Atomistry » Zinc » PDB 4d9w-4dr4 » 4dl9
Atomistry »
  Zinc »
    PDB 4d9w-4dr4 »
      4dl9 »

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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy