Nickel in PDB 3l6t: Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain

The structure of Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain, PDB code: 3l6t was solved by M.R.Redinbo, R.P.Nash, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.37 / 1.93
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.385, 58.656, 86.532, 90.00, 95.01, 90.00
R / Rfree (%)	16.8 / 20.4

The structure of Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Nickel atom in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain (pdb code 3l6t). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain, PDB code: 3l6t:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain


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 An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni314 b:33.2 occ:1.00 NE2 A:HIS162 2.1 29.4 1.0 O5 A:CIT300 2.2 32.0 1.0 ND1 A:HIS149 2.2 32.8 1.0 NE2 A:HIS160 2.2 24.8 1.0 O7 A:CIT300 2.2 33.2 1.0 O4 A:CIT300 2.4 35.7 1.0 C6 A:CIT300 2.9 36.0 1.0 C3 A:CIT300 3.0 37.5 1.0 CE1 A:HIS149 3.0 33.3 1.0 CE1 A:HIS162 3.1 31.6 1.0 CD2 A:HIS162 3.1 26.5 1.0 CD2 A:HIS160 3.1 26.2 1.0 C5 A:CIT300 3.2 38.5 1.0 CE1 A:HIS160 3.2 30.1 1.0 CG A:HIS149 3.2 34.1 1.0 C4 A:CIT300 3.6 36.1 1.0 CB A:HIS149 3.7 34.0 1.0 O1 A:CIT300 4.0 43.5 1.0 O6 A:CIT300 4.0 38.8 1.0 O A:HOH360 4.1 0.6 1.0 NE2 A:HIS149 4.2 35.4 1.0 ND1 A:HIS162 4.2 26.5 1.0 CG A:HIS162 4.2 27.6 1.0 C2 A:CIT300 4.3 42.2 1.0 CG A:HIS160 4.3 28.6 1.0 ND1 A:HIS160 4.3 29.9 1.0 CD2 A:HIS149 4.3 35.9 1.0 O3 A:CIT300 4.4 43.3 1.0 C1 A:CIT300 4.6 46.4 1.0 CG2 A:VAL16 4.7 54.0 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain


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 An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni308 b:48.4 occ:1.00 NE2 B:HIS160 2.2 36.1 1.0 NE2 B:HIS162 2.2 39.2 1.0 O2 B:EDO302 2.4 53.4 1.0 ND1 B:HIS149 2.5 65.4 1.0 O B:HOH323 2.5 56.5 1.0 O1 B:EDO302 2.7 68.6 1.0 CE1 B:HIS162 3.1 37.5 1.0 CE1 B:HIS160 3.1 40.1 1.0 CD2 B:HIS160 3.2 35.7 1.0 CD2 B:HIS162 3.3 39.2 1.0 C2 B:EDO302 3.4 58.8 1.0 CE1 B:HIS149 3.4 67.2 1.0 C1 B:EDO302 3.4 65.6 1.0 CG B:HIS149 3.5 67.9 1.0 O B:HOH330 3.7 86.5 1.0 CB B:HIS149 3.7 66.0 1.0 O B:HOH365 4.2 68.8 0.5 ND1 B:HIS160 4.3 38.6 1.0 ND1 B:HIS162 4.3 37.9 1.0 CG B:HIS160 4.3 33.2 1.0 CG B:HIS162 4.4 37.5 1.0 NE2 B:HIS149 4.5 69.5 1.0 CD2 B:HIS149 4.6 70.3 1.0 O B:HOH435 4.9 49.6 0.4 O B:HOH435 5.0 55.0 0.6

R.P.Nash, S.Habibi, Y.Cheng, S.A.Lujan, M.R.Redinbo. The Mechanism and Control of Dna Transfer By the Conjugative Relaxase of Resistance Plasmid PCU1. Nucleic Acids Res. V. 38 5929 2010.
ISSN: ISSN 0305-1048
PubMed: 20448025
DOI: 10.1093/NAR/GKQ303