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Zinc in PDB 8iq1: Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State

Enzymatic activity of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State

All present enzymatic activity of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State, PDB code: 8iq1 was solved by J.H.Zhou, W.X.Huang, R.X.Cheng, P.J.Zhang, Y.C.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.28 / 1.80
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 46.126, 69.961, 91.345, 98.69, 94.83, 103.31
R / Rfree (%) 18.4 / 21.7

Other elements in 8iq1:

The structure of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms
Copper (Cu) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State (pdb code 8iq1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State, PDB code: 8iq1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8iq1

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Zinc binding site 1 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:15.7
occ:1.00
ND1 A:HIS61 2.0 17.4 1.0
OD1 A:ASP81 2.0 18.6 1.0
ND1 A:HIS69 2.1 16.5 1.0
ND1 A:HIS78 2.1 14.3 1.0
CG A:ASP81 2.8 14.1 1.0
CE1 A:HIS61 2.9 18.4 1.0
CE1 A:HIS69 2.9 18.3 1.0
CE1 A:HIS78 3.0 15.6 1.0
CG A:HIS61 3.0 15.1 1.0
OD2 A:ASP81 3.0 14.2 1.0
CG A:HIS78 3.2 14.2 1.0
CG A:HIS69 3.2 17.7 1.0
CB A:HIS61 3.4 14.2 1.0
CB A:HIS78 3.6 14.3 1.0
CB A:HIS69 3.7 15.6 1.0
O A:LYS134 3.9 19.5 1.0
CA A:HIS69 4.0 15.9 1.0
NE2 A:HIS61 4.0 17.4 1.0
NE2 A:HIS78 4.1 14.6 1.0
CD2 A:HIS61 4.1 15.9 1.0
NE2 A:HIS69 4.1 19.4 1.0
CD2 A:HIS78 4.2 13.6 1.0
CB A:ASP81 4.2 14.0 1.0
CD2 A:HIS69 4.3 18.2 1.0
CA A:ASP81 4.7 13.8 1.0
O A:HOH364 4.7 20.8 1.0
N A:GLY70 4.8 17.4 1.0
N A:HIS78 4.8 13.3 1.0
CA A:HIS78 4.8 13.0 1.0
C A:LYS134 4.9 20.3 1.0
CA A:HIS61 4.9 14.0 1.0
CD2 A:HIS44 4.9 15.3 1.0
C A:HIS69 5.0 20.2 1.0
N A:ASP81 5.0 13.3 1.0

Zinc binding site 2 out of 8 in 8iq1

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Zinc binding site 2 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:18.6
occ:1.00
ND1 B:HIS78 1.9 19.5 1.0
OD1 B:ASP81 2.0 19.7 1.0
ND1 B:HIS69 2.0 21.7 1.0
ND1 B:HIS61 2.2 22.4 1.0
CE1 B:HIS78 2.7 20.1 1.0
CG B:ASP81 2.8 18.0 1.0
CE1 B:HIS69 2.9 21.5 1.0
OD2 B:ASP81 2.9 19.5 1.0
CG B:HIS78 3.0 19.0 1.0
CG B:HIS69 3.1 22.6 1.0
CG B:HIS61 3.2 22.6 1.0
CE1 B:HIS61 3.2 24.8 1.0
CB B:HIS61 3.4 17.4 1.0
CB B:HIS78 3.5 16.6 1.0
CB B:HIS69 3.6 23.8 1.0
NE2 B:HIS78 3.9 21.2 1.0
O B:LYS134 3.9 28.8 1.0
CA B:HIS69 3.9 19.9 1.0
CD2 B:HIS78 4.0 19.5 1.0
NE2 B:HIS69 4.1 22.8 1.0
CB B:ASP81 4.2 19.7 1.0
CD2 B:HIS69 4.2 24.1 1.0
NE2 B:HIS61 4.3 24.3 1.0
CD2 B:HIS61 4.3 24.6 1.0
N B:HIS78 4.7 16.8 1.0
CA B:ASP81 4.7 17.2 1.0
N B:GLY70 4.7 19.8 1.0
CA B:HIS78 4.7 16.2 1.0
C B:HIS69 4.9 22.2 1.0
N B:ASP81 4.9 15.5 1.0
C B:LYS134 4.9 30.4 1.0
O B:HOH378 4.9 33.1 1.0
N B:HIS69 4.9 21.2 1.0
CA B:HIS61 5.0 17.6 1.0

