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Sodium 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:

Nickel (Ni) 2 atoms
Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain, PDB code: 3l6t:

Sodium binding site 1 out of 1 in 3l6t

Go back to Sodium Binding Sites List in 3l6t
Sodium binding site 1 out of 1 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 Sodium with other atoms in the Na 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:Na321

b:52.9
occ:1.00
N A:LYS91 3.0 31.2 0.2
N A:LYS91 3.0 29.8 0.8
O3 A:PO4319 3.1 0.5 1.0
O B:HOH357 3.2 58.9 0.5
O A:HOH524 3.2 44.9 0.5
O2 A:PO4319 3.3 0.4 1.0
CB A:LYS91 3.5 36.9 0.2
P A:PO4319 3.6 0.9 1.0
CG A:LYS91 3.7 49.0 0.8
CB A:LYS91 3.7 39.0 0.8
CA A:PRO90 3.7 31.6 1.0
C A:PRO90 3.9 32.0 1.0
CA A:LYS91 3.9 33.8 0.2
CE B:LYS215 3.9 61.3 1.0
O1 A:PO4319 3.9 0.5 1.0
CA A:LYS91 4.0 32.9 0.8
CD A:LYS91 4.0 60.2 0.8
O A:HOH501 4.0 42.5 0.5
OD2 A:ASP220 4.1 33.5 1.0
CB A:PRO90 4.2 30.4 1.0
O A:HOH524 4.4 46.7 0.5
NZ B:LYS215 4.5 66.0 1.0
O A:HOH429 4.5 34.3 1.0
CE A:LYS91 4.6 67.3 0.8
CG A:LYS91 4.8 39.2 0.2
O A:HOH501 4.9 37.7 0.5

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: Tue Dec 15 06:16:34 2020

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