Nickel in PDB 4wwf: High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs

The structure of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs, PDB code: 4wwf was solved by A.Volbeda, J.Coves, A.P.Maillard, S.Kinnemann, C.Grosse, G.Schleuder, I.Petit-Hurtlein, E.De Rosny, D.H.Nies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.79 / 1.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	43.910, 47.520, 193.740, 90.00, 90.00, 90.00
R / Rfree (%)	11.5 / 14.5

The structure of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Nickel atom in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs (pdb code 4wwf). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs, PDB code: 4wwf:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:5.7 occ:1.00 NE2 A:HIS42 2.0 6.1 1.0 NE2 A:HIS46 2.1 7.0 1.0 NE2 A:HIS119 2.1 5.2 1.0 O A:HOH428 2.1 7.1 1.0 OE2 A:GLU63 2.1 6.3 1.0 OE1 A:GLU63 2.2 6.1 1.0 CD A:GLU63 2.5 5.8 1.0 CE1 A:HIS42 3.0 6.9 1.0 CE1 A:HIS46 3.0 11.2 1.0 CD2 A:HIS119 3.1 5.1 1.0 CD2 A:HIS42 3.1 6.0 1.0 CD2 A:HIS46 3.1 6.1 1.0 CE1 A:HIS119 3.1 5.0 1.0 HE1 A:HIS42 3.1 6.8 1.0 HG A:CYS123 3.2 7.3 1.0 HD2 A:HIS119 3.2 4.7 1.0 HE1 A:HIS46 3.2 8.4 1.0 HD2 A:HIS46 3.3 5.9 1.0 HD2 A:HIS42 3.3 5.8 1.0 HE1 A:HIS119 3.3 4.8 1.0 CG A:GLU63 4.0 6.5 1.0 ND1 A:HIS42 4.1 8.0 1.0 SG A:CYS123 4.1 6.6 1.0 ND1 A:HIS46 4.2 11.4 1.0 O A:HOH435 4.2 12.4 1.0 CG A:HIS42 4.2 6.4 1.0 O A:HOH447 4.2 14.4 1.0 ND1 A:HIS119 4.2 4.8 1.0 CG A:HIS46 4.2 7.6 1.0 CG A:HIS119 4.2 4.9 1.0 O A:HOH433 4.3 10.1 1.0 HA A:GLU63 4.3 5.4 1.0 HD2 A:PHE66 4.4 6.9 1.0 HG2 A:GLU63 4.4 6.7 1.0 HG3 A:GLU63 4.4 6.3 1.0 HB3 A:GLU63 4.8 6.4 1.0 HD1 A:HIS42 4.9 6.1 1.0 CB A:GLU63 4.9 6.2 1.0 CD2 A:PHE66 4.9 7.0 1.0 HD1 A:HIS46 5.0 7.9 1.0 HB3 A:PHE66 5.0 6.4 1.0

