Chlorine in PDB 3myr: Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
Enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
All present enzymatic activity of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State:
1.12.99.6;
Protein crystallography data
The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr
was solved by
H.Ogata,
P.Kellers,
W.Lubitz,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
2.10
|
Space group
|
P 21 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
205.750,
216.960,
119.800,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
13.8 /
16.8
|
Other elements in 3myr:
The structure of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
(pdb code 3myr). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the
Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State, PDB code: 3myr:
Jump to Chlorine binding site number:
1;
2;
3;
4;
Chlorine binding site 1 out
of 4 in 3myr
Go back to
Chlorine Binding Sites List in 3myr
Chlorine binding site 1 out
of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl2004
b:20.5
occ:1.00
|
O
|
A:HOH3328
|
3.1
|
17.5
|
1.0
|
N
|
A:ASN236
|
3.2
|
14.8
|
1.0
|
O
|
A:HOH3314
|
3.3
|
16.3
|
1.0
|
N
|
A:ASP237
|
3.3
|
16.0
|
1.0
|
N
|
A:MET154
|
3.6
|
17.1
|
1.0
|
CB
|
A:PRO153
|
3.6
|
13.8
|
1.0
|
CD
|
A:PRO153
|
3.6
|
12.8
|
1.0
|
CA
|
A:ASN236
|
3.7
|
14.6
|
1.0
|
CG
|
A:PRO153
|
3.7
|
13.1
|
1.0
|
CG2
|
A:ILE152
|
3.8
|
16.1
|
1.0
|
N
|
A:PRO153
|
3.9
|
17.1
|
1.0
|
CB
|
A:MET154
|
4.0
|
17.2
|
1.0
|
C
|
A:ASN236
|
4.1
|
15.8
|
1.0
|
CG
|
A:MET154
|
4.1
|
20.9
|
1.0
|
C
|
A:TRP235
|
4.1
|
15.4
|
1.0
|
CE
|
A:MET154
|
4.2
|
29.8
|
1.0
|
CA
|
A:PRO153
|
4.3
|
17.0
|
1.0
|
CA
|
A:ASP237
|
4.3
|
19.6
|
1.0
|
C
|
A:PRO153
|
4.4
|
20.2
|
1.0
|
CA
|
A:MET154
|
4.4
|
17.7
|
1.0
|
CA
|
A:TRP235
|
4.5
|
14.8
|
1.0
|
O
|
A:LYS234
|
4.6
|
15.8
|
1.0
|
C
|
A:ILE152
|
4.9
|
16.7
|
1.0
|
SD
|
A:MET154
|
5.0
|
31.2
|
1.0
|
|
Chlorine binding site 2 out
of 4 in 3myr
Go back to
Chlorine Binding Sites List in 3myr
Chlorine binding site 2 out
of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl2004
b:20.5
occ:1.00
|
O
|
C:HOH3354
|
3.1
|
16.5
|
1.0
|
O
|
C:HOH3577
|
3.2
|
16.1
|
1.0
|
N
|
C:ASN236
|
3.2
|
18.5
|
1.0
|
N
|
C:ASP237
|
3.4
|
19.2
|
1.0
|
N
|
C:MET154
|
3.5
|
16.9
|
1.0
|
CB
|
C:PRO153
|
3.6
|
14.6
|
1.0
|
CA
|
C:ASN236
|
3.7
|
17.6
|
1.0
|
CD
|
C:PRO153
|
3.7
|
12.2
|
1.0
|
CG
|
C:PRO153
|
3.8
|
17.8
|
1.0
|
CG2
|
C:ILE152
|
3.8
|
17.6
|
1.0
|
CB
|
C:MET154
|
3.9
|
20.7
|
1.0
|
CE
|
C:MET154
|
4.0
|
27.8
|
1.0
|
CG
|
C:MET154
|
4.1
|
25.8
|
1.0
|
C
|
C:ASN236
|
4.1
|
17.9
|
1.0
|
N
|
C:PRO153
|
4.1
|
15.4
|
1.0
|
C
|
C:TRP235
|
4.2
|
19.5
|
1.0
|
CA
|
C:ASP237
|
4.3
|
21.6
|
1.0
|
CA
|
C:PRO153
|
4.3
|
14.6
|
1.0
|
CA
|
C:MET154
