Zinc in PDB 8co4: Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina

Enzymatic activity of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina

All present enzymatic activity of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina:
1.1.1.1; 1.1.1.284;

Protein crystallography data

The structure of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina, PDB code: 8co4 was solved by S.Fermani, S.Fanti, G.Carloni, J.Rossi, G.Falini, M.Zaffagnini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.92 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.6, 93.927, 167.484, 90, 90, 90
R / Rfree (%) 16.1 / 21.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina (pdb code 8co4). 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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina, PDB code: 8co4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8co4

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Zinc binding site 1 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.0
occ:0.99
 SG A:CYS105 2.3 22.1 1.0
SG A:CYS113 2.3 21.7 1.0
SG A:CYS99 2.4 21.4 1.0
SG A:CYS102 2.4 21.9 1.0
CB A:CYS113 3.2 19.8 1.0
CB A:CYS105 3.3 22.9 1.0
CB A:CYS102 3.4 24.8 1.0
CB A:CYS99 3.4 24.4 1.0
N A:CYS99 3.5 16.0 1.0
CA A:CYS113 3.7 22.8 1.0
N A:CYS102 3.8 20.8 1.0
CA A:CYS99 3.9 22.7 1.0
N A:ARG100 3.9 16.1 1.0
N A:GLY114 4.1 26.6 1.0
N A:CYS105 4.1 24.2 1.0
CA A:CYS102 4.2 26.2 1.0
C A:CYS113 4.3 31.3 1.0
C A:CYS99 4.3 24.4 1.0
CA A:CYS105 4.3 26.0 1.0
N A:GLU101 4.4 19.7 1.0
CB A:LYS115 4.5 24.4 1.0
N A:LYS115 4.5 29.8 1.0
C A:GLU98 4.7 21.3 1.0
C A:CYS102 4.9 23.7 1.0
CA A:ARG100 4.9 21.9 1.0
O A:LEU112 4.9 29.6 1.0
N A:CYS113 5.0 23.9 1.0
C A:GLU101 5.0 27.5 1.0

Zinc binding site 2 out of 8 in 8co4

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Zinc binding site 2 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:39.8
occ:0.85
 O A:HOH504 1.6 23.9 1.0
O A:HOH658 1.6 33.4 1.0
NE2 A:HIS69 2.2 31.6 1.0
SG A:CYS177 2.3 37.5 1.0
SG A:CYS47 2.3 29.5 1.0
CD2 A:HIS69 3.1 25.8 1.0
CE1 A:HIS69 3.3 26.1 1.0
CB A:CYS177 3.3 36.5 1.0
CB A:CYS47 3.4 31.7 1.0
OE2 A:GLU70 3.7 33.5 1.0
CB A:THR49 4.0 32.4 1.0
OG1 A:THR49 4.0 30.3 1.0
CG A:HIS69 4.3 22.3 1.0
ND1 A:HIS69 4.3 21.6 1.0
CG A:GLU70 4.4 29.7 1.0
O A:HOH764 4.5 48.2 1.0
CD A:GLU70 4.5 32.8 1.0
NH2 A:ARG372 4.5 27.1 1.0
CA A:CYS177 4.7 23.6 1.0
CG2 A:THR49 4.8 28.3 1.0
N A:GLY178 4.8 26.5 1.0
CA A:CYS47 4.8 38.4 1.0
N A:THR49 5.0 25.1 1.0
C A:CYS177 5.0 24.8 1.0

Zinc binding site 3 out of 8 in 8co4

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Zinc binding site 3 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:19.8
occ:0.97
 SG B:CYS105 2.3 21.5 1.0
SG B:CYS99 2.3 21.0 1.0
SG B:CYS102 2.4 19.5 1.0
SG B:CYS113 2.4 18.8 1.0
CB B:CYS113 3.2 22.0 1.0
CB B:CYS102 3.3 20.2 1.0
CB B:CYS105 3.3 25.0 1.0
CB B:CYS99 3.4 19.1 1.0
N B:CYS99 3.6 16.1 1.0
CA B:CYS113 3.7 23.4 1.0
N B:CYS102 3.7 21.5 1.0
CA B:CYS99 3.9 17.8 1.0
N B:ARG100 3.9 15.6 1.0
N B:GLY114 4.0 24.9 1.0
CA B:CYS102 4.1 25.9 1.0
N B:CYS105 4.1 17.1 1.0
C B:CYS113 4.2 24.7 1.0
C B:CYS99 4.3 19.6 1.0
N B:GLU101 4.3 26.4 1.0
CA B:CYS105 4.3 22.0 1.0
N B:LYS115 4.4 21.6 1.0
CB B:LYS115 4.4 18.3 1.0
C B:GLU98 4.7 15.5 1.0
C B:GLU101 4.9 28.6 1.0
C B:CYS102 4.9 19.6 1.0
CA B:ARG100 4.9 24.4 1.0
CA B:LYS115 5.0 16.1 1.0
N B:CYS113 5.0 20.7 1.0

