
|
1.0
|
CB
|
G:HIS56
|
4.0
|
73.9
|
1.0
|
CA
|
G:LEU55
|
4.0
|
55.7
|
1.0
|
C
|
G:THR105
|
4.1
|
29.6
|
1.0
|
CE1
|
G:HIS56
|
4.2
|
78.0
|
1.0
|
ND1
|
G:HIS56
|
4.2
|
79.2
|
1.0
|
O
|
G:LYS104
|
4.2
|
34.0
|
1.0
|
O
|
G:LEU55
|
4.3
|
66.1
|
1.0
|
CB
|
G:THR105
|
4.4
|
31.8
|
1.0
|
CA
|
G:HIS56
|
4.5
|
72.8
|
1.0
|
OD1
|
G:ASP54
|
4.5
|
53.9
|
1.0
|
O
|
G:HOH366
|
4.6
|
50.2
|
1.0
|
CG2
|
G:THR105
|
4.8
|
31.7
|
1.0
|
C
|
G:ASP54
|
4.9
|
45.1
|
1.0
|
N
|
G:THR105
|
5.0
|
28.4
|
1.0
|
|
Zinc binding site 7 out
of 7 in 6kua
Go back to
Zinc Binding Sites List in 6kua
Zinc binding site 7 out
of 7 in the Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Zn201
b:0.2
occ:1.00
|
NE2
|
H:HIS56
|
2.1
|
72.3
|
1.0
|
OD2
|
H:ASP54
|
2.8
|
66.0
|
1.0
|
CE1
|
H:HIS56
|
2.8
|
70.6
|
1.0
|
CD2
|
H:HIS56
|
3.1
|
74.1
|
1.0
|
CG
|
H:ASP54
|
3.6
|
61.9
|
1.0
|
ND1
|
H:HIS56
|
3.9
|
72.2
|
1.0
|
OD1
|
H:ASP54
|
4.0
|
64.3
|
1.0
|
CG
|
H:HIS56
|
4.1
|
73.6
|
1.0
|
CZ
|
H:PHE15
|
4.7
|
51.5
|
1.0
|
CB
|
H:ASP54
|
4.8
|
42.8
|
1.0
|
|
Reference:
F.Shang,
J.Lan,
L.Wang,
Y.Xu,
Y.Chen.
Crystal Structure of the Nicotinamidase Sapnca From Staphylococcus Aureus To Be Published.
Page generated: Tue Oct 29 02:06:17 2024
|