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
|