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Chlorine in PDB 5j2f: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus

Enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus, PDB code: 5j2f was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 79.900, 55.500, 90.00, 107.70, 90.00
R / Rfree (%) 19.8 / 26.1

Other elements in 5j2f:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus (pdb code 5j2f). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus, PDB code: 5j2f:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5j2f

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Chlorine binding site 1 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:41.4
occ:1.00
 O A:HOH526 3.1 28.4 1.0
N A:CYS267 3.2 21.1 1.0
CA A:GLN264 3.4 23.8 1.0
C A:GLN264 3.4 24.5 1.0
O A:GLN264 3.5 25.7 1.0
N A:TYR266 3.7 24.1 1.0
CB A:CYS267 3.8 24.3 1.0
CB A:TYR266 3.8 27.8 1.0
SG A:CYS267 3.8 23.7 1.0
CB A:VAL313 3.9 26.8 1.0
O A:ASP263 3.9 26.7 1.0
CG1 A:VAL313 3.9 28.0 1.0
CA A:TYR266 4.0 24.1 1.0
N A:TYR265 4.0 24.9 1.0
C A:TYR266 4.1 22.5 1.0
CA A:CYS267 4.1 21.3 1.0
CB A:GLN264 4.3 24.2 1.0
O A:TYR296 4.4 23.8 1.0
N A:GLN264 4.4 24.3 1.0
CD2 A:TYR266 4.5 33.8 1.0
C A:TYR265 4.5 24.3 1.0
C A:ASP263 4.6 24.9 1.0
O A:VAL313 4.6 28.3 1.0
CG2 A:VAL313 4.6 27.5 1.0
CG A:TYR266 4.6 31.6 1.0
CG A:GLN264 4.8 23.6 1.0
CA A:TYR265 4.8 24.1 1.0

Chlorine binding site 2 out of 5 in 5j2f

Go back to Chlorine Binding Sites List in 5j2f
Chlorine binding site 2 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:40.6
occ:1.00
 N A:HIS34 3.3 29.9 1.0
CB A:ALA32 3.4 29.3 1.0
C A:ALA32 3.4 30.8 1.0
CB A:HIS34 3.4 30.8 1.0
N A:LYS35 3.5 27.5 1.0
CA A:ALA32 3.5 31.0 1.0
O A:ALA32 3.6 29.3 1.0
CA A:HIS34 3.8 30.0 1.0
N A:ILE33 3.9 30.3 1.0
CD2 A:HIS34 4.0 33.7 1.0
CG A:HIS34 4.1 34.0 1.0
CG A:LYS35 4.1 27.2 1.0
C A:HIS34 4.1 29.8 1.0
O A:HOH665 4.2 43.8 1.0
C A:ILE33 4.3 31.5 1.0
CB A:LYS35 4.4 25.1 1.0
CA A:LYS35 4.5 25.3 1.0
CA A:ILE33 4.6 31.8 1.0
O6 D:DG1 4.8 27.3 1.0
CG2 A:ILE33 5.0 33.5 1.0
N A:ALA32 5.0 30.0 1.0

Chlorine binding site 3 out of 5 in 5j2f

Go back to Chlorine Binding Sites List in 5j2f
Chlorine binding site 3 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:42.0
occ:1.00
 N A:LEU82 3.2 28.8 1.0
O A:HOH760 3.5 38.5 1.0
NH2 A:ARG89 3.5 48.3 1.0
NH1 A:ARG89 3.6 47.3 1.0
CA A:LYS81 3.7 31.1 1.0
CB A:LYS81 3.7 34.1 1.0
C A:LYS81 3.9 29.1 1.0
CZ A:ARG89 4.0 46.8 1.0
CB A:LEU82 4.1 29.4 1.0
O A:LEU82 4.2 32.1 1.0
CA A:LEU82 4.2 30.2 1.0
CB A:LEU85 4.2 27.8 1.0
CD1 A:LEU85 4.2 24.7 1.0
C A:LEU82 4.6 32.0 1.0
CG A:LEU85 4.8 26.0 1.0
CE1 A:PHE76 4.9 27.7 1.0
O A:GLY80 4.9 29.9 1.0
CG A:GLU86 4.9 42.4 1.0
N A:LYS81 5.0 29.9 1.0

Chlorine binding site 4 out of 5 in 5j2f

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Chlorine binding site 4 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:31.7
occ:1.00
 NH2 A:ARG299 3.0 37.9 1.0
ND2 A:ASN294 3.2 21.0 1.0
NE A:ARG299 3.2 36.5 1.0
OG1 A:THR297 3.2 27.6 1.0
CZ A:ARG299 3.5 37.9 1.0
O A:HOH631 3.5 31.1 1.0
OD1 A:ASN294 4.0 21.6 1.0
CG A:ASN294 4.0 21.9 1.0
CB A:TYR296 4.0 25.2 1.0
CD2 A:TYR296 4.3 24.9 1.0
CB A:THR297 4.4 29.4 1.0
CD A:ARG299 4.4 32.7 1.0
CG2 A:THR297 4.5 29.1 1.0
O A:HOH677 4.6 28.0 1.0
CG A:TYR296 4.6 25.0 1.0
N A:THR297 4.7 25.6 1.0
NH1 A:ARG299 4.8 40.6 1.0

Chlorine binding site 5 out of 5 in 5j2f

Go back to Chlorine Binding Sites List in 5j2f
Chlorine binding site 5 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:A Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:30.1
occ:1.00
 OH A:TYR271 3.1 26.1 1.0
NH1 A:ARG258 3.1 20.7 1.0
O P:HOH110 3.3 25.5 1.0
CE2 A:TYR271 3.8 23.2 1.0
CE1 A:PHE272 3.8 17.1 1.0
CZ A:TYR271 3.9 23.1 1.0
CD A:LYS234 3.9 22.7 1.0
C1' P:DA10 4.0 37.7 1.0
CD A:ARG258 4.1 23.4 1.0
C2' P:DA10 4.1 36.5 1.0
CZ A:ARG258 4.2 21.3 1.0
O A:HOH516 4.4 24.1 1.0
CZ A:PHE272 4.5 18.9 1.0
CD1 A:PHE272 4.6 15.7 1.0
NE A:ARG258 4.6 22.1 1.0
C8 P:DA10 4.7 37.0 1.0
N9 P:DA10 4.8 38.2 1.0
CG A:ARG258 4.8 23.3 1.0
CG A:LYS234 4.8 19.1 1.0
NZ A:LYS234 4.9 23.0 1.0
O4' P:DA10 4.9 38.3 1.0

Reference:

V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Mispaired Dna Termini Transitioning to Pre-Catalytic Complexes Support An Induced-Fit Fidelity Mechanism. Structure V. 24 1863 2016.
ISSN: ISSN 0969-2126
PubMed: 27642161
DOI: 10.1016/J.STR.2016.08.006
Page generated: Fri Jul 26 09:41:45 2024

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