Magnesium in PDB 6g94: Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
Enzymatic activity of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
All present enzymatic activity of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B:
1.12.99.6;
Protein crystallography data
The structure of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B, PDB code: 6g94
was solved by
A.Volbeda,
J.C.Fontecilla-Camps,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
25.00 /
2.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
124.410,
165.030,
206.220,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
22.2 /
25.3
|
Other elements in 6g94:
The structure of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
(pdb code 6g94). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B, PDB code: 6g94:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6g94
Go back to
Magnesium Binding Sites List in 6g94
Magnesium binding site 1 out
of 4 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
L:Mg603
b:42.9
occ:1.00
|
O
|
L:HOH770
|
2.0
|
42.5
|
1.0
|
O
|
L:HOH799
|
2.0
|
45.4
|
1.0
|
O
|
L:HOH745
|
2.0
|
46.9
|
1.0
|
OE1
|
L:GLU57
|
2.0
|
45.2
|
1.0
|
O
|
L:CYS528
|
2.1
|
44.8
|
1.0
|
NE2
|
L:HIS582
|
2.2
|
44.8
|
1.0
|
CD
|
L:GLU57
|
3.0
|
46.5
|
1.0
|
CE1
|
L:HIS582
|
3.0
|
43.4
|
1.0
|
C
|
L:CYS528
|
3.2
|
44.1
|
1.0
|
CD2
|
L:HIS582
|
3.2
|
43.3
|
1.0
|
OE2
|
L:GLU57
|
3.4
|
48.4
|
1.0
|
N
|
L:CYS528
|
3.7
|
44.1
|
1.0
|
CA
|
L:CYS528
|
3.8
|
43.3
|
1.0
|
CB
|
L:CYS528
|
4.1
|
43.4
|
1.0
|
ND1
|
L:HIS582
|
4.2
|
40.6
|
1.0
|
OE1
|
L:GLN527
|
4.2
|
49.3
|
1.0
|
O
|
L:HOH753
|
4.2
|
38.4
|
1.0
|
OE2
|
L:GLU347
|
4.3
|
44.9
|
1.0
|
CG
|
L:HIS582
|
4.3
|
40.2
|
1.0
|
N
|
L:VAL529
|
4.3
|
44.8
|
1.0
|
CG
|
L:GLU57
|
4.3
|
46.4
|
1.0
|
O
|
L:HOH764
|
4.3
|
39.2
|
1.0
|
OE1
|
L:GLU347
|
4.4
|
45.7
|
1.0
|
NZ
|
L:LYS399
|
4.4
|
40.8
|
1.0
|
CD
|
L:LYS399
|
4.6
|
43.4
|
1.0
|
CA
|
L:VAL529
|
4.7
|
42.2
|
1.0
|
CD
|
L:GLU347
|
4.8
|
45.8
|
1.0
|
CE
|
L:LYS399
|
4.8
|
42.3
|
1.0
|
C
|
L:GLN527
|
4.9
|
41.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6g94
Go back to
Magnesium Binding Sites List in 6g94
Magnesium binding site 2 out
of 4 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
M:Mg603
b:50.5
occ:1.00
|
O
|
M:HOH770
|
2.0
|
43.3
|
1.0
|
O
|
M:HOH755
|
2.0
|
44.0
|
1.0
|
O
|
M:HOH784
|
2.0
|
46.0
|
1.0
|
NE2
|
M:HIS582
|
2.1
|
56.7
|
1.0
|
O
|
M:CYS528
|
2.1
|
46.1
|
1.0
|
OE1
|
M:GLU57
|
2.3
|
49.8
|
1.0
|
CE1
|
M:HIS582
|
2.9
|
54.8
|
1.0
|
CD2
|
M:HIS582
|
3.2
|
53.7
|
1.0
|
CD
|
M:GLU57
|
3.2
|
47.0
|
1.0
|
C
|
M:CYS528
|
3.3
|
47.7
|
1.0
|
OE2
|
M:GLU57
|
3.5
|
45.6
|
1.0
|
N
|
M:CYS528
|
3.9
|
48.4
|
1.0
|
CA
|
M:CYS528
|
4.0
|
48.1
|
1.0
|
OE2
|
M:GLU347
|
4.0
|
52.4
|
1.0
|
O
|
M:HOH763
|
4.0
|
41.0
|
1.0
|
ND1
|
M:HIS582
|
4.0
|
52.8
|
1.0
|
O
|
M:HOH788
|
4.2
|
36.4
|
1.0
|
CB
|
M:CYS528
|
4.2
|
49.4
|
1.0
|
CG
|
M:HIS582
|
4.2
|
51.7
|
1.0
|
N
|
M:VAL529
|
4.3
|
48.0
|
1.0
|
OE1
|
M:GLN527
|
4.4
|
49.7
|
1.0
|
NZ
|
M:LYS399
|
4.4
|
48.6
|
1.0
|
OE1
|
M:GLU347
|
4.4
|
52.2
|
1.0
|
CG
|
M:GLU57
|
4.5
|
46.6
|
1.0
|
CD
|
M:LYS399
