Magnesium in PDB 7qhf: [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
Enzymatic activity of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
All present enzymatic activity of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S:
1.12.7.2;
Protein crystallography data
The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S, PDB code: 7qhf
was solved by
C.Brocks,
J.Duan,
E.Hofmann,
T.Happe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.53 /
1.63
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.49,
72.22,
102.92,
90,
97.32,
90
|
R / Rfree (%)
|
16.9 /
19.2
|
Other elements in 7qhf:
The structure of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
(pdb code 7qhf). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
[Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S, PDB code: 7qhf:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7qhf
Go back to
Magnesium Binding Sites List in 7qhf
Magnesium binding site 1 out
of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg607
b:35.2
occ:1.00
|
O
|
A:HOH801
|
2.0
|
31.9
|
1.0
|
O
|
A:HOH894
|
2.0
|
36.2
|
1.0
|
O
|
A:LEU218
|
2.0
|
31.2
|
1.0
|
O
|
A:HOH761
|
2.1
|
28.3
|
1.0
|
O
|
A:HOH915
|
2.1
|
32.2
|
1.0
|
O
|
A:HOH892
|
2.1
|
33.8
|
1.0
|
C
|
A:LEU218
|
3.1
|
30.9
|
1.0
|
CA
|
A:LEU218
|
3.7
|
27.9
|
1.0
|
O
|
A:ALA220
|
4.0
|
31.4
|
1.0
|
OD2
|
A:ASP263
|
4.0
|
29.2
|
1.0
|
O
|
A:HOH763
|
4.1
|
28.5
|
1.0
|
O
|
A:ALA217
|
4.2
|
27.1
|
1.0
|
N
|
A:ASN219
|
4.3
|
28.9
|
1.0
|
O
|
A:LYS223
|
4.3
|
27.8
|
1.0
|
OD1
|
A:ASP263
|
4.4
|
31.3
|
1.0
|
CB
|
A:LEU218
|
4.5
|
25.6
|
1.0
|
O
|
A:HOH1105
|
4.5
|
49.8
|
1.0
|
O
|
A:GLY261
|
4.6
|
29.8
|
1.0
|
CG
|
A:ASP263
|
4.7
|
32.6
|
1.0
|
CA
|
A:ASN219
|
4.7
|
34.1
|
1.0
|
C
|
A:ASN219
|
4.8
|
31.8
|
1.0
|
N
|
A:LEU218
|
4.8
|
26.0
|
1.0
|
N
|
A:ALA220
|
4.8
|
29.0
|
1.0
|
C
|
A:ALA220
|
4.9
|
31.1
|
1.0
|
CG2
|
A:VAL225
|
4.9
|
26.4
|
1.0
|
C
|
A:ALA217
|
4.9
|
28.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7qhf
Go back to
Magnesium Binding Sites List in 7qhf
Magnesium binding site 2 out
of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg609
b:27.8
occ:1.00
|
OD1
|
A:ASP42
|
2.0
|
29.6
|
1.0
|
O
|
A:HOH830
|
2.0
|
30.4
|
1.0
|
OD1
|
A:ASN40
|
2.0
|
27.3
|
1.0
|
O
|
A:HOH859
|
2.1
|
29.9
|
1.0
|
O
|
A:HOH964
|
2.1
|
32.1
|
1.0
|
O
|
A:HOH888
|
2.2
|
31.4
|
1.0
|
CG
|
A:ASP42
|
3.1
|
34.3
|
1.0
|
CG
|
A:ASN40
|
3.2
|
27.8
|
1.0
|
OD2
|
A:ASP42
|
3.7
|
40.1
|
1.0
|
ND2
|
A:ASN40
|
3.8
|
28.0
|
1.0
|
O
|
A:HOH713
|
3.9
|
32.4
|
1.0
|
N
|
A:ASN40
|
4.0
|
26.0
|
1.0
|
O
|
B:HOH723
|
4.1
|
38.3
|
1.0
|
O
|
A:HOH1031
|
4.2
|
38.3
|
1.0
|
O
|
A:ASN40
|
4.2
|
27.3
|
1.0
|
O
|
A:HOH918
|
4.3
|
38.2
|
1.0
|
CB
|
A:ASP42
|
4.3
|
29.3
|
1.0
|
OD2
|
A:ASP63
|
4.3
|
30.0
|
1.0
|
O
|
B:HOH720
|
4.4
|
41.1
|
1.0
|
OD1
|
B:ASN452
|
4.4
|
38.7
|
1.0
|
CB
|
A:ASN40
|
4.4
|
25.6
|
1.0
|
CB
|
A:ASP63
|
4.4
|
28.1
|
1.0
|
C
|
A:ASN40
|