Zinc binding site 4 out of 8 in 8co4

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Zinc binding site 4 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:30.5
occ:0.90
 O B:HOH527 1.7 21.7 1.0
O B:HOH547 1.8 25.2 1.0
NE2 B:HIS69 2.2 34.5 1.0
SG B:CYS177 2.3 28.6 1.0
SG B:CYS47 2.3 27.2 1.0
CE1 B:HIS69 3.1 25.4 1.0
CD2 B:HIS69 3.3 28.4 1.0
CB B:CYS177 3.3 24.6 1.0
CB B:CYS47 3.4 27.6 1.0
OG1 B:THR49 3.9 26.6 1.0
CB B:THR49 4.0 23.0 1.0
OE2 B:GLU70 4.1 31.5 1.0
ND1 B:HIS69 4.2 25.0 1.0
CG B:HIS69 4.4 20.0 1.0
CG B:GLU70 4.7 26.8 1.0
CA B:CYS177 4.7 22.1 1.0
O B:HOH736 4.7 46.6 1.0
NH2 B:ARG372 4.7 23.3 1.0
CG2 B:THR49 4.8 27.3 1.0
CD B:GLU70 4.8 35.1 1.0
CA B:CYS47 4.9 30.3 1.0
N B:GLY178 4.9 26.1 1.0
N B:THR49 4.9 21.3 1.0

Zinc binding site 5 out of 8 in 8co4

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Zinc binding site 5 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:20.6
occ:1.00
 SG C:CYS99 2.3 20.9 1.0
SG C:CYS105 2.3 20.2 1.0
SG C:CYS113 2.4 18.7 1.0
SG C:CYS102 2.4 18.7 1.0
CB C:CYS113 3.2 20.9 1.0
CB C:CYS102 3.4 18.4 1.0
CB C:CYS99 3.4 14.6 1.0
CB C:CYS105 3.4 19.3 1.0
N C:CYS99 3.6 15.9 1.0
CA C:CYS113 3.7 21.0 1.0
N C:CYS102 3.7 17.9 1.0
N C:ARG100 3.9 20.4 1.0
CA C:CYS99 3.9 13.9 1.0
N C:GLY114 4.0 24.1 1.0
CA C:CYS102 4.1 19.6 1.0
N C:CYS105 4.2 18.1 1.0
C C:CYS99 4.3 20.7 1.0
C C:CYS113 4.3 29.9 1.0
N C:LYS115 4.3 17.7 1.0
CB C:LYS115 4.3 24.1 1.0
N C:GLU101 4.4 17.5 1.0
CA C:CYS105 4.4 18.3 1.0
C C:GLU98 4.7 15.7 1.0
C C:CYS102 4.8 19.6 1.0
CA C:ARG100 4.9 18.9 1.0
C C:GLU101 4.9 30.8 1.0
CA C:LYS115 4.9 25.1 1.0
O C:CYS102 4.9 19.7 1.0