|
4.5
|
49.3
|
1.0
|
CA
|
M:VAL529
|
4.6
|
46.6
|
1.0
|
CD
|
M:GLU347
|
4.7
|
54.4
|
1.0
|
CE
|
M:LYS399
|
4.8
|
49.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6g94
Go back to
Magnesium Binding Sites List in 6g94
Magnesium binding site 3 out
of 4 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Mg603
b:44.0
occ:1.00
|
O
|
J:HOH738
|
1.9
|
47.8
|
1.0
|
O
|
J:HOH707
|
1.9
|
42.0
|
1.0
|
O
|
J:HOH788
|
2.0
|
51.7
|
1.0
|
OE1
|
J:GLU57
|
2.0
|
48.4
|
1.0
|
O
|
J:CYS528
|
2.1
|
50.2
|
1.0
|
NE2
|
J:HIS582
|
2.2
|
48.6
|
1.0
|
CD
|
J:GLU57
|
3.0
|
50.1
|
1.0
|
CE1
|
J:HIS582
|
3.1
|
46.8
|
1.0
|
OE2
|
J:GLU57
|
3.2
|
50.6
|
1.0
|
C
|
J:CYS528
|
3.3
|
49.1
|
1.0
|
CD2
|
J:HIS582
|
3.3
|
46.4
|
1.0
|
N
|
J:CYS528
|
3.7
|
54.4
|
1.0
|
CA
|
J:CYS528
|
3.9
|
50.4
|
1.0
|
CB
|
J:CYS528
|
4.2
|
47.3
|
1.0
|
OE1
|
J:GLN527
|
4.2
|
59.8
|
1.0
|
O
|
J:HOH755
|
4.2
|
38.9
|
1.0
|
NZ
|
J:LYS399
|
4.2
|
49.8
|
1.0
|
ND1
|
J:HIS582
|
4.3
|
46.5
|
1.0
|
OE1
|
J:GLU347
|
4.3
|
48.4
|
1.0
|
OE2
|
J:GLU347
|
4.3
|
56.9
|
1.0
|
O
|
J:HOH774
|
4.3
|
36.4
|
1.0
|
CG
|
J:GLU57
|
4.3
|
48.3
|
1.0
|
N
|
J:VAL529
|
4.4
|
49.2
|
1.0
|
CG
|
J:HIS582
|
4.4
|
46.5
|
1.0
|
CD
|
J:LYS399
|
4.5
|
46.7
|
1.0
|
CE
|
J:LYS399
|
4.7
|
48.9
|
1.0
|
CD
|
J:GLU347
|
4.7
|
50.1
|
1.0
|
CA
|
J:VAL529
|
4.8
|
48.4
|
1.0
|
C
|
J:GLN527
|
4.8
|
52.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6g94
Go back to
Magnesium Binding Sites List in 6g94
Magnesium binding site 4 out
of 4 in the Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of E. Coli Hydrogenase-1 C19G Variant in Complex with Cytochrome B within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
K:Mg603
b:45.0
occ:1.00
|
O
|
K:HOH769
|
1.9
|
43.2
|
1.0
|
O
|
K:HOH731
|
2.0
|
55.2
|
1.0
|
O
|
K:HOH802
|
2.0
|
54.2
|
1.0
|
OE1
|
K:GLU57
|
2.1
|
50.3
|
1.0
|
NE2
|
K:HIS582
|
2.2
|
46.4
|
1.0
|
O
|
K:CYS528
|
2.2
|
49.8
|
1.0
|
CD
|
K:GLU57
|
3.0
|
49.8
|
1.0
|
CE1
|
K:HIS582
|
3.0
|
47.7
|
1.0
|
CD2
|
K:HIS582
|
3.3
|
45.5
|
1.0
|
OE2
|
K:GLU57
|
3.3
|
49.0
|
1.0
|
C
|
K:CYS528
|
3.4
|
48.9
|
1.0
|
N
|
K:CYS528
|
3.8
|
46.6
|
1.0
|
CA
|
K:CYS528
|
4.0
|
47.3
|
1.0
|
O
|
K:HOH753
|
4.1
|
40.5
|
1.0
|
ND1
|
K:HIS582
|
4.2
|
48.0
|
1.0
|
NZ
|
K:LYS399
|
4.2
|
49.1
|
1.0
|
OE2
|
K:GLU347
|
4.2
|
48.3
|
1.0
|
OE1
|
K:GLN527
|
4.2
|
42.6
|
1.0
|
O
|
K:HOH780
|
4.3
|
35.7
|
1.0
|
CB
|
K:CYS528
|
4.3
|
45.5
|
1.0
|
CG
|
K:GLU57
|
4.3
|
45.7
|
1.0
|
CG
|
K:HIS582
|
4.3
|
46.2
|
1.0
|
OE1
|
K:GLU347
|
4.4
|
44.7
|
1.0
|
N
|
K:VAL529
|
4.5
|
46.8
|
1.0
|
CD
|
K:LYS399
|
4.5
|
45.7
|
1.0
|
CE
|
K:LYS399
|
4.6
|
48.7
|
1.0
|
CD
|
K:GLU347
|
4.8
|
46.6
|
1.0
|
CA
|
K:VAL529
|
4.8
|
44.4
|
1.0
|
C
|
K:GLN527
|
4.9
|
45.2
|
1.0
|
|
Reference:
A.Volbeda,
J.M.Mouesca,
C.Darnault,
M.M.Roessler,
A.Parkin,
F.A.Armstrong,
J.C.Fontecilla-Camps.
X-Ray Structural, Functional and Computational Studies of the O2-Sensitive E. Coli Hydrogenase-1 C19G Variant Reveal An Unusual [4FE-4S] Cluster. Chem. Commun. (Camb.) V. 54 7175 2018.
ISSN: ESSN 1364-548X
PubMed: 29888350
DOI: 10.1039/C8CC02896F
Page generated: Tue Oct 1 01:03:09 2024
|