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Chlorine 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
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of An N-Terminal Mutant of the Plasmid PCU1 Trai Relaxase Domain, PDB code: 3l6t:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 3l6t

Go back to Chlorine Binding Sites List in 3l6t
Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl315

b:85.5
occ:1.00
N A:ASN181 3.2 41.0 1.0
O A:HOH450 3.2 57.7 1.0
O2 A:EDO310 3.3 90.0 1.0
O A:HOH334 3.3 96.6 1.0
CG A:ASN181 3.4 43.6 1.0
C2 A:EDO310 3.4 89.8 1.0
O A:HOH418 3.4 38.8 1.0
OD1 A:ASN181 3.5 45.0 1.0
ND2 A:ASN181 3.5 45.8 1.0
O1 A:EDO310 3.5 91.0 1.0
C1 A:EDO310 3.5 91.5 1.0
O A:LEU179 3.6 43.2 1.0
CA A:LYS180 3.9 45.0 1.0
CB A:ASN181 3.9 37.0 1.0
C A:LYS180 4.0 45.2 1.0
CA A:ASN181 4.1 37.7 1.0
OD1 A:ASP182 4.4 52.6 1.0
OH A:TYR83 4.6 36.6 1.0
C A:LEU179 4.6 40.8 1.0
NH1 A:ARG127 4.7 72.3 1.0
N A:LYS180 4.8 40.1 1.0
N A:ASP182 4.8 41.5 1.0
CG A:LYS180 4.9 47.3 1.0
O A:HOH399 4.9 50.5 1.0
C A:ASN181 4.9 37.2 1.0
NH1 A:ARG80 4.9 68.0 1.0
CB A:LYS180 4.9 46.0 1.0

Chlorine binding site 2 out of 3 in 3l6t

Go back to Chlorine Binding Sites List in 3l6t
Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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
A:Cl316

b:65.3
occ:1.00
O A:LYS111 2.7 24.7 1.0
NH1 A:ARG118 2.8 36.0 0.7
NH2 A:ARG118 3.1 42.0 0.7
O A:HOH335 3.2 50.9 0.5
O A:HOH443 3.3 41.2 1.0
CZ A:ARG118 3.4 41.6 0.7
C A:LYS111 3.5 27.0 1.0
NH2 A:ARG118 3.6 40.5 0.3
CA A:LYS111 3.7 24.5 1.0
N A:ALA115 3.7 25.2 1.0
CB A:LYS111 3.9 27.7 1.0
CB A:ALA114 3.9 25.9 1.0
CB A:ALA115 4.1 27.4 1.0
CA A:ALA115 4.3 25.9 1.0
C A:ALA114 4.3 25.5 1.0
CG A:LYS111 4.4 34.0 1.0
NE A:ARG118 4.5 44.0 0.3
CZ A:ARG118 4.5 43.3 0.3
CA A:ALA114 4.6 26.0 1.0
NE A:ARG118 4.7 45.5 0.7
N A:ALA112 4.7 24.3 1.0
O A:HOH455 5.0 51.5 1.0

Chlorine binding site 3 out of 3 in 3l6t

Go back to Chlorine Binding Sites List in 3l6t
Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl317

b:73.0
occ:1.00
CB A:VAL16 2.8 49.5 1.0
O A:VAL16 3.0 43.9 1.0
N A:VAL16 3.3 37.5 1.0
CA A:VAL16 3.3 34.4 1.0
C A:VAL16 3.5 38.0 1.0
CG1 A:VAL16 3.7 48.9 1.0
CG2 A:VAL16 3.7 54.0 1.0
O A:HOH386 3.8 48.2 1.0
CB A:PHE164 3.8 31.0 1.0
CG2 A:VAL15 3.8 41.0 1.0
CD1 A:PHE164 3.9 34.3 1.0
CD2 A:PHE147 4.0 26.1 1.0
CB A:HIS162 4.0 28.0 1.0
CE2 A:PHE147 4.1 34.0 1.0
OD2 A:ASP84 4.1 27.2 1.0
CG A:PHE164 4.2 33.2 1.0
C A:VAL15 4.4 38.6 1.0
CG A:ASP84 4.5 29.0 1.0
CG A:HIS162 4.6 27.6 1.0
CZ A:PHE55 4.6 31.2 1.0
N A:GLY17 4.7 35.5 1.0
ND1 A:HIS162 4.7 26.5 1.0
CG A:PHE147 4.8 28.0 1.0
CA A:PHE164 4.9 28.3 1.0
CB A:ASP84 4.9 24.1 1.0
CB A:VAL15 4.9 36.1 1.0
CE1 A:PHE164 4.9 35.3 1.0
CA A:VAL15 4.9 37.7 1.0
OD1 A:ASP84 5.0 29.7 1.0
CZ A:PHE147 5.0 36.4 1.0

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: Sat Dec 12 09:52:33 2020

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