Nickel in PDB 5bnc: Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis

The structure of Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis, PDB code: 5bnc was solved by F.H.Ahmed, P.D.Carr, C.J.Jackson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.77 / 2.25
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	62.100, 62.100, 301.406, 90.00, 90.00, 120.00
R / Rfree (%)	18.5 / 23

The structure of Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis (pdb code 5bnc). 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 Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis, PDB code: 5bnc:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:26.9 occ:1.00 NE2 A:HIS190 2.0 25.9 1.0 NE2 A:HIS195 2.2 34.0 1.0 O A:HOH488 2.3 26.4 1.0 CD2 A:HIS190 2.9 26.9 1.0 CD2 A:HIS195 3.0 31.0 1.0 CE1 A:HIS190 3.1 27.0 1.0 CE1 A:HIS195 3.3 35.4 1.0 O A:HOH409 4.1 47.5 1.0 CG A:HIS190 4.1 24.2 1.0 ND1 A:HIS190 4.1 26.5 1.0 CG A:HIS195 4.2 34.2 1.0 ND1 A:HIS195 4.3 35.6 1.0 CD2 A:LEU191 5.0 31.9 1.0

Nickel binding site 2 out of 2 in the Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Structure of Heme Binding Protein MSMEG_6519 From Mycobacterium Smegmatis within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:28.7 occ:1.00 O B:HOH501 1.9 26.5 1.0 NE2 B:HIS190 2.0 25.9 1.0 NE2 B:HIS195 2.1 32.7 1.0 CE1 B:HIS195 2.9 34.0 1.0 CD2 B:HIS190 2.9 27.4 1.0 CE1 B:HIS190 3.0 28.6 1.0 CD2 B:HIS195 3.3 29.4 1.0 ND1 B:HIS190 4.0 28.0 1.0 CG B:HIS190 4.0 26.2 1.0 ND1 B:HIS195 4.1 33.3 1.0 CG B:HIS195 4.3 31.2 1.0 CB B:ASP194 4.7 32.6 1.0

F.H.Ahmed, P.D.Carr, B.M.Lee, L.Afriat-Jurnou, A.E.Mohamed, N.S.Hong, J.Flanagan, M.C.Taylor, C.Greening, C.J.Jackson. Sequence-Structure-Function Classification of A Catalytically Diverse Oxidoreductase Superfamily in Mycobacteria. J.Mol.Biol. V. 427 3554 2015.
ISSN: ESSN 1089-8638
PubMed: 26434506
DOI: 10.1016/J.JMB.2015.09.021