Nickel binding site 2 out of 3 in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:9.6 occ:0.50 NI B:NI201 0.0 9.6 0.5 NI B:NI201 0.7 14.9 0.5 OE2 B:GLU63 1.7 15.5 0.5 O B:HOH426 2.0 12.4 0.5 NE2 B:HIS42 2.0 17.1 0.5 NE2 B:HIS46 2.1 16.0 0.5 OE2 B:GLU63 2.1 11.3 0.5 O B:HOH426 2.1 9.4 0.5 NE2 B:HIS119 2.1 10.8 0.5 NE2 B:HIS119 2.1 9.6 0.5 OE1 B:GLU63 2.2 11.9 0.5 OE1 B:GLU63 2.3 9.8 0.5 NE2 B:HIS46 2.3 20.3 0.5 CD B:GLU63 2.3 11.4 0.5 CD B:GLU63 2.4 10.2 0.5 ND1 B:HIS42 2.8 19.9 0.5 CE1 B:HIS42 3.0 20.8 0.5 CE1 B:HIS46 3.0 23.3 0.5 CE1 B:HIS119 3.0 10.4 0.5 CD2 B:HIS42 3.1 22.0 0.5 CD2 B:HIS46 3.1 18.5 0.5 CE1 B:HIS119 3.1 10.1 0.5 CD2 B:HIS46 3.1 17.3 0.5 CD2 B:HIS119 3.1 9.9 0.5 HD2 B:HIS46 3.1 19.3 0.5 HE1 B:HIS42 3.1 33.0 0.5 HE1 B:HIS46 3.2 20.8 0.5 CD2 B:HIS119 3.2 9.8 0.5 HE1 B:HIS119 3.2 9.9 0.5 HE1 B:HIS119 3.2 9.6 0.5 HE1 B:HIS42 3.3 23.8 0.5 HG B:CYS123 3.3 11.7 1.0 HD2 B:HIS42 3.3 22.6 0.5 HD2 B:HIS46 3.3 18.8 0.5 HD2 B:HIS119 3.3 9.7 0.5 HD2 B:HIS119 3.3 9.5 0.5 CE1 B:HIS46 3.4 15.1 0.5 CE1 B:HIS42 3.4 27.4 0.5 O B:HOH472 3.6 10.5 0.3 HE1 B:HIS46 3.6 14.4 0.5 CG B:GLU63 3.8 11.4 0.5 CG B:GLU63 3.9 10.8 0.5 CG B:HIS42 4.0 15.8 0.5 HB2 B:HIS42 4.0 17.3 0.5 O B:HIS42 4.1 17.4 0.5 HG3 B:GLU63 4.1 11.1 0.5 ND1 B:HIS42 4.1 22.4 0.5 ND1 B:HIS46 4.1 20.6 0.5 HG2 B:GLU63 4.1 10.6 0.5 ND1 B:HIS119 4.2 9.4 0.5 SG B:CYS123 4.2 12.6 1.0 CG B:HIS42 4.2 24.4 0.5 CG B:HIS46 4.2 14.7 0.5 ND1 B:HIS119 4.2 9.3 0.5 O B:HOH435 4.2 19.8 0.7 CG B:HIS119 4.3 9.0 0.5 HG3 B:GLU63 4.3 10.7 0.5 HA B:GLU63 4.3 8.8 0.5 CG B:HIS119 4.3 8.9 0.5 O B:HOH422 4.3 22.0 1.0 HG2 B:GLU63 4.3 10.1 0.5 CG B:HIS46 4.3 19.1 0.5 HA B:GLU63 4.3 8.6 0.5 ND1 B:HIS46 4.4 20.8 0.5 CB B:HIS42 4.5 17.1 0.5 HD2 B:PHE66 4.5 14.3 1.0 O B:HOH413 4.6 13.4 1.0 NE2 B:HIS42 4.6 24.1 0.5 CB B:GLU63 4.8 8.8 0.5 HB3 B:GLU63 4.8 8.7 0.5 C B:HIS42 4.8 18.4 0.5 HB3 B:GLU63 4.9 8.5 0.5 CB B:GLU63 4.9 8.5 0.5 HD1 B:HIS46 4.9 18.9 0.5 HD1 B:HIS42 4.9 22.8 0.5 HD1 B:HIS119 4.9 9.3 0.5 CD2 B:HIS42 5.0 21.6 0.5 HD1 B:HIS119 5.0 9.3 0.5

