Nickel in PDB 3lgh: Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination

The structure of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination, PDB code: 3lgh was solved by E.Pozharski, F.St John, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.34 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.479, 105.056, 48.185, 90.00, 90.00, 90.00
R / Rfree (%)	26 / 31.8

The structure of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Nickel atom in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination (pdb code 3lgh). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination, PDB code: 3lgh:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni149 b:27.9 occ:1.00 ND1 A:HIS101 2.1 29.9 1.0 NE2 A:HIS99 2.1 29.4 1.0 SG A:CYS107 2.3 34.6 1.0 CE1 A:HIS101 2.9 27.9 1.0 CE1 A:HIS99 3.0 29.9 1.0 CD2 A:HIS99 3.0 27.9 1.0 CG A:HIS101 3.1 31.3 1.0 CA A:HIS101 3.3 33.5 1.0 CB A:CYS107 3.4 34.7 1.0 CB A:HIS101 3.5 32.7 1.0 N A:HIS101 3.9 32.8 1.0 O A:ILE100 4.0 32.0 1.0 NE2 A:HIS101 4.1 29.1 1.0 CA A:CYS107 4.1 34.5 1.0 ND1 A:HIS99 4.1 29.9 1.0 CD2 A:HIS101 4.2 30.3 1.0 CG A:HIS99 4.2 29.7 1.0 C A:ILE100 4.2 32.2 1.0 C A:HIS101 4.6 34.8 1.0 O A:ASN106 4.6 36.1 1.0 N A:MET102 4.9 36.1 1.0 N A:CYS107 4.9 35.3 1.0

Nickel binding site 2 out of 4 in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni149 b:33.1 occ:1.00 NE2 B:HIS99 2.1 29.3 1.0 ND1 B:HIS101 2.1 30.1 1.0 SG B:CYS107 2.3 35.3 1.0 CE1 B:HIS101 3.0 28.6 1.0 CE1 B:HIS99 3.0 29.8 1.0 CD2 B:HIS99 3.1 28.1 1.0 CG B:HIS101 3.2 31.2 1.0 CB B:CYS107 3.3 34.8 1.0 CA B:HIS101 3.5 33.5 1.0 CB B:HIS101 3.6 32.8 1.0 N B:HIS101 3.9 32.7 1.0 CA B:CYS107 4.0 34.6 1.0 NE2 B:HIS101 4.1 29.5 1.0 ND1 B:HIS99 4.1 30.1 1.0 O B:ILE100 4.2 32.2 1.0 CD2 B:HIS101 4.2 30.7 1.0 CG B:HIS99 4.2 29.7 1.0 C B:ILE100 4.3 32.1 1.0 O B:ASN106 4.7 35.8 1.0 C B:HIS101 4.8 34.8 1.0 N B:CYS107 4.8 35.3 1.0

Nickel binding site 3 out of 4 in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni149 b:49.6 occ:1.00 NE2 C:HIS101 2.1 46.2 1.0 NE2 C:HIS74 2.1 45.7 1.0 CE1 C:HIS101 3.0 44.7 1.0 CE1 C:HIS74 3.0 44.9 1.0 CD2 C:HIS101 3.2 45.0 1.0 CD2 C:HIS74 3.2 44.5 1.0 ND1 C:HIS101 4.1 45.5 1.0 ND1 C:HIS74 4.2 44.8 1.0 CG C:HIS101 4.2 44.8 1.0 CG C:HIS74 4.3 43.4 1.0

Nickel binding site 4 out of 4 in the Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Nikr From Helicobacter Pylori with Variable Ni Site Coordination within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni149 b:45.8 occ:1.00 O D:HOH171 2.0 32.0 1.0 NE2 D:HIS74 2.1 45.0 1.0 O D:HOH170 2.1 24.3 1.0 NE2 D:HIS101 2.1 45.9 1.0 CE1 D:HIS74 2.9 44.7 1.0 CE1 D:HIS101 3.1 44.5 1.0 CD2 D:HIS101 3.2 44.6 1.0 CD2 D:HIS74 3.2 44.1 1.0 ND1 D:HIS74 4.1 44.7 1.0 ND1 D:HIS101 4.2 45.1 1.0 CG D:HIS74 4.3 43.2 1.0 CG D:HIS101 4.3 44.5 1.0

A.L.West, F.St John, P.E.Lopes, A.D.Mackerell, E.Pozharski, S.L.Michel. Holo-Ni(II)Hpnikr Is An Asymmetric Tetramer Containing Two Different Nickel-Binding Sites. J.Am.Chem.Soc. V. 132 14447 2010.
ISSN: ISSN 0002-7863
PubMed: 20863122
DOI: 10.1021/JA104118R