Nickel in PDB 5lmm: Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q

All present enzymatic activity of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q:
1.12.99.6;

The structure of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q, PDB code: 5lmm was solved by S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, F.A.Armstrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	91.74 / 1.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	93.981, 97.799, 183.474, 90.00, 90.00, 90.00
R / Rfree (%)	11.8 / 14.6

The structure of Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Iron	(Fe)	26 atoms
Chlorine	(Cl)	3 atoms

The binding sites of Nickel atom in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q (pdb code 5lmm). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q, PDB code: 5lmm:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


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 Hyd-1 Mutant E28Q within 5.0Å range: probe atom residue distance (Å) B Occ L:Ni603 b:14.3 occ:0.90 OD L:CSO79 1.8 16.0 0.5 O L:HOH1030 1.8 16.9 1.0 SG L:CYS576 2.1 19.8 1.0 SG L:CYS76 2.2 16.1 1.0 SG L:CYS579 2.6 9.9 1.0 SG L:CSO79 2.7 13.6 1.0 FE L:FCO602 3.0 9.7 1.0 CB L:CYS76 3.1 12.9 1.0 CB L:CYS576 3.2 14.8 1.0 CB L:CYS579 3.7 9.5 1.0 CB L:CSO79 3.8 10.6 1.0 N L:CSO79 3.8 10.9 1.0 C1 L:FCO602 4.0 9.5 1.0 C2 L:FCO602 4.2 8.5 1.0 CA L:CSO79 4.4 10.2 1.0 CB L:VAL78 4.5 12.3 1.0 N L:CYS579 4.5 8.7 1.0 CA L:CYS76 4.5 9.8 1.0 CA L:CYS576 4.5 11.1 1.0 C3 L:FCO602 4.5 9.9 1.0 CA L:CYS579 4.6 8.8 1.0 NH1 L:ARG509 4.7 15.1 1.0 O L:HOH705 4.7 11.2 0.3 CZ L:ARG509 4.8 13.3 1.0 C L:VAL78 4.8 11.5 1.0 N1 L:FCO602 4.9 10.7 1.0 N L:VAL78 4.9 9.9 1.0 NE L:ARG509 4.9 13.3 1.0 CA L:VAL78 4.9 11.1 1.0 CD L:ARG509 5.0 12.0 1.0

Nickel binding site 2 out of 2 in the Structure of E Coli Hydrogenase Hyd-1 Mutant E28Q


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 Hyd-1 Mutant E28Q within 5.0Å range: probe atom residue distance (Å) B Occ M:Ni602 b:14.4 occ:0.90 OD M:CSO79 1.8 14.6 0.5 O M:HOH994 1.8 15.8 1.0 SG M:CYS576 2.1 19.7 1.0 SG M:CYS76 2.2 13.8 0.8 SG M:CYS579 2.6 9.8 1.0 SG M:CSO79 2.7 13.6 1.0 FE M:FCO601 3.0 9.4 1.0 CB M:CYS76 3.0 12.7 1.0 CB M:CYS576 3.2 16.2 1.0 CB M:CYS579 3.7 10.1 1.0 CB M:CSO79 3.7 10.3 1.0 N M:CSO79 3.8 10.8 1.0 C1 M:FCO601 4.0 9.0 1.0 C2 M:FCO601 4.2 8.4 1.0 CA M:CSO79 4.4 10.9 1.0 CA M:CYS76 4.5 10.2 1.0 CB M:VAL78 4.5 12.7 1.0 CA M:CYS576 4.5 11.5 1.0 N M:CYS579 4.5 8.8 1.0 C3 M:FCO601 4.6 9.2 1.0 CA M:CYS579 4.6 9.1 1.0 NH1 M:ARG509 4.7 13.7 1.0 O M:HOH701 4.7 10.5 0.3 CZ M:ARG509 4.7 12.8 1.0 C M:VAL78 4.8 12.4 1.0 N M:VAL78 4.9 10.7 1.0 NE M:ARG509 4.9 14.0 1.0 N1 M:FCO601 4.9 10.0 1.0 CA M:VAL78 5.0 12.2 1.0 CD M:ARG509 5.0 12.5 1.0

S.B.Carr, S.E.V.Phillips, R.M.Evans, E.J.Brooke, S.T.A.Islam, G.M.Roberts, S.A.M.Wehlin, F.A.Armstrong. Kinetic Consequences of Re-Engineering the Outer Shell "Canopy" Above the Active Site of A [Nife]-Hydrogenase. To Be Published.