Zinc binding site 3 out of 8 in 8iq1

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Zinc binding site 3 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:19.7
occ:1.00
OD1 C:ASP81 1.9 18.1 1.0
ND1 C:HIS78 1.9 18.8 1.0
ND1 C:HIS61 2.0 20.5 1.0
ND1 C:HIS69 2.1 23.2 1.0
CG C:ASP81 2.7 19.2 1.0
CE1 C:HIS78 2.8 18.7 1.0
OD2 C:ASP81 2.9 19.0 1.0
CE1 C:HIS69 3.0 22.4 1.0
CE1 C:HIS61 3.0 20.6 1.0
CG C:HIS78 3.0 17.3 1.0
CG C:HIS61 3.0 20.0 1.0
CG C:HIS69 3.2 23.6 1.0
CB C:HIS61 3.4 15.3 1.0
CB C:HIS78 3.5 16.6 1.0
CB C:HIS69 3.7 22.2 1.0
NE2 C:HIS78 3.9 16.9 1.0
CA C:HIS69 4.0 21.8 1.0
O C:LYS134 4.0 23.6 1.0
CD2 C:HIS78 4.1 17.1 1.0
NE2 C:HIS61 4.1 21.8 1.0
CB C:ASP81 4.1 17.5 1.0
NE2 C:HIS69 4.1 24.7 1.0
CD2 C:HIS61 4.2 19.4 1.0
CD2 C:HIS69 4.3 24.0 1.0
CA C:ASP81 4.7 18.6 1.0
N C:HIS78 4.7 18.5 1.0
N C:GLY70 4.7 21.4 1.0
CA C:HIS78 4.7 17.7 1.0
O C:HOH378 4.8 24.1 1.0
C C:HIS69 4.9 24.0 1.0
CA C:HIS61 4.9 15.0 1.0
N C:ASP81 4.9 19.5 1.0

Zinc binding site 4 out of 8 in 8iq1

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Zinc binding site 4 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:16.4
occ:1.00
OD1 D:ASP81 2.0 13.4 1.0
ND1 D:HIS69 2.0 16.9 1.0
ND1 D:HIS78 2.0 16.4 1.0
ND1 D:HIS61 2.1 14.7 1.0
CG D:ASP81 2.7 14.2 1.0
CE1 D:HIS78 2.8 18.5 1.0
CE1 D:HIS69 2.8 16.7 1.0
OD2 D:ASP81 2.9 17.1 1.0
CE1 D:HIS61 3.1 15.2 1.0
CG D:HIS61 3.1 16.0 1.0
CG D:HIS78 3.1 17.4 1.0
CG D:HIS69 3.1 18.0 1.0
CB D:HIS61 3.4 14.6 1.0
CB D:HIS69 3.6 18.9 1.0
CB D:HIS78 3.7 15.9 1.0
NE2 D:HIS78 3.9 17.4 1.0
CA D:HIS69 4.0 20.9 1.0
O D:LYS134 4.0 24.6 1.0
NE2 D:HIS69 4.0 16.9 1.0
CD2 D:HIS78 4.1 17.4 1.0
CB D:ASP81 4.2 13.8 1.0
CD2 D:HIS69 4.2 17.9 1.0
NE2 D:HIS61 4.2 17.3 1.0
CD2 D:HIS61 4.2 15.9 1.0
O D:HOH350 4.6 22.0 1.0
CA D:ASP81 4.7 13.4 1.0
N D:HIS78 4.7 15.6 1.0
N D:GLY70 4.7 19.9 1.0
CA D:HIS78 4.8 14.0 1.0
CD2 D:HIS44 4.9 11.9 1.0
C D:HIS69 4.9 21.0 1.0
C D:LYS134 4.9 22.9 1.0
CA D:HIS61 5.0 15.9 1.0
N D:HIS69 5.0 20.0 1.0
N D:ASP81 5.0 10.3 1.0

