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Zinc in PDB 4dl9: Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+

Enzymatic activity of Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+

All present enzymatic activity of Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+:
1.1.1.1;

Protein crystallography data

The structure of Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+, PDB code: 4dl9 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) 24.88 / 1.85
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.114, 125.076, 76.761, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 21.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+ (pdb code 4dl9). 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 From Tomato (Solanum Lycopersicum) in Complex with Nad+, PDB code: 4dl9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4dl9

Go back to Zinc Binding Sites List in 4dl9
Zinc binding site 1 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+


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 From Tomato (Solanum Lycopersicum) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:26.8
occ:1.00
 OE2 A:GLU70 2.0 29.1 1.0
NE2 A:HIS69 2.1 25.7 1.0
SG A:CYS47 2.2 25.5 1.0
SG A:CYS177 2.3 26.7 1.0
CE1 A:HIS69 3.0 25.3 1.0
CD A:GLU70 3.1 32.8 1.0
CD2 A:HIS69 3.1 25.6 1.0
CB A:CYS47 3.2 23.4 1.0
CB A:CYS177 3.2 22.3 1.0
CG A:GLU70 3.5 31.9 1.0
NH2 A:ARG372 3.6 23.2 1.0
O A:HOH684 3.8 32.9 1.0
O A:HOH504 4.1 22.6 1.0
ND1 A:HIS69 4.2 25.1 1.0
CG A:HIS69 4.2 23.0 1.0
OE1 A:GLU70 4.2 25.7 1.0
CA A:CYS47 4.4 24.2 1.0
OG1 A:THR49 4.4 24.2 1.0
CZ A:ARG372 4.4 33.6 1.0
CA A:CYS177 4.6 22.1 1.0
N A:CYS47 4.6 24.9 1.0
CB A:THR49 4.7 29.8 1.0
N A:GLY178 4.7 22.3 1.0
NE A:ARG372 4.7 23.7 1.0
C5N A:NAD403 4.9 29.6 1.0
CB A:GLU70 4.9 23.9 1.0

Zinc binding site 2 out of 4 in 4dl9

Go back to Zinc Binding Sites List in 4dl9
Zinc binding site 2 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+


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 From Tomato (Solanum Lycopersicum) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:25.9
occ:1.00
 SG A:CYS113 2.2 25.4 1.0
SG A:CYS102 2.3 31.2 1.0
SG A:CYS105 2.3 26.6 1.0
SG A:CYS99 2.4 26.6 1.0
CB A:CYS113 3.1 21.7 1.0
CB A:CYS102 3.2 29.1 1.0
N A:CYS99 3.4 23.0 1.0
CB A:CYS99 3.5 22.2 1.0
CB A:CYS105 3.5 24.8 1.0
CA A:CYS113 3.7 21.8 1.0
N A:CYS102 3.8 34.6 1.0
CA A:CYS99 3.9 22.3 1.0
N A:ARG100 3.9 21.4 1.0
CA A:CYS102 4.1 31.6 1.0
N A:CYS105 4.1 26.8 1.0
C A:CYS99 4.2 26.6 1.0
CA A:CYS105 4.4 26.6 1.0
N A:GLU101 4.5 31.3 1.0
N A:GLY114 4.5 24.1 1.0
C A:CYS113 4.5 23.6 1.0
C A:GLU98 4.6 25.9 1.0
CB A:LYS115 4.7 25.9 1.0
C A:CYS102 4.8 37.4 1.0
N A:LYS115 4.8 22.9 1.0
CA A:GLU98 4.9 21.9 1.0
CA A:ARG100 4.9 23.2 1.0
N A:CYS113 4.9 23.7 1.0
C A:GLU101 5.0 40.7 1.0

Zinc binding site 3 out of 4 in 4dl9

Go back to Zinc Binding Sites List in 4dl9
Zinc binding site 3 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+


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 From Tomato (Solanum Lycopersicum) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:30.9
occ:1.00
 OE2 B:GLU70 2.0 33.3 1.0
SG B:CYS47 2.2 24.7 1.0
NE2 B:HIS69 2.2 24.9 1.0
SG B:CYS177 2.3 29.2 1.0
CD B:GLU70 3.0 36.0 1.0
CE1 B:HIS69 3.2 24.3 1.0
CB B:CYS47 3.2 23.6 1.0
CB B:CYS177 3.2 24.3 1.0
CD2 B:HIS69 3.2 24.9 1.0
CG B:GLU70 3.4 27.4 1.0
NH2 B:ARG372 3.6 26.0 1.0
O B:HOH806 3.6 43.1 1.0
O B:HOH509 4.1 24.5 1.0
OE1 B:GLU70 4.2 25.6 1.0
ND1 B:HIS69 4.3 23.7 1.0
CG B:HIS69 4.3 22.4 1.0
CA B:CYS47 4.4 24.9 1.0
CZ B:ARG372 4.4 28.3 1.0
OG1 B:THR49 4.5 26.9 1.0
CA B:CYS177 4.6 22.2 1.0
N B:GLY178 4.6 21.5 1.0
N B:CYS47 4.7 25.7 1.0
CB B:THR49 4.7 30.2 1.0
NE B:ARG372 4.7 22.7 1.0
CB B:GLU70 4.9 19.6 1.0
C5N B:NAD403 5.0 31.3 1.0

Zinc binding site 4 out of 4 in 4dl9

Go back to Zinc Binding Sites List in 4dl9
Zinc binding site 4 out of 4 in the Crystal Structure of S-Nitrosoglutathione Reductase From Tomato (Solanum Lycopersicum) in Complex with Nad+


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 From Tomato (Solanum Lycopersicum) in Complex with Nad+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:27.8
occ:1.00
 SG B:CYS113 2.2 29.4 1.0
SG B:CYS102 2.2 28.2 1.0
SG B:CYS105 2.3 26.7 1.0
SG B:CYS99 2.4 27.7 1.0
CB B:CYS113 3.1 25.2 1.0
CB B:CYS102 3.2 26.8 1.0
CB B:CYS99 3.4 24.2 1.0
CB B:CYS105 3.5 24.2 1.0
N B:CYS99 3.5 24.1 1.0
CA B:CYS113 3.7 24.4 1.0
CA B:CYS99 3.8 24.0 1.0
N B:CYS102 3.9 31.9 1.0
N B:ARG100 4.0 24.6 1.0
N B:CYS105 4.1 28.2 1.0
CA B:CYS102 4.1 29.3 1.0
C B:CYS99 4.3 28.9 1.0
CA B:CYS105 4.4 26.5 1.0
N B:GLU101 4.4 32.9 1.0
N B:GLY114 4.5 24.9 1.0
C B:CYS113 4.5 27.5 1.0
C B:GLU98 4.6 27.7 1.0
CB B:LYS115 4.7 30.2 1.0
N B:LYS115 4.8 27.5 1.0
C B:GLU101 4.8 40.9 1.0
C B:CYS102 4.9 36.9 1.0
CA B:GLU98 4.9 25.1 1.0
N B:CYS113 4.9 25.8 1.0
CA B:ARG100 5.0 26.4 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 21:28:09 2024

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