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Zinc in PDB 4dla: Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)

Enzymatic activity of Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)

All present enzymatic activity of Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum):
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum), PDB code: 4dla was solved by D.Kopecny, M.Tylichova, P.Briozzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.25 / 2.14
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 83.710, 125.000, 77.150, 90.00, 90.00, 90.00
R / Rfree (%) 23.7 / 29.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum) (pdb code 4dla). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum), PDB code: 4dla:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dla

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Zinc binding site 1 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)


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 S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:40.2
occ:1.00
 O A:HOH701 1.9 33.0 1.0
NE2 A:HIS69 2.1 33.1 1.0
SG A:CYS177 2.2 31.3 1.0
SG A:CYS47 2.3 34.4 1.0
CD2 A:HIS69 3.0 33.0 1.0
CE1 A:HIS69 3.2 32.8 1.0
CB A:CYS47 3.2 30.7 1.0
CB A:CYS177 3.2 28.0 1.0
OG1 A:THR49 3.9 29.8 1.0
O A:HOH544 4.1 35.6 1.0
CG A:HIS69 4.1 31.5 1.0
CB A:THR49 4.2 34.2 1.0
ND1 A:HIS69 4.2 33.5 1.0
O A:HOH702 4.4 42.3 1.0
CA A:CYS177 4.6 28.7 1.0
OE2 A:GLU70 4.7 30.5 1.0
CA A:CYS47 4.7 30.9 1.0
N A:GLY178 4.7 31.0 1.0
NH2 A:ARG372 4.7 26.2 1.0
O A:HOH545 4.8 35.3 1.0
CE1 A:TYR95 4.9 38.6 1.0

Zinc binding site 2 out of 4 in 4dla

Go back to Zinc Binding Sites List in 4dla
Zinc binding site 2 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)


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 S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:30.9
occ:1.00
 SG A:CYS113 2.2 31.5 1.0
SG A:CYS99 2.4 29.9 1.0
SG A:CYS102 2.4 35.7 1.0
SG A:CYS105 2.4 37.9 1.0
CB A:CYS113 3.0 27.4 1.0
CB A:CYS105 3.3 34.5 1.0
CB A:CYS102 3.4 32.3 1.0
CB A:CYS99 3.4 25.1 1.0
N A:CYS99 3.5 25.0 1.0
CA A:CYS99 3.8 24.5 1.0
N A:CYS102 3.8 34.0 1.0
CA A:CYS113 3.9 26.8 1.0
N A:ARG100 4.0 28.1 1.0
CA A:CYS102 4.2 32.8 1.0
N A:CYS105 4.2 33.6 1.0
C A:CYS99 4.3 29.3 1.0
CA A:CYS105 4.3 34.5 1.0
N A:GLU101 4.4 32.1 1.0
C A:GLU98 4.6 28.6 1.0
N A:GLY114 4.6 27.4 1.0
C A:CYS113 4.6 28.1 1.0
C A:CYS102 4.8 36.7 1.0
CB A:LYS115 4.9 28.5 1.0
N A:LYS115 4.9 28.1 1.0
CA A:GLU98 4.9 25.1 1.0
C A:GLU101 4.9 38.0 1.0
CA A:ARG100 5.0 29.3 1.0
O A:CYS102 5.0 36.0 1.0

Zinc binding site 3 out of 4 in 4dla

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Zinc binding site 3 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)


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 S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:36.3
occ:1.00
 O B:HOH551 1.9 23.2 1.0
NE2 B:HIS69 2.1 29.8 1.0
SG B:CYS177 2.2 26.5 1.0
SG B:CYS47 2.5 34.0 1.0
CD2 B:HIS69 3.0 30.0 1.0
CE1 B:HIS69 3.3 29.5 1.0
CB B:CYS177 3.3 23.1 1.0
CB B:CYS47 3.4 30.4 1.0
OG1 B:THR49 3.8 26.2 1.0
O B:HOH555 3.8 37.7 1.0
CB B:THR49 4.1 34.6 1.0
CG B:HIS69 4.2 28.1 1.0
ND1 B:HIS69 4.3 30.1 1.0
CA B:CYS177 4.7 23.8 1.0
OE2 B:GLU70 4.8 30.7 1.0
CA B:CYS47 4.8 29.9 1.0
N B:GLY178 4.8 24.9 1.0
CG B:GLU70 4.8 23.8 1.0
CG2 B:THR49 4.9 29.2 1.0
NH2 B:ARG372 4.9 27.1 1.0

Zinc binding site 4 out of 4 in 4dla

Go back to Zinc Binding Sites List in 4dla
Zinc binding site 4 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum)


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 S-Nitrosoglutathione Reductase Apoenzyme From Tomato (Solanum Lycopersicum) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:28.8
occ:1.00
 SG B:CYS102 2.3 35.3 1.0
SG B:CYS113 2.3 28.6 1.0
SG B:CYS99 2.4 29.9 1.0
SG B:CYS105 2.4 37.5 1.0
CB B:CYS113 3.2 25.0 1.0
CB B:CYS105 3.4 34.4 1.0
N B:CYS99 3.4 25.8 1.0
CB B:CYS102 3.4 32.2 1.0
CB B:CYS99 3.4 25.8 1.0
CA B:CYS99 3.8 25.8 1.0
N B:CYS102 3.8 33.2 1.0
CA B:CYS113 3.9 25.5 1.0
N B:ARG100 4.1 27.1 1.0
CA B:CYS102 4.1 33.0 1.0
N B:CYS105 4.2 36.1 1.0
C B:CYS99 4.3 30.8 1.0
CA B:CYS105 4.4 35.5 1.0
O B:HOH658 4.4 39.5 1.0
C B:GLU98 4.5 29.7 1.0
N B:GLU101 4.5 30.7 1.0
N B:GLY114 4.7 26.1 1.0
C B:CYS113 4.7 28.4 1.0
C B:CYS102 4.8 40.3 1.0
CA B:GLU98 4.8 26.6 1.0
CB B:LYS115 4.9 28.9 1.0
C B:GLU101 4.9 37.0 1.0
O B:CYS102 5.0 40.4 1.0

Reference:

L.Kubienova, D.Kopecny, M.Tylichova, P.Briozzo, J.Skopalova, M.Sebela, M.Navratil, R.Tache, L.Luhova, J.B.Barroso, M.Petrivalsky. Structural and Functional Characterization of A Plant S-Nitrosoglutathione Reductase From Solanum Lycopersicum. Biochimie V. 95 889 2013.
ISSN: ISSN 0300-9084
PubMed: 23274177
DOI: 10.1016/J.BIOCHI.2012.12.009
Page generated: Sat Oct 26 21:28:50 2024

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