Nickel in PDB 4gd3: Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B

All present enzymatic activity of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B:
1.12.99.6;

The structure of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3 was solved by A.Volbeda, J.C.Fontecilla-Camps, C.Darnault, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 3.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	126.000, 165.300, 212.800, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 23.6

The structure of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	54 atoms
Chlorine	(Cl)	10 atoms

The binding sites of Nickel atom in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B (pdb code 4gd3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B, PDB code: 4gd3:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni602 b:91.4 occ:1.00 SG L:CYS76 2.1 84.7 1.0 SG L:CYS576 2.1 87.7 1.0 SG L:CYS79 2.2 88.5 1.0 FE L:FCO601 2.5 88.9 1.0 SG L:CYS579 2.7 90.2 1.0 CB L:CYS76 2.9 84.2 1.0 CB L:CYS579 3.3 90.7 1.0 CB L:CYS79 3.4 91.8 1.0 CB L:CYS576 3.5 89.9 1.0 C1 L:FCO601 3.7 95.0 1.0 N L:CYS79 3.7 89.5 1.0 C2 L:FCO601 3.8 93.6 1.0 C3 L:FCO601 4.0 90.1 1.0 CA L:CYS79 4.1 90.6 1.0 CA L:CYS76 4.4 83.1 1.0 CA L:CYS579 4.4 90.9 1.0 NH1 L:ARG509 4.5 96.8 1.0 N L:CYS579 4.6 90.3 1.0 N1 L:FCO601 4.6 99.6 1.0 CB L:VAL78 4.7 85.8 1.0 OE1 L:GLU28 4.7 96.3 1.0 N2 L:FCO601 4.7 98.4 1.0 CZ L:ARG509 4.8 97.2 1.0 CD L:ARG509 4.8 95.6 1.0 C L:VAL78 4.8 87.3 1.0 CA L:CYS576 4.8 90.4 1.0 NE L:ARG509 4.9 96.2 1.0 C L:CYS76 4.9 81.7 1.0 C L:CYS79 4.9 90.2 1.0 CG L:GLU28 5.0 90.8 1.0

Nickel binding site 2 out of 4 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni603 b:89.4 occ:1.00 SG M:CYS576 2.0 85.0 1.0 SG M:CYS76 2.2 83.7 1.0 SG M:CYS79 2.3 82.1 1.0 FE M:FCO602 2.5 81.9 1.0 SG M:CYS579 2.7 84.8 1.0 CB M:CYS76 3.0 83.3 1.0 CB M:CYS579 3.2 88.4 1.0 CB M:CYS576 3.4 89.2 1.0 CB M:CYS79 3.5 85.6 1.0 C1 M:FCO602 3.6 89.6 1.0 N M:CYS79 3.8 85.4 1.0 C2 M:FCO602 3.8 86.2 1.0 C3 M:FCO602 4.1 83.2 1.0 CA M:CYS79 4.2 85.0 1.0 CA M:CYS579 4.3 89.6 1.0 CA M:CYS76 4.4 83.0 1.0 NH1 M:ARG509 4.5 91.4 1.0 N M:CYS579 4.5 90.5 1.0 N1 M:FCO602 4.5 93.5 1.0 OE1 M:GLU28 4.6 99.8 1.0 CZ M:ARG509 4.7 93.6 1.0 CA M:CYS576 4.7 91.9 1.0 CB M:VAL78 4.7 85.4 1.0 CD M:ARG509 4.7 91.1 1.0 NE M:ARG509 4.8 93.3 1.0 N2 M:FCO602 4.8 90.1 1.0 CG M:GLU28 4.9 94.2 1.0 C M:VAL78 4.9 84.1 1.0

Nickel binding site 3 out of 4 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ J:Ni602 b:81.8 occ:1.00 SG J:CYS79 2.1 83.5 1.0 SG J:CYS576 2.2 79.8 1.0 SG J:CYS76 2.2 78.5 1.0 FE J:FCO601 2.5 81.2 1.0 SG J:CYS579 2.6 80.8 1.0 CB J:CYS76 3.0 75.8 1.0 CB J:CYS79 3.3 84.4 1.0 CB J:CYS579 3.3 80.8 1.0 CB J:CYS576 3.5 80.2 1.0 N J:CYS79 3.6 81.3 1.0 C1 J:FCO601 3.7 85.4 1.0 C2 J:FCO601 3.7 84.5 1.0 C3 J:FCO601 4.0 80.8 1.0 CA J:CYS79 4.1 83.4 1.0 NH1 J:ARG509 4.3 87.5 1.0 CA J:CYS76 4.4 75.1 1.0 CA J:CYS579 4.5 80.7 1.0 CB J:VAL78 4.6 77.2 1.0 N1 J:FCO601 4.6 89.4 1.0 N2 J:FCO601 4.6 89.4 1.0 CZ J:ARG509 4.7 87.5 1.0 OE1 J:GLU28 4.7 86.7 1.0 CD J:ARG509 4.7 85.7 1.0 N J:CYS579 4.7 80.1 1.0 C J:VAL78 4.7 79.4 1.0 CA J:CYS576 4.8 80.6 1.0 NE J:ARG509 4.8 86.4 1.0 C J:CYS76 4.9 74.3 1.0 C J:CYS79 4.9 83.4 1.0

Nickel binding site 4 out of 4 in the Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Structure of E. Coli Hydrogenase-1 in Complex with Cytochrome B within 5.0Å range: probe atom residue distance (Å) B Occ K:Ni603 b:92.4 occ:1.00 SG K:CYS576 2.1 90.0 1.0 SG K:CYS76 2.1 88.0 1.0 SG K:CYS79 2.2 90.7 1.0 SG K:CYS579 2.5 89.5 1.0 FE K:FCO602 2.5 91.1 1.0 CB K:CYS76 2.8 87.0 1.0 CB K:CYS579 3.1 91.6 1.0 CB K:CYS79 3.6 91.9 1.0 CB K:CYS576 3.6 91.9 1.0 C1 K:FCO602 3.7 94.5 1.0 N K:CYS79 3.8 91.3 1.0 C2 K:FCO602 3.9 92.3 1.0 C3 K:FCO602 4.0 89.4 1.0 CA K:CYS76 4.2 86.9 1.0 CA K:CYS79 4.3 91.4 1.0 CA K:CYS579 4.3 92.4 1.0 N K:CYS579 4.4 92.6 1.0 NH1 K:ARG509 4.6 96.2 1.0 OE1 K:GLU28 4.6 1.0 1.0 N1 K:FCO602 4.7 97.9 1.0 CB K:VAL78 4.8 89.3 1.0 CA K:CYS576 4.8 93.4 1.0 C K:CYS76 4.8 86.2 1.0 CD K:ARG509 4.9 94.8 1.0 CZ K:ARG509 4.9 97.1 1.0 C K:VAL78 4.9 89.7 1.0 CG K:GLU28 4.9 96.1 1.0 N2 K:FCO602 4.9 95.7 1.0 NE K:ARG509 4.9 96.8 1.0

A.Volbeda, C.Darnault, A.Parkin, F.Sargent, F.A.Armstrong, J.C.Fontecilla-Camps. Crystal Structure of the O(2)-Tolerant Membrane-Bound Hydrogenase 1 From Escherichia Coli in Complex with Its Cognate Cytochrome B. Structure V. 21 184 2013.
ISSN: ISSN 0969-2126
PubMed: 23260654
DOI: 10.1016/J.STR.2012.11.010