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Chlorine in PDB 5j2g: Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G Mismatch at the Primer Terminus

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

All present enzymatic activity of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus, PDB code: 5j2g 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 (°) 50.670, 80.480, 55.420, 90.00, 108.04, 90.00
R / Rfree (%) 20.6 / 26.5

Other elements in 5j2g:

The structure of Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus (pdb code 5j2g). 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:G Mismatch at the Primer Terminus, PDB code: 5j2g:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5j2g

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Chlorine binding site 1 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:29.4
occ:1.00
 O A:HOH520 3.0 28.2 1.0
N A:CYS267 3.2 21.4 1.0
C A:GLN264 3.5 21.2 1.0
CA A:GLN264 3.5 21.1 1.0
N A:TYR266 3.5 21.6 1.0
CB A:TYR266 3.7 24.3 1.0
O A:GLN264 3.7 22.1 1.0
SG A:CYS267 3.8 20.5 1.0
CB A:CYS267 3.8 20.0 1.0
CG1 A:VAL313 3.8 27.9 1.0
CB A:VAL313 3.8 28.6 1.0
O A:ASP263 3.9 23.0 1.0
N A:TYR265 3.9 21.9 1.0
CA A:TYR266 3.9 23.5 1.0
C A:TYR266 4.0 21.9 1.0
CA A:CYS267 4.1 20.8 1.0
CD2 A:TYR266 4.3 29.0 1.0
C A:TYR265 4.3 22.3 1.0
O A:TYR296 4.4 18.4 1.0
CB A:GLN264 4.4 21.2 1.0
O A:VAL313 4.5 29.9 1.0
N A:GLN264 4.5 22.2 1.0
CG A:TYR266 4.5 27.9 1.0
C A:ASP263 4.6 22.7 1.0
CG2 A:VAL313 4.6 26.0 1.0
CA A:TYR265 4.7 21.8 1.0
C A:VAL313 4.9 30.0 1.0

Chlorine binding site 2 out of 5 in 5j2g

Go back to Chlorine Binding Sites List in 5j2g
Chlorine binding site 2 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:37.7
occ:1.00
 O T:HOH113 3.1 41.7 1.0
CE A:LYS280 3.2 20.3 1.0
OD1 A:ASN37 3.3 21.6 1.0
ND2 A:ASN37 3.4 14.0 1.0
N6 T:DA6 3.4 10.6 1.0
NH2 A:ARG40 3.5 21.1 1.0
CG A:ASN37 3.8 19.4 1.0
O A:HOH665 3.9 31.1 1.0
CD A:LYS280 4.0 17.9 1.0
N2 P:DG10 4.0 25.9 1.0
CE2 A:TYR36 4.2 19.3 1.0
N7 T:DA6 4.2 16.8 1.0
NZ A:LYS280 4.3 21.1 1.0
O A:HOH753 4.4 23.2 1.0
C6 T:DA6 4.4 13.9 1.0
O T:HOH126 4.7 32.6 1.0
CD2 A:TYR36 4.7 20.4 1.0
C5 T:DA6 4.7 13.7 1.0
CZ A:ARG40 4.7 22.9 1.0
O T:HOH108 4.7 42.1 1.0
CD1 A:ILE33 4.7 29.3 1.0
CG1 A:ILE33 4.8 27.2 1.0
C2 P:DG10 5.0 26.8 1.0

Chlorine binding site 3 out of 5 in 5j2g

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Chlorine binding site 3 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:29.8
occ:1.00
 O A:HOH704 3.0 36.4 1.0
ND2 A:ASN294 3.1 22.1 1.0
OG1 A:THR297 3.2 23.6 1.0
O A:HOH659 3.2 31.0 1.0
NH2 A:ARG299 3.7 40.5 1.0
CZ A:ARG299 3.7 39.5 1.0
NE A:ARG299 3.8 36.7 1.0
CB A:TYR296 3.9 21.5 1.0
CG A:ASN294 4.0 21.6 1.0
OD1 A:ASN294 4.0 20.5 1.0
CD2 A:TYR296 4.1 20.1 1.0
NH1 A:ARG299 4.3 41.9 1.0
CG A:TYR296 4.5 21.8 1.0
CB A:THR297 4.5 24.9 1.0
CD A:ARG299 4.6 32.3 1.0
O A:HOH613 4.6 23.2 1.0
N A:THR297 4.6 21.2 1.0
CG2 A:THR297 4.7 25.4 1.0

Chlorine binding site 4 out of 5 in 5j2g

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Chlorine binding site 4 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:46.0
occ:1.00
 N A:LEU82 3.1 28.9 1.0
NH2 A:ARG89 3.1 45.6 1.0
O A:HOH684 3.1 32.9 1.0
NH1 A:ARG89 3.2 44.4 1.0
CZ A:ARG89 3.5 44.0 1.0
CD1 A:LEU85 3.7 25.4 1.0
CA A:LYS81 3.7 33.9 1.0
CB A:LYS81 3.7 35.7 1.0
O A:LEU82 3.8 28.7 1.0
O A:HOH709 3.8 33.6 1.0
C A:LYS81 3.8 31.9 1.0
CB A:LEU85 3.9 25.9 1.0
CA A:LEU82 4.0 29.0 1.0
CB A:LEU82 4