4.4
|
26.8
|
1.0
|
CA
|
A:ASP42
|
4.5
|
30.0
|
1.0
|
CA
|
A:ASN40
|
4.5
|
25.7
|
1.0
|
CG
|
B:ASN452
|
4.6
|
34.0
|
1.0
|
N
|
A:ASP42
|
4.7
|
27.2
|
1.0
|
O
|
B:HOH942
|
4.8
|
31.6
|
1.0
|
CB
|
B:ASN452
|
4.9
|
26.3
|
1.0
|
CG
|
A:ASP63
|
4.9
|
29.4
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7qhf
Go back to
Magnesium Binding Sites List in 7qhf
Magnesium binding site 3 out
of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg607
b:32.2
occ:1.00
|
O
|
B:HOH823
|
1.9
|
26.2
|
1.0
|
O
|
B:HOH944
|
2.0
|
32.4
|
1.0
|
O
|
B:HOH798
|
2.1
|
27.7
|
1.0
|
O
|
B:HOH907
|
2.1
|
35.1
|
1.0
|
O
|
B:LEU218
|
2.2
|
29.9
|
1.0
|
O
|
B:HOH841
|
2.3
|
33.3
|
1.0
|
C
|
B:LEU218
|
3.2
|
27.7
|
1.0
|
CA
|
B:LEU218
|
3.8
|
25.9
|
1.0
|
O
|
B:HOH783
|
4.0
|
29.7
|
1.0
|
OD2
|
B:ASP263
|
4.0
|
28.1
|
1.0
|
O
|
B:ALA220
|
4.0
|
30.6
|
1.0
|
O
|
B:LYS223
|
4.1
|
28.5
|
1.0
|
O
|
B:ALA217
|
4.2
|
28.5
|
1.0
|
OD1
|
B:ASP263
|
4.3
|
28.3
|
1.0
|
N
|
B:ASN219
|
4.4
|
27.9
|
1.0
|
CG
|
B:ASP263
|
4.6
|
31.1
|
1.0
|
CB
|
B:LEU218
|
4.7
|
27.7
|
1.0
|
O
|
B:GLY261
|
4.7
|
28.4
|
1.0
|
CA
|
B:ASN219
|
4.8
|
33.3
|
1.0
|
C
|
B:ASN219
|
4.8
|
33.0
|
1.0
|
O
|
B:HOH741
|
4.8
|
42.1
|
1.0
|
N
|
B:ALA220
|
4.9
|
30.2
|
1.0
|
C
|
B:ALA220
|
4.9
|
33.5
|
1.0
|
N
|
B:LEU218
|
4.9
|
24.0
|
1.0
|
CG2
|
B:VAL225
|
4.9
|
26.7
|
1.0
|
O
|
B:HOH972
|
5.0
|
47.9
|
1.0
|
C
|
B:ALA217
|
5.0
|
28.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7qhf
Go back to
Magnesium Binding Sites List in 7qhf
Magnesium binding site 4 out
of 4 in the [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of [Fefe]-Hydrogenase I From Clostridium Pasteurianum (Cpi), Variant G302S within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg609
b:38.4
occ:1.00
|
O
|
B:HOH970
|
1.9
|
42.8
|
1.0
|
O
|
B:HOH817
|
2.0
|
35.0
|
1.0
|
OD1
|
B:ASP42
|
2.0
|
36.5
|
1.0
|
OD1
|
B:ASN40
|
2.1
|
32.4
|
1.0
|
O
|
B:HOH967
|
2.2
|
37.4
|
1.0
|
O
|
B:HOH761
|
2.3
|
41.7
|
1.0
|
CG
|
B:ASP42
|
3.2
|
36.0
|
1.0
|
CG
|
B:ASN40
|
3.2
|
31.3
|
1.0
|
O
|
B:HOH707
|
3.7
|
41.0
|
1.0
|
OD2
|
B:ASP42
|
3.8
|
41.3
|
1.0
|
ND2
|
B:ASN40
|
3.9
|
34.2
|
1.0
|
N
|
B:ASN40
|
4.0
|
29.3
|
1.0
|
O
|
B:ASN40
|
4.2
|
29.5
|
1.0
|
OD2
|
B:ASP63
|
4.3
|
36.6
|
1.0
|
O
|
A:HOH819
|
4.3
|
38.5
|
1.0
|
CB
|
B:ASP42
|
4.4
|
35.2
|
1.0
|
CB
|
B:ASN40
|
4.4
|
26.0
|
1.0
|
C
|
B:ASN40
|
4.5
|
25.2
|
1.0
|
CA
|
B:ASN40
|
4.5
|
29.4
|
1.0
|
CA
|
B:ASP42
|
4.5
|
32.5
|
1.0
|
ND2
|
A:ASN452
|
4.6
|
40.2
|
1.0
|
CG
|
A:ASN452
|
4.7
|
36.4
|
1.0
|
CB
|
B:ASP63
|
4.8
|
35.9
|
1.0
|
N
|
B:ASP42
|
4.8
|
29.1
|
1.0
|
OD1
|
A:ASN452
|
4.9
|
39.4
|
1.0
|
O
|
A:HOH984
|
4.9
|
38.1
|
1.0
|
CB
|
A:ASN452
|
5.0
|
30.5
|
1.0
|
|
Reference:
C.Brocks,
C.K.Das,
J.Duan,
E.Hofmann,
M.Winkler,
L.Schaefer,
V.Engelbrecht,
T.Happe.
Intruder Protection: Manipulating the Pathways of Ros Diffusion in [Fefe]-Hydrogenases To Be Published.
Page generated: Thu Oct 3 05:06:42 2024
|