|
4.4
|
18.9
|
1.0
|
C
|
C:PRO153
|
4.4
|
18.2
|
1.0
|
CA
|
C:TRP235
|
4.5
|
19.4
|
1.0
|
O
|
C:LYS234
|
4.6
|
19.7
|
1.0
|
SD
|
C:MET154
|
4.9
|
30.9
|
1.0
|
C
|
C:ILE152
|
4.9
|
15.8
|
1.0
|
|
Chlorine binding site 3 out
of 4 in 3myr
Go back to
Chlorine Binding Sites List in 3myr
Chlorine binding site 3 out
of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl2004
b:24.4
occ:1.00
|
O
|
E:HOH3206
|
3.1
|
17.4
|
1.0
|
O
|
E:HOH3216
|
3.1
|
20.6
|
1.0
|
N
|
E:ASN236
|
3.2
|
20.6
|
1.0
|
N
|
E:ASP237
|
3.3
|
21.6
|
1.0
|
N
|
E:MET154
|
3.6
|
20.5
|
1.0
|
CB
|
E:PRO153
|
3.6
|
18.5
|
1.0
|
CD
|
E:PRO153
|
3.7
|
19.6
|
1.0
|
CA
|
E:ASN236
|
3.8
|
21.6
|
1.0
|
CG2
|
E:ILE152
|
3.8
|
18.8
|
1.0
|
CG
|
E:PRO153
|
3.8
|
20.0
|
1.0
|
CE
|
E:MET154
|
3.9
|
29.2
|
1.0
|
CB
|
E:MET154
|
4.0
|
23.1
|
1.0
|
N
|
E:PRO153
|
4.1
|
21.3
|
1.0
|
C
|
E:ASN236
|
4.1
|
21.2
|
1.0
|
C
|
E:TRP235
|
4.1
|
21.4
|
1.0
|
CG
|
E:MET154
|
4.2
|
24.8
|
1.0
|
CA
|
E:ASP237
|
4.2
|
24.6
|
1.0
|
CA
|
E:PRO153
|
4.3
|
21.0
|
1.0
|
C
|
E:PRO153
|
4.4
|
21.7
|
1.0
|
CA
|
E:MET154
|
4.4
|
22.1
|
1.0
|
CA
|
E:TRP235
|
4.5
|
22.0
|
1.0
|
O
|
E:LYS234
|
4.6
|
23.2
|
1.0
|
C
|
E:ILE152
|
4.9
|
21.2
|
1.0
|
SD
|
E:MET154
|
5.0
|
31.8
|
1.0
|
|
Chlorine binding site 4 out
of 4 in 3myr
Go back to
Chlorine Binding Sites List in 3myr
Chlorine binding site 4 out
of 4 in the Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Crystal Structure of [Nife] Hydrogenase From Allochromatium Vinosum in Its Ni-A State within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Cl2004
b:21.2
occ:1.00
|
O
|
G:HOH3053
|
3.1
|
19.1
|
1.0
|
N
|
G:ASN236
|
3.2
|
18.1
|
1.0
|
O
|
G:HOH3104
|
3.3
|
18.1
|
1.0
|
N
|
G:ASP237
|
3.4
|
21.3
|
1.0
|
N
|
G:MET154
|
3.5
|
16.7
|
1.0
|
CB
|
G:PRO153
|
3.5
|
16.2
|
1.0
|
CA
|
G:ASN236
|
3.7
|
19.6
|
1.0
|
CD
|
G:PRO153
|
3.7
|
15.1
|
1.0
|
CG2
|
G:ILE152
|
3.9
|
19.5
|
1.0
|
CG
|
G:PRO153
|
3.9
|
15.2
|
1.0
|
CB
|
G:MET154
|
3.9
|
20.7
|
1.0
|
CE
|
G:MET154
|
4.0
|
31.4
|
1.0
|
N
|
G:PRO153
|
4.0
|
19.1
|
1.0
|
C
|
G:ASN236
|
4.1
|
19.3
|
1.0
|
C
|
G:TRP235
|
4.2
|
20.1
|
1.0
|
CA
|
G:PRO153
|
4.2
|
17.9
|
1.0
|
CG
|
G:MET154
|
4.3
|
20.9
|
1.0
|
C
|
G:PRO153
|
4.3
|
19.1
|
1.0
|
CA
|
G:ASP237
|
4.4
|
23.8
|
1.0
|
CA
|
G:MET154
|
4.4
|
19.3
|
1.0
|
CA
|
G:TRP235
|
4.5
|
19.1
|
1.0
|
O
|
G:LYS234
|
4.6
|
18.6
|
1.0
|
C
|
G:ILE152
|
4.9
|
19.4
|
1.0
|
SD
|
G:MET154
|
4.9
|
30.1
|
1.0
|
|
Reference:
H.Ogata,
P.Kellers,
W.Lubitz.
The Crystal Structure of the [Nife] Hydrogenase From the Photosynthetic Bacterium Allochromatium Vinosum: Characterization of the Oxidized Enzyme (Ni-A State). J.Mol.Biol. V. 402 428 2010.
ISSN: ISSN 0022-2836
PubMed: 20673834
DOI: 10.1016/J.JMB.2010.07.041
Page generated: Sun Jul 21 00:27:36 2024
|