Nickel in PDB 4ue2: Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase

All present enzymatic activity of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase:
1.12.2.1;

The structure of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue2 was solved by A.Volbeda, L.Martin, P.-P.Liebgott, J.C.Fontecilla-Camps, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.91 / 2.02
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.090, 99.650, 184.170, 90.00, 91.16, 90.00
R / Rfree (%)	16.381 / 19.135

The structure of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Iron	(Fe)	36 atoms

The binding sites of Nickel atom in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase (pdb code 4ue2). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase, PDB code: 4ue2:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ni1551 b:12.7 occ:1.00 O Q:HOH2074 1.9 12.1 0.5 SG Q:CYS75 2.2 11.8 1.0 SG Q:CYS72 2.2 11.4 1.0 SG Q:CSO543 2.3 20.1 1.0 SG Q:CYS546 2.5 13.2 1.0 FE Q:FCO1550 2.6 11.3 1.0 CB Q:CYS72 3.0 10.6 1.0 OD Q:CSO543 3.2 18.0 0.4 CB Q:CSO543 3.3 15.7 1.0 CB Q:CYS75 3.3 11.9 1.0 CB Q:CYS546 3.6 12.1 1.0 N Q:CYS75 3.6 12.2 1.0 C1 Q:FCO1550 3.7 11.4 1.0 C2 Q:FCO1550 3.8 12.0 1.0 CA Q:CYS75 4.0 11.5 1.0 C3 Q:FCO1550 4.2 11.9 1.0 NH1 Q:ARG476 4.3 13.2 1.0 CA Q:CYS72 4.5 10.7 1.0 CD Q:ARG476 4.6 12.5 1.0 CZ Q:ARG476 4.6 13.0 1.0 CB Q:VAL74 4.6 11.9 1.0 N1 Q:FCO1550 4.7 10.9 1.0 CA Q:CSO543 4.7 15.1 1.0 CA Q:CYS546 4.7 12.0 1.0 NE Q:ARG476 4.7 12.5 1.0 C Q:VAL74 4.8 12.3 1.0 C Q:CYS75 4.8 11.7 1.0 N2 Q:FCO1550 4.8 12.8 1.0 N Q:CYS546 4.8 10.9 1.0 O Q:CYS75 4.8 10.9 1.0 N Q:VAL74 5.0 11.4 1.0

Nickel binding site 2 out of 3 in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ R:Ni1551 b:15.1 occ:1.00 O R:HOH2066 1.8 15.2 0.5 SG R:CYS72 2.2 15.0 1.0 SG R:CYS75 2.2 14.1 1.0 SG R:CSO543 2.2 20.9 1.0 SG R:CYS546 2.5 15.0 1.0 FE R:FCO1550 2.7 15.2 1.0 CB R:CYS72 3.0 15.5 1.0 OD R:CSO543 3.2 19.9 0.4 CB R:CYS75 3.2 14.7 1.0 CB R:CSO543 3.3 18.3 1.0 CB R:CYS546 3.6 14.0 1.0 N R:CYS75 3.6 15.1 1.0 C1 R:FCO1550 3.8 14.9 1.0 C2 R:FCO1550 3.9 14.9 1.0 CA R:CYS75 4.0 15.7 1.0 C3 R:FCO1550 4.2 15.8 1.0 NH1 R:ARG476 4.4 14.5 1.0 CA R:CYS72 4.5 16.1 1.0 CD R:ARG476 4.7 14.3 1.0 CB R:VAL74 4.7 14.9 1.0 CZ R:ARG476 4.7 15.2 1.0 CA R:CYS546 4.7 14.0 1.0 CA R:CSO543 4.7 16.5 1.0 N1 R:FCO1550 4.7 14.8 1.0 NE R:ARG476 4.7 14.8 1.0 C R:CYS75 4.7 16.4 1.0 O R:CYS75 4.7 17.2 1.0 C R:VAL74 4.8 15.5 1.0 N R:CYS546 4.8 13.6 1.0 N2 R:FCO1550 4.8 14.6 1.0

Nickel binding site 3 out of 3 in the Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Structure of Air-Treated Anaerobically Purified D. Fructosovorans Nife-Hydrogenase within 5.0Å range: probe atom residue distance (Å) B Occ S:Ni1551 b:18.2 occ:1.00 O S:HOH2050 1.8 16.7 0.5 SG S:CYS72 2.2 17.9 1.0 SG S:CSO543 2.2 22.0 1.0 SG S:CYS75 2.2 15.8 1.0 SG S:CYS546 2.5 16.6 1.0 FE S:FCO1550 2.6 16.8 1.0 CB S:CYS72 3.1 16.1 1.0 OD S:CSO543 3.2 21.1 0.4 CB S:CYS75 3.2 15.6 1.0 CB S:CSO543 3.3 18.9 1.0 CB S:CYS546 3.6 16.3 1.0 C1 S:FCO1550 3.7 16.5 1.0 N S:CYS75 3.7 14.6 1.0 C2 S:FCO1550 3.8 17.0 1.0 CA S:CYS75 4.0 15.6 1.0 C3 S:FCO1550 4.2 17.0 1.0 NH1 S:ARG476 4.5 17.4 1.0 CA S:CYS72 4.5 14.6 1.0 N1 S:FCO1550 4.6 17.0 1.0 CD S:ARG476 4.6 17.1 1.0 CA S:CSO543 4.7 18.7 1.0 CA S:CYS546 4.7 16.6 1.0 CB S:VAL74 4.7 13.6 1.0 CZ S:ARG476 4.7 17.6 1.0 O S:CYS75 4.7 16.6 1.0 NE S:ARG476 4.7 16.5 1.0 N2 S:FCO1550 4.7 18.4 1.0 C S:CYS75 4.7 15.9 1.0 N S:CYS546 4.8 15.6 1.0 C S:VAL74 4.8 15.1 1.0

A.Volbeda, L.Martin, P.-P.Liebgott, A.L.De Lacey, J.C.Fontecilla-Camps. [Nife]-Hydrogenases Revisited: Nickel-Carboxamido Bond Formation in A Variant with Accrued O2-Tolerance and A Tentative Re-Interpretation of Ni-Si States. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25780984
DOI: 10.1039/C4MT00309H