Zinc binding site 5 out of 8 in 8iq1

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Zinc binding site 5 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:16.8
occ:1.00
OD1 E:ASP81 1.9 14.1 1.0
ND1 E:HIS69 2.0 15.4 1.0
ND1 E:HIS61 2.0 15.0 1.0
ND1 E:HIS78 2.1 15.8 1.0
CG E:ASP81 2.6 17.5 1.0
OD2 E:ASP81 2.7 14.3 1.0
CE1 E:HIS69 2.8 17.2 1.0
CE1 E:HIS61 2.9 15.3 1.0
CE1 E:HIS78 2.9 17.2 1.0
CG E:HIS61 3.1 16.5 1.0
CG E:HIS78 3.1 15.4 1.0
CG E:HIS69 3.1 17.0 1.0
CB E:HIS61 3.4 14.4 1.0
CB E:HIS78 3.6 15.0 1.0
CB E:HIS69 3.6 17.3 1.0
CA E:HIS69 3.9 17.2 1.0
NE2 E:HIS69 4.0 17.6 1.0
O E:LYS134 4.0 19.4 1.0
CB E:ASP81 4.0 13.5 1.0
NE2 E:HIS78 4.0 18.3 1.0
NE2 E:HIS61 4.1 16.5 1.0
CD2 E:HIS78 4.2 14.9 1.0
CD2 E:HIS61 4.2 17.2 1.0
CD2 E:HIS69 4.2 17.4 1.0
N E:GLY70 4.6 15.5 1.0
CA E:ASP81 4.6 13.1 1.0
N E:HIS78 4.6 14.1 1.0
CA E:HIS78 4.7 15.6 1.0
C E:HIS69 4.8 17.3 1.0
CD2 E:HIS44 4.9 14.2 1.0
N E:ASP81 4.9 12.9 1.0
O E:HOH378 4.9 19.9 1.0
N E:HIS69 5.0 16.8 1.0
CA E:HIS61 5.0 16.4 1.0
O E:GLY70 5.0 18.4 1.0

Zinc binding site 6 out of 8 in 8iq1

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Zinc binding site 6 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:20.5
occ:1.00
ND1 F:HIS61 2.0 20.5 1.0
ND1 F:HIS78 2.0 18.5 1.0
OD1 F:ASP81 2.1 21.0 1.0
ND1 F:HIS69 2.2 24.3 1.0
CE1 F:HIS78 2.8 22.4 1.0
CG F:ASP81 2.8 20.0 1.0
CE1 F:HIS61 2.9 21.8 1.0
CG F:HIS61 3.0 20.2 1.0
CE1 F:HIS69 3.0 24.6 1.0
OD2 F:ASP81 3.0 20.7 1.0
CG F:HIS78 3.1 19.5 1.0
CG F:HIS69 3.3 25.8 1.0
CB F:HIS61 3.4 18.6 1.0
CB F:HIS78 3.6 18.8 1.0
CB F:HIS69 3.7 25.2 1.0
NE2 F:HIS78 4.0 19.9 1.0
NE2 F:HIS61 4.0 22.0 1.0
O F:LYS134 4.0 27.8 1.0
CA F:HIS69 4.0 25.1 1.0
CD2 F:HIS61 4.1 21.2 1.0
CD2 F:HIS78 4.1 18.4 1.0
NE2 F:HIS69 4.2 27.3 1.0
CB F:ASP81 4.3 18.4 1.0
CD2 F:HIS69 4.3 26.6 1.0
CA F:ASP81 4.7 18.3 1.0
N F:HIS78 4.8 20.6 1.0
N F:GLY70 4.8 26.0 1.0
CA F:HIS78 4.8 19.9 1.0
CA F:HIS61 4.9 17.6 1.0
CD2 F:HIS44 4.9 20.9 1.0
O F:HOH378 5.0 28.0 1.0
C F:HIS69 5.0 26.8 1.0

Zinc binding site 7 out of 8 in 8iq1

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Zinc binding site 7 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


