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
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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
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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: Sat Oct 26 21:28:50 2024
|