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

Protein crystallography data

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

Other elements in 3l6t:

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

Nickel Binding Sites:

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 3l6t

Go back to Nickel Binding Sites List in 3l6t
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 3l6t

Go back to Nickel Binding Sites List in 3l6t
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

Reference:

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
Page generated: Thu Oct 29 06:20:37 2020
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