Zinc binding site 6 out of 8 in 8co4

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Zinc binding site 6 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:25.2
occ:0.90
 O C:HOH531 1.7 26.9 1.0
O C:HOH558 1.9 28.8 1.0
NE2 C:HIS69 2.2 22.6 1.0
SG C:CYS177 2.3 25.6 1.0
SG C:CYS47 2.4 27.1 1.0
CE1 C:HIS69 3.1 24.9 1.0
CD2 C:HIS69 3.2 20.4 1.0
CB C:CYS177 3.4 25.2 1.0
CB C:CYS47 3.4 22.7 1.0
OG1 C:THR49 3.8 28.6 1.0
CB C:THR49 3.9 24.3 1.0
O C:HOH716 4.1 33.7 1.0
OE1 C:GLU70 4.2 33.7 1.0
O C:HOH741 4.2 36.7 1.0
ND1 C:HIS69 4.2 20.7 1.0
CG C:HIS69 4.3 15.2 1.0
CG2 C:THR49 4.7 25.6 1.0
CA C:CYS177 4.8 21.6 1.0
CG C:GLU70 4.8 30.2 1.0
N C:THR49 4.8 18.6 1.0
CE1 C:TYR95 4.8 27.6 1.0
CA C:CYS47 4.8 25.4 1.0
OH C:TYR95 4.9 34.2 1.0
CD C:GLU70 4.9 27.0 1.0
N C:GLY178 5.0 25.3 1.0
CA C:THR49 5.0 21.8 1.0

Zinc binding site 7 out of 8 in 8co4

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Zinc binding site 7 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:22.0
occ:1.00
 SG D:CYS113 2.3 19.3 1.0
SG D:CYS105 2.3 20.1 1.0
SG D:CYS99 2.3 20.4 1.0
SG D:CYS102 2.3 19.5 1.0
CB D:CYS113 3.2 18.4 1.0
CB D:CYS102 3.3 23.8 1.0
CB D:CYS105 3.4 22.9 1.0
CB D:CYS99 3.4 20.2 1.0
N D:CYS99 3.6 17.5 1.0
CA D:CYS113 3.6 22.3 1.0
N D:CYS102 3.8 20.8 1.0
N D:GLY114 3.9 27.3 1.0
CA D:CYS99 3.9 19.2 1.0
N D:ARG100 3.9 16.6 1.0
CA D:CYS102 4.1 25.2 1.0
N D:CYS105 4.2 15.2 1.0
C D:CYS113 4.2 23.2 1.0
C D:CYS99 4.3 23.5 1.0
CA D:CYS105 4.4 21.2 1.0
N D:GLU101 4.4 21.8 1.0
N D:LYS115 4.6 20.6 1.0
CB D:LYS115 4.7 24.8 1.0
C D:GLU98 4.7 18.5 1.0
C D:CYS102 4.8 24.5 1.0
CA D:ARG100 4.9 19.8 1.0
C D:GLU101 4.9 32.6 1.0
N D:CYS113 4.9 21.8 1.0
O D:CYS102 5.0 23.2 1.0

Zinc binding site 8 out of 8 in 8co4

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Zinc binding site 8 out of 8 in the Crystal Structure of Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina


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 Apo S-Nitrosoglutathione Reductase From Arabidopsis Thalina within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:34.5
occ:0.95
 NE2 D:HIS69 2.2 29.1 1.0
O D:HOH514 2.2 29.2 1.0
SG D:CYS177 2.3 28.9 1.0
SG D:CYS47 2.3 35.4 1.0
CE1 D:HIS69 3.1 23.2 1.0
CD2 D:HIS69 3.2 27.4 1.0
CB D:CYS47 3.4 21.8 1.0
CB D:CYS177 3.4 31.5 1.0
OG1 D:THR49 3.9 34.8 1.0
OE2 D:GLU70 4.1 33.5 1.0
CB D:THR49 4.1 27.8 1.0
ND1 D:HIS69 4.3 24.0 1.0
CG D:HIS69 4.3 20.6 1.0
CG D:GLU70 4.6 27.5 1.0
NH2 D:ARG372 4.7 25.6 1.0
O D:HOH504 4.7 41.9 1.0
CD D:GLU70 4.8 35.9 1.0
CA D:CYS177 4.8 25.3 1.0
CA D:CYS47 4.8 30.4 1.0
N D:GLY178 4.9 26.1 1.0
N D:THR49 4.9 32.9 1.0

Reference:

M.Meloni, J.Rossi, S.Fanti, G.Carloni, D.Tedesco, P.Treffon, L.Piccinini, G.Falini, P.Trost, E.Vierling, F.Licausi, B.Giuntoli, F.Musiani, S.Fermani, M.Zaffagnini. Structural and Biochemical Characterization of Arabidopsis Alcohol Dehydrogenases Reveals Distinct Functional Properties But Similar Redox Sensitivity. Plant J. 2024.
ISSN: ESSN 1365-313X
PubMed: 38308388
DOI: 10.1111/TPJ.16651
Page generated: Wed Oct 30 18:52:18 2024

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