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Zinc in PDB 1f1g: Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide

Enzymatic activity of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide

All present enzymatic activity of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide:
1.15.1.1;

Protein crystallography data

The structure of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide, PDB code: 1f1g was solved by P.J.Hart, N.L.Ogihara, H.Liu, A.M.Nersissian, J.S.Valentine, D.Eisenberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 72.500, 72.480, 72.470, 109.20, 109.55, 109.21
R / Rfree (%) n/a / n/a

Other elements in 1f1g:

The structure of Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide also contains other interesting chemical elements:

Copper (Cu) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide (pdb code 1f1g). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide, PDB code: 1f1g:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1f1g

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Zinc binding site 1 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4002

b:11.0
occ:1.00
OD1 A:ASP83 1.9 9.4 1.0
ND1 A:HIS63 2.0 11.0 1.0
ND1 A:HIS71 2.0 10.2 1.0
ND1 A:HIS80 2.0 10.2 1.0
CG A:ASP83 2.7 8.9 1.0
CE1 A:HIS80 2.9 10.4 1.0
CE1 A:HIS71 2.9 10.8 1.0
OD2 A:ASP83 2.9 12.0 1.0
CE1 A:HIS63 2.9 10.5 1.0
CG A:HIS63 3.0 9.5 1.0
CG A:HIS80 3.1 10.5 1.0
CG A:HIS71 3.1 10.7 1.0
CB A:HIS63 3.4 9.5 1.0
CB A:HIS80 3.6 9.5 1.0
CB A:HIS71 3.6 10.6 1.0
CA A:HIS71 3.9 11.2 1.0
NE2 A:HIS80 4.0 10.6 1.0
O A:LYS136 4.0 12.1 1.0
NE2 A:HIS63 4.0 11.5 1.0
NE2 A:HIS71 4.1 10.6 1.0
CD2 A:HIS80 4.1 11.6 1.0
CD2 A:HIS63 4.1 12.6 1.0
CB A:ASP83 4.2 10.6 1.0
CD2 A:HIS71 4.2 10.8 1.0
CA A:ASP83 4.7 10.2 1.0
CD2 A:HIS46 4.7 10.5 1.0
N A:GLY72 4.8 11.2 1.0
N A:HIS80 4.8 10.2 1.0
CA A:HIS80 4.8 10.1 1.0
C A:HIS71 4.9 11.6 1.0
N A:HIS71 4.9 11.9 1.0
N A:ASP83 4.9 8.8 1.0
CA A:HIS63 4.9 9.7 1.0
C A:LYS136 5.0 12.7 1.0

Zinc binding site 2 out of 6 in 1f1g

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Zinc binding site 2 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4004

b:10.9
occ:1.00
OD1 B:ASP238 2.0 10.1 1.0
ND1 B:HIS226 2.0 10.0 1.0
ND1 B:HIS218 2.0 10.0 1.0
ND1 B:HIS235 2.1 10.0 1.0
CG B:ASP238 2.7 9.6 1.0
CE1 B:HIS226 2.9 9.8 1.0
CE1 B:HIS235 2.9 10.1 1.0
OD2 B:ASP238 2.9 10.8 1.0
CE1 B:HIS218 3.0 11.2 1.0
CG B:HIS218 3.0 9.9 1.0
CG B:HIS235 3.1 10.0 1.0
CG B:HIS226 3.2 10.1 1.0
CB B:HIS218 3.4 9.8 1.0
CB B:HIS235 3.6 9.3 1.0
CB B:HIS226 3.6 10.3 1.0
CA B:HIS226 3.9 10.6 1.0
NE2 B:HIS235 4.0 10.4 1.0
O B:LYS291 4.0 12.7 1.0
NE2 B:HIS226 4.1 10.2 1.0
NE2 B:HIS218 4.1 10.8 1.0
CD2 B:HIS235 4.1 11.9 1.0
CD2 B:HIS218 4.1 10.9 1.0
CB B:ASP238 4.2 11.2 1.0
CD2 B:HIS226 4.2 9.9 1.0
CA B:ASP238 4.7 10.9 1.0
CD2 B:HIS201 4.7 11.2 1.0
N B:HIS235 4.8 9.5 1.0
N B:GLY227 4.8 11.5 1.0
CA B:HIS235 4.8 10.3 1.0
C B:HIS226 4.9 10.3 1.0
N B:HIS226 4.9 11.2 1.0
CA B:HIS218 4.9 9.5 1.0
N B:ASP238 4.9 9.4 1.0
C B:LYS291 5.0 11.6 1.0