Nickel binding site 3 out of 3 in the High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of High-Resolution Structure of Two Ni-Bound Forms of the M123C Mutant of C. Metallidurans Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:14.9 occ:0.50 NI B:NI201 0.0 14.9 0.5 NI B:NI201 0.7 9.6 0.5 NE2 B:HIS42 1.4 17.1 0.5 O B:HOH426 2.0 12.4 0.5 ND1 B:HIS42 2.1 19.9 0.5 NE2 B:HIS119 2.1 10.8 0.5 NE2 B:HIS46 2.2 16.0 0.5 OE1 B:GLU63 2.2 11.9 0.5 NE2 B:HIS119 2.2 9.6 0.5 NE2 B:HIS46 2.2 20.3 0.5 OE1 B:GLU63 2.3 9.8 0.5 CE1 B:HIS42 2.3 20.8 0.5 OE2 B:GLU63 2.3 15.5 0.5 O B:HOH426 2.5 9.4 0.5 HE1 B:HIS42 2.5 33.0 0.5 CD2 B:HIS42 2.6 22.0 0.5 CD B:GLU63 2.6 11.4 0.5 HE1 B:HIS42 2.7 23.8 0.5 OE2 B:GLU63 2.7 11.3 0.5 CE1 B:HIS42 2.7 27.4 0.5 CD B:GLU63 2.8 10.2 0.5 CE1 B:HIS46 2.8 23.3 0.5 HE1 B:HIS46 2.9 20.8 0.5 HD2 B:HIS42 3.0 22.6 0.5 CD2 B:HIS119 3.0 9.9 0.5 CD2 B:HIS119 3.0 9.8 0.5 HD2 B:HIS119 3.1 9.7 0.5 HD2 B:HIS119 3.1 9.5 0.5 CE1 B:HIS46 3.1 15.1 0.5 CE1 B:HIS119 3.2 10.4 0.5 CD2 B:HIS46 3.2 17.3 0.5 HE1 B:HIS46 3.2 14.4 0.5 CE1 B:HIS119 3.3 10.1 0.5 CD2 B:HIS46 3.3 18.5 0.5 CG B:HIS42 3.4 15.8 0.5 ND1 B:HIS42 3.4 22.4 0.5 HD2 B:HIS46 3.4 19.3 0.5 HE1 B:HIS119 3.5 9.9 0.5 HE1 B:HIS119 3.5 9.6 0.5 CG B:HIS42 3.6 24.4 0.5 HB2 B:HIS42 3.6 17.3 0.5 HD2 B:HIS46 3.6 18.8 0.5 O B:HIS42 3.8 17.4 0.5 HG B:CYS123 3.9 11.7 1.0 NE2 B:HIS42 4.0 24.1 0.5 CB B:HIS42 4.0 17.1 0.5 HD2 B:PHE66 4.0 14.3 1.0 ND1 B:HIS46 4.0 20.6 0.5 O B:HOH472 4.0 10.5 0.3 CG B:GLU63 4.1 11.4 0.5 HD1 B:HIS42 4.2 22.8 0.5 CG B:HIS119 4.2 9.0 0.5 CG B:HIS119 4.2 8.9 0.5 O B:HOH413 4.3 13.4 1.0 ND1 B:HIS46 4.3 20.8 0.5 CD2 B:HIS42 4.3 21.6 0.5 ND1 B:HIS119 4.3 9.4 0.5 CG B:HIS46 4.3 14.7 0.5 CG B:GLU63 4.3 10.8 0.5 ND1 B:HIS119 4.3 9.3 0.5 CG B:HIS46 4.4 19.1 0.5 HA B:GLU63 4.4 8.8 0.5 C B:HIS42 4.4 18.4 0.5 HA B:GLU63 4.4 8.6 0.5 HG3 B:GLU63 4.5 11.1 0.5 CD2 B:PHE66 4.6 16.0 1.0 HG2 B:GLU63 4.6 10.6 0.5 HG3 B:GLU63 4.6 10.7 0.5 HE2 B:HIS42 4.6 23.9 0.5 CA B:HIS42 4.7 16.0 0.5 HE2 B:PHE66 4.7 20.0 1.0 HD1 B:HIS46 4.7 18.9 0.5 SG B:CYS123 4.8 12.6 1.0 HA B:HIS42 4.8 14.1 0.5 HG2 B:GLU63 4.8 10.1 0.5 HB3 B:HIS42 4.8 16.0 0.5 HB3 B:GLU63 4.9 8.7 0.5 O B:HOH422 4.9 22.0 1.0 O B:HOH435 4.9 19.8 0.7 HB3 B:GLU63 4.9 8.5 0.5 HB3 B:PHE66 4.9 13.0 1.0 CE2 B:PHE66 5.0 23.1 1.0 CB B:GLU63 5.0 8.8 0.5

A.P.Maillard, S.Kunnemann, C.Groe, A.Volbeda, G.Schleuder, I.Petit-Hartlein, E.De Rosny, D.H.Nies, J.Coves. Response of Cnrx From Cupriavidus Metallidurans CH34 to Nickel Binding. Metallomics 2015.
ISSN: ESSN 1756-591X
PubMed: 25628016
DOI: 10.1039/C4MT00293H