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Zinc in PDB 4dlb: Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione

Enzymatic activity of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione

All present enzymatic activity of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione:
1.1.1.1;

Protein crystallography data

The structure of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione, PDB code: 4dlb 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) 28.79 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.640, 78.040, 124.260, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 24.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 4dlb

Go back to Zinc Binding Sites List in 4dlb
Zinc binding site 1 out of 4 in the Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:50.4
occ:1.00
O A:HOH699 1.9 32.1 1.0
SG A:CYS177 2.3 37.9 1.0
NE2 A:HIS69 2.3 28.8 1.0
SG A:CYS47 2.3 37.6 1.0
CB A:CYS47 3.0 33.0 1.0
CB A:CYS177 3.1 33.6 1.0
CD2 A:HIS69 3.2 28.3 1.0
CE1 A:HIS69 3.4 28.3 1.0
OE2 A:GLU70 3.9 52.9 1.0
CG A:GLU70 3.9 32.8 1.0
C5N A:NAD403 4.0 45.9 1.0
CD A:GLU70 4.1 51.6 1.0
NH2 A:ARG372 4.2 26.7 1.0
CG A:HIS69 4.3 25.8 1.0
N A:GLY178 4.3 28.0 1.0
CB A:THR49 4.4 38.2 1.0
ND1 A:HIS69 4.4 28.4 1.0
CA A:CYS177 4.4 33.3 1.0
C6N A:NAD403 4.5 46.4 1.0
CA A:CYS47 4.5 31.6 1.0
OG1 A:THR49 4.6 37.5 1.0
C A:CYS177 4.7 33.8 1.0
OE1 A:GLU70 4.9 56.5 1.0
C4N A:NAD403 4.9 45.3 1.0
CE1 A:TYR95 4.9 37.1 1.0

Zinc binding site 2 out of 4 in 4dlb

Go back to Zinc Binding Sites List in 4dlb
Zinc binding site 2 out of 4 in the Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.9
occ:1.00
SG A:CYS113 2.3 25.8 1.0
SG A:CYS99 2.3 25.8 1.0
SG A:CYS105 2.4 36.5 1.0
SG A:CYS102 2.4 34.1 1.0
CB A:CYS113 3.0 22.1 1.0
CB A:CYS102 3.3 31.4 1.0
N A:CYS99 3.5 23.9 1.0
CB A:CYS105 3.5 34.2 1.0
CB A:CYS99 3.5 22.8 1.0
CA A:CYS113 3.7 21.6 1.0
N A:CYS102 3.9 34.3 1.0
CA A:CYS99 3.9 23.6 1.0
N A:ARG100 4.0 27.2 1.0
CA A:CYS102 4.1 33.4 1.0
N A:CYS105 4.3 37.3 1.0
C A:CYS99 4.3 27.9 1.0
CA A:CYS105 4.4 36.1 1.0
N A:GLU101 4.5 34.8 1.0
C A:CYS113 4.6 26.0 1.0
C A:GLU98 4.6 26.9 1.0
N A:GLY114 4.6 23.7 1.0
CB A:LYS115 4.6 24.1 1.0
CA A:GLU98 4.8 20.9 1.0
C A:CYS102 4.9 42.8 1.0
N A:LYS115 4.9 22.0 1.0
N A:CYS113 4.9 23.2 1.0

Zinc binding site 3 out of 4 in 4dlb

Go back to Zinc Binding Sites List in 4dlb
Zinc binding site 3 out of 4 in the Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:45.5
occ:1.00
O B:HOH659 1.9 19.9 1.0
NE2 B:HIS69 2.3 26.3 1.0
SG B:CYS47 2.4 33.5 1.0
OE2 B:GLU70 2.4 46.6 1.0
SG B:CYS177 2.4 29.7 1.0
CB B:CYS47 2.8 29.6 1.0
CE1 B:HIS69 3.1 26.1 1.0
CB B:CYS177 3.1 25.0 1.0
CD2 B:HIS69 3.3 25.9 1.0
CD B:GLU70 3.3 42.7 1.0
CG B:GLU70 3.4 31.3 1.0
NH2 B:ARG372 3.9 25.7 1.0
ND1 B:HIS69 4.2 25.4 1.0
CG B:HIS69 4.3 24.1 1.0
CA B:CYS47 4.3 28.4 1.0
OG1 B:THR49 4.4 36.4 1.0
C5N B:NAD403 4.5 42.7 1.0
OE1 B:GLU70 4.5 30.8 1.0
N B:GLY178 4.5 23.4 1.0
CA B:CYS177 4.5 24.2 1.0
CB B:THR49 4.7 34.8 1.0
CZ B:ARG372 4.8 29.5 1.0
C B:CYS177 4.9 27.1 1.0
CB B:GLU70 4.9 24.7 1.0
C6N B:NAD403 4.9 43.7 1.0

Zinc binding site 4 out of 4 in 4dlb

Go back to Zinc Binding Sites List in 4dlb
Zinc binding site 4 out of 4 in the Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) Crystallized in Presence of Nadh and Glutathione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:28.1
occ:1.00
SG B:CYS113 2.3 25.1 1.0
SG B:CYS105 2.4 27.6 1.0
SG B:CYS102 2.4 34.0 1.0
SG B:CYS99 2.4 25.6 1.0
CB B:CYS113 3.0 22.0 1.0
CB B:CYS99 3.4 21.6 1.0
N B:CYS99 3.4 20.0 1.0
CB B:CYS105 3.4 25.6 1.0
CB B:CYS102 3.6 30.7 1.0
CA B:CYS113 3.8 22.4 1.0
CA B:CYS99 3.8 21.1 1.0
N B:CYS102 3.9 34.2 1.0
N B:ARG100 4.1 24.6 1.0
N B:CYS105 4.3 31.1 1.0
CA B:CYS102 4.3 32.3 1.0
C B:CYS99 4.3 26.0 1.0
CA B:CYS105 4.4 28.6 1.0
C B:GLU98 4.6 23.8 1.0
N B:GLU101 4.6 33.5 1.0
C B:CYS113 4.6 27.8 1.0
N B:GLY114 4.7 24.4 1.0
CB B:LYS115 4.9 22.6 1.0
C B:CYS102 4.9 40.3 1.0
CA B:GLU98 4.9 20.7 1.0
N B:CYS113 4.9 23.7 1.0
O B:CYS102 5.0 41.0 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: Wed Dec 16 05:11:36 2020

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