Zinc binding site 3 out of 6 in 1f1g

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Zinc binding site 3 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn4006

b:11.1
occ:1.00
OD1 C:ASP393 2.0 9.6 1.0
ND1 C:HIS373 2.0 12.1 1.0
ND1 C:HIS390 2.0 10.3 1.0
ND1 C:HIS381 2.0 10.9 1.0
CG C:ASP393 2.7 9.0 1.0
CE1 C:HIS390 2.9 10.7 1.0
OD2 C:ASP393 2.9 11.5 1.0
CE1 C:HIS373 2.9 10.4 1.0
CE1 C:HIS381 3.0 10.9 1.0
CG C:HIS373 3.0 10.3 1.0
CG C:HIS390 3.1 9.9 1.0
CG C:HIS381 3.1 10.1 1.0
CB C:HIS373 3.4 9.9 1.0
CB C:HIS390 3.5 9.6 1.0
CB C:HIS381 3.6 10.9 1.0
CA C:HIS381 3.9 10.8 1.0
NE2 C:HIS390 4.0 10.8 1.0
O C:LYS446 4.0 12.6 1.0
NE2 C:HIS373 4.0 11.4 1.0
CD2 C:HIS390 4.1 11.6 1.0
CD2 C:HIS373 4.1 13.7 1.0
NE2 C:HIS381 4.1 11.2 1.0
CB C:ASP393 4.2 10.6 1.0
CD2 C:HIS381 4.2 11.2 1.0
CA C:ASP393 4.6 10.5 1.0
CD2 C:HIS356 4.7 11.0 1.0
N C:HIS390 4.8 10.7 1.0
CA C:HIS390 4.8 10.2 1.0
N C:GLY382 4.8 11.9 1.0
C C:HIS381 4.9 11.2 1.0
CA C:HIS373 4.9 10.1 1.0
N C:ASP393 4.9 8.9 1.0
N C:HIS381 4.9 11.8 1.0
C C:LYS446 5.0 12.3 1.0

Zinc binding site 4 out of 6 in 1f1g

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Zinc binding site 4 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn4008

b:10.6
occ:1.00
OD1 D:ASP548 2.0 10.2 1.0
ND1 D:HIS536 2.0 10.1 1.0
ND1 D:HIS528 2.0 9.8 1.0
ND1 D:HIS545 2.0 10.0 1.0
CG D:ASP548 2.8 9.7 1.0
CE1 D:HIS536 2.9 10.1 1.0
CE1 D:HIS545 2.9 10.3 1.0
OD2 D:ASP548 2.9 10.8 1.0
CE1 D:HIS528 3.0 11.3 1.0
CG D:HIS528 3.0 9.8 1.0
CG D:HIS545 3.1 10.3 1.0
CG D:HIS536 3.1 9.8 1.0
CB D:HIS528 3.4 10.4 1.0
CB D:HIS545 3.6 9.8 1.0
CB D:HIS536 3.6 10.2 1.0
CA D:HIS536 3.9 10.3 1.0
NE2 D:HIS545 4.0 9.8 1.0
NE2 D:HIS536 4.1 10.1 1.0
O D:LYS601 4.1 12.3 1.0
CD2 D:HIS545 4.1 11.8 1.0
NE2 D:HIS528 4.1 11.8 1.0
CD2 D:HIS528 4.1 11.2 1.0
CD2 D:HIS536 4.2 9.8 1.0
CB D:ASP548 4.2 10.1 1.0
CA D:ASP548 4.7 10.2 1.0
CD2 D:HIS511 4.8 10.7 1.0
N D:HIS545 4.8 9.4 1.0
N D:GLY537 4.8 11.5 1.0
CA D:HIS545 4.8 10.2 1.0
C D:HIS536 4.8 10.4 1.0
N D:HIS536 4.9 11.3 1.0
CA D:HIS528 4.9 10.5 1.0
N D:ASP548 4.9 9.4 1.0
C D:LYS601 5.0 11.6 1.0

