Nickel in PDB 3zg1: Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs

The structure of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs, PDB code: 3zg1 was solved by E.Girard, J.Coves, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.737 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.846, 79.125, 93.475, 90.00, 90.10, 90.00
R / Rfree (%)	17.63 / 22.24

The structure of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs (pdb code 3zg1). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs, PDB code: 3zg1:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni150 b:34.1 occ:0.55 OE2 A:GLU63 1.8 33.5 1.0 NE2 A:HIS42 2.4 61.2 1.0 CD2 A:HIS42 2.7 60.2 1.0 CD A:GLU63 2.8 32.5 1.0 NE2 A:HIS119 2.8 31.7 1.0 OE1 A:GLU63 3.1 30.2 1.0 CD2 A:HIS119 3.3 28.9 1.0 CE1 A:HIS42 3.6 62.4 1.0 CE1 A:HIS119 4.0 27.5 1.0 CG A:HIS42 4.0 60.6 1.0 CG A:GLU63 4.1 31.0 1.0 CD2 A:HIS46 4.3 55.9 1.0 ND1 A:HIS42 4.4 62.7 1.0 CB A:HIS46 4.5 54.2 1.0 CG A:HIS119 4.6 26.0 1.0 O A:HIS42 4.6 56.1 1.0 CG A:HIS46 4.8 56.2 1.0 ND1 A:HIS119 4.9 23.9 1.0 CA A:HIS46 4.9 52.5 1.0

Nickel binding site 2 out of 4 in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni150 b:32.5 occ:1.00 OE2 B:GLU63 1.9 35.4 1.0 NE2 B:HIS42 2.0 26.5 1.0 NE2 B:HIS119 2.1 25.8 1.0 O B:HOH2003 2.2 42.4 1.0 NE2 B:HIS46 2.2 41.0 1.0 OE1 B:GLU63 2.3 33.6 1.0 CD B:GLU63 2.4 34.0 1.0 CD2 B:HIS42 2.9 24.1 1.0 CD2 B:HIS119 3.0 23.6 1.0 CE1 B:HIS42 3.1 30.7 1.0 CD2 B:HIS46 3.1 40.1 1.0 CE1 B:HIS119 3.1 24.9 1.0 CE1 B:HIS46 3.2 41.7 1.0 CG B:GLU63 3.9 33.2 1.0 CG B:HIS42 4.1 29.0 1.0 ND1 B:HIS42 4.1 31.4 1.0 CG B:HIS119 4.2 22.9 1.0 ND1 B:HIS119 4.2 23.5 1.0 CG B:HIS46 4.3 38.6 1.0 ND1 B:HIS46 4.3 40.2 1.0 CB B:GLU63 4.8 31.9 1.0 CB B:ALA123 4.9 21.8 1.0

Nickel binding site 3 out of 4 in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni150 b:39.2 occ:0.60 NE2 C:HIS42 2.1 41.4 1.0 OE1 C:GLU63 2.3 42.3 1.0 NE2 C:HIS119 2.4 29.3 1.0 CD2 C:HIS42 2.5 40.4 1.0 O C:HOH2037 2.8 54.4 1.0 CD2 C:HIS119 3.0 26.3 1.0 CD C:GLU63 3.3 38.9 1.0 CE1 C:HIS42 3.3 42.7 1.0 CE1 C:HIS119 3.6 27.7 1.0 OE2 C:GLU63 3.6 42.7 1.0 CD2 C:HIS46 3.7 51.5 1.0 CG C:HIS42 3.8 40.9 1.0 ND1 C:HIS42 4.2 43.6 1.0 O C:HOH2007 4.3 29.8 1.0 CG C:HIS119 4.3 25.0 1.0 ND1 C:HIS119 4.5 26.8 1.0 CG C:HIS46 4.6 51.8 1.0 CG C:GLU63 4.6 31.9 1.0 NE2 C:HIS46 4.7 55.2 1.0 O C:HOH2013 4.7 34.8 1.0 O C:HIS42 4.7 43.6 1.0 CB C:HIS46 4.8 48.5 1.0

Nickel binding site 4 out of 4 in the Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Ni-Bound Form of M123A Mutant of Cupriavidus Metallidurans CH34 Cnrxs within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni150 b:40.6 occ:0.75 NE2 D:HIS119 1.9 35.2 1.0 NE2 D:HIS46 2.0 63.4 1.0 OE2 D:GLU63 2.2 47.8 1.0 O D:HOH2002 2.5 58.2 1.0 NE2 D:HIS42 2.5 51.3 1.0 CE1 D:HIS119 2.5 30.1 1.0 OE1 D:GLU63 2.6 51.9 1.0 CD D:GLU63 2.7 48.9 1.0 CD2 D:HIS46 2.8 61.7 1.0 CD2 D:HIS42 3.0 47.0 1.0 CE1 D:HIS46 3.1 65.4 1.0 CD2 D:HIS119 3.2 30.6 1.0 CE1 D:HIS42 3.7 54.4 1.0 ND1 D:HIS119 3.8 27.5 1.0 CG D:HIS46 4.0 62.5 1.0 ND1 D:HIS46 4.1 65.1 1.0 CG D:HIS119 4.1 26.8 1.0 CG D:GLU63 4.2 47.2 1.0 O D:HOH2012 4.2 31.7 1.0 CG D:HIS42 4.3 47.7 1.0 ND1 D:HIS42 4.6 47.3 1.0 CD2 D:PHE66 4.9 34.2 1.0

J.Trepreau, C.Grosse, J.-M.Mouesca, G.Sarret, E.Girard, I.Petit-Haertlein, S.Kuennemann, C.Desbourdes, E.De Rosny, A.P.Maillard, D.H.Nies, J.Coves. Metal Sensing and Signal Transduction By Cnrx From Cupriavidus Metallidurans CH34: Role of the Only Methionine Assessed By A Functional, Spectroscopic, and Theoretical Study Metallomics V. 6 263 2014.
ISSN: ISSN 1756-5901
PubMed: 24154823
DOI: 10.1039/C3MT00248A