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 Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:19.6
occ:1.00
ND1 G:HIS78 1.9 20.1 1.0
ND1 G:HIS61 2.0 19.4 1.0
ND1 G:HIS69 2.1 21.5 1.0
OD1 G:ASP81 2.1 16.4 1.0
CE1 G:HIS78 2.6 22.2 1.0
CG G:ASP81 2.8 17.0 1.0
OD2 G:ASP81 2.9 19.4 1.0
CE1 G:HIS69 2.9 22.7 1.0
CE1 G:HIS61 3.0 19.7 1.0
CG G:HIS61 3.1 18.2 1.0
CG G:HIS78 3.1 21.1 1.0
CG G:HIS69 3.1 22.8 1.0
CB G:HIS61 3.4 16.1 1.0
CB G:HIS69 3.5 25.8 1.0
CB G:HIS78 3.7 18.9 1.0
NE2 G:HIS78 3.8 20.8 1.0
O G:LYS134 3.8 30.0 1.0
CA G:HIS69 3.8 27.9 1.0
CD2 G:HIS78 4.0 20.1 1.0
NE2 G:HIS69 4.1 22.1 1.0
NE2 G:HIS61 4.1 20.6 1.0
CD2 G:HIS61 4.2 19.0 1.0
CD2 G:HIS69 4.2 23.4 1.0
CB G:ASP81 4.3 14.8 1.0
N G:GLY70 4.7 29.9 1.0
N G:HIS78 4.7 19.2 1.0
CA G:ASP81 4.8 18.3 1.0
CA G:HIS78 4.8 20.5 1.0
N G:HIS69 4.8 28.7 1.0
C G:LYS134 4.8 31.9 1.0
C G:HIS69 4.8 32.3 1.0
CD2 G:HIS44 4.9 19.6 1.0
CA G:HIS61 4.9 16.7 1.0

Zinc binding site 8 out of 8 in 8iq1

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Zinc binding site 8 out of 8 in the Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Hydrogen Sulfide-Bound Superoxide Dismutase in Reduced State within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:18.4
occ:1.00
OD1 H:ASP81 1.8 20.4 1.0
ND1 H:HIS61 2.1 20.9 1.0
ND1 H:HIS78 2.2 21.9 1.0
ND1 H:HIS69 2.2 27.5 1.0
CG H:ASP81 2.6 20.5 1.0
OD2 H:ASP81 2.8 22.8 1.0
CE1 H:HIS69 3.0 27.2 1.0
CG H:HIS78 3.0 22.1 1.0
CG H:HIS61 3.0 22.8 1.0
CE1 H:HIS78 3.1 21.0 1.0
CE1 H:HIS61 3.2 22.3 1.0
CG H:HIS69 3.3 29.6 1.0
CB H:HIS61 3.3 23.3 1.0
CB H:HIS78 3.3 20.7 1.0
CB H:HIS69 3.7 27.2 1.0
CA H:HIS69 4.0 25.5 1.0
CB H:ASP81 4.0 20.2 1.0
CD2 H:HIS78 4.2 20.2 1.0
NE2 H:HIS78 4.2 21.9 1.0
NE2 H:HIS69 4.2 27.6 1.0
CD2 H:HIS61 4.2 22.7 1.0
NE2 H:HIS61 4.2 24.8 1.0
O H:LYS134 4.3 31.0 1.0
CD2 H:HIS69 4.3 28.6 1.0
CA H:ASP81 4.5 20.3 1.0
N H:HIS78 4.5 23.1 1.0
CA H:HIS78 4.5 22.2 1.0
N H:GLY70 4.8 26.7 1.0
N H:ASP81 4.8 19.4 1.0
O1 H:EDO203 4.8 34.3 1.0
CA H:HIS61 4.8 25.8 1.0
CD2 H:HIS44 4.8 21.6 1.0
C H:HIS69 4.9 27.8 1.0

Reference:

D.D.Wu, S.Jin, R.X.Cheng, W.J.Cai, W.L.Xue, Q.Q.Zhang, L.J.Yang, Q.Zhu, M.Y.Li, G.Lin, Y.Z.Wang, X.P.Mu, Y.Wang, I.Y.Zhang, Q.Zhang, Y.Chen, S.Y.Cai, B.Tan, Y.Li, Y.Q.Chen, P.J.Zhang, C.Sun, Y.Yin, M.J.Wang, Y.Z.Zhu, B.B.Tao, J.H.Zhou, W.X.Huang, Y.C.Zhu. Hydrogen Sulfide Functions As A Micro-Modulator Bound at the Copper Active Site of Cu/Zn-Sod to Regulate the Catalytic Activity of the Enzyme. Cell Rep V. 42 12750 2023.
ISSN: ESSN 2211-1247
PubMed: 37421623
DOI: 10.1016/J.CELREP.2023.112750
Page generated: Thu Dec 28 13:17:46 2023

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