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:

Nickel (Ni) 4 atoms
Iron (Fe) 50 atoms
Chlorine (Cl) 4 atoms

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: Mon Dec 14 22:44:09 2020

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