Zinc binding site 5 out of 6 in 1f1g

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Zinc binding site 5 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn4010

b:10.7
occ:1.00
OD1 E:ASP703 2.0 10.3 1.0
ND1 E:HIS691 2.0 10.3 1.0
ND1 E:HIS700 2.0 9.8 1.0
ND1 E:HIS683 2.0 10.9 1.0
CG E:ASP703 2.8 8.6 1.0
CE1 E:HIS700 2.9 10.4 1.0
OD2 E:ASP703 2.9 10.5 1.0
CE1 E:HIS691 2.9 11.3 1.0
CE1 E:HIS683 3.0 10.7 1.0
CG E:HIS683 3.0 10.4 1.0
CG E:HIS700 3.1 9.9 1.0
CG E:HIS691 3.1 10.3 1.0
CB E:HIS683 3.4 10.0 1.0
CB E:HIS700 3.5 9.8 1.0
CB E:HIS691 3.6 10.4 1.0
CA E:HIS691 3.9 10.2 1.0
NE2 E:HIS700 4.0 10.1 1.0
CD2 E:HIS700 4.1 10.9 1.0
O E:LYS756 4.1 11.4 1.0
NE2 E:HIS683 4.1 11.3 1.0
NE2 E:HIS691 4.1 10.2 1.0
CD2 E:HIS683 4.2 12.8 1.0
CB E:ASP703 4.2 9.8 1.0
CD2 E:HIS691 4.2 10.3 1.0
CA E:ASP703 4.7 10.2 1.0
CD2 E:HIS666 4.7 10.4 1.0
N E:GLY692 4.8 10.8 1.0
N E:HIS700 4.8 9.7 1.0
CA E:HIS700 4.8 10.0 1.0
C E:HIS691 4.9 9.4 1.0
N E:HIS691 4.9 11.4 1.0
N E:ASP703 4.9 9.3 1.0
CA E:HIS683 5.0 10.6 1.0
C E:LYS756 5.0 11.8 1.0

Zinc binding site 6 out of 6 in 1f1g

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Zinc binding site 6 out of 6 in the Crystal Structure of Yeast Cuznsod Exposed to Nitric Oxide


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 Yeast Cuznsod Exposed to Nitric Oxide within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn4012

b:10.6
occ:1.00
ND1 F:HIS846 2.0 9.8 1.0
OD1 F:ASP858 2.0 9.9 1.0
ND1 F:HIS838 2.0 10.5 1.0
ND1 F:HIS855 2.0 9.7 1.0
CG F:ASP858 2.8 9.4 1.0
CE1 F:HIS855 2.9 10.1 1.0
CE1 F:HIS846 2.9 10.9 1.0
OD2 F:ASP858 2.9 9.6 1.0
CE1 F:HIS838 3.0 10.4 1.0
CG F:HIS838 3.0 10.5 1.0
CG F:HIS855 3.1 9.8 1.0
CG F:HIS846 3.1 9.9 1.0
CB F:HIS838 3.4 9.9 1.0
CB F:HIS855 3.6 10.0 1.0
CB F:HIS846 3.6 10.7 1.0
CA F:HIS846 3.9 10.3 1.0
NE2 F:HIS855 4.0 10.6 1.0
O F:LYS911 4.1 12.0 1.0
CD2 F:HIS855 4.1 10.6 1.0
NE2 F:HIS838 4.1 11.2 1.0
NE2 F:HIS846 4.1 10.2 1.0
CD2 F:HIS838 4.1 11.8 1.0
CD2 F:HIS846 4.2 10.2 1.0
CB F:ASP858 4.2 10.4 1.0
CA F:ASP858 4.7 10.8 1.0
CD2 F:HIS821 4.7 11.2 1.0
N F:GLY847 4.8 11.4 1.0
N F:HIS855 4.8 9.8 1.0
CA F:HIS855 4.8 9.6 1.0
C F:HIS846 4.9 9.5 1.0
N F:ASP858 4.9 9.0 1.0
N F:HIS846 4.9 11.9 1.0
CA F:HIS838 4.9 10.2 1.0
C F:LYS911 5.0 11.6 1.0

Reference:

P.J.Hart, M.M.Balbirnie, N.L.Ogihara, A.M.Nersissian, M.S.Weiss, J.S.Valentine, D.Eisenberg. A Structure-Based Mechanism For Copper-Zinc Superoxide Dismutase. Biochemistry V. 38 2167 1999.
ISSN: ISSN 0006-2960
PubMed: 10026301
DOI: 10.1021/BI982284U
Page generated: Wed Dec 16 02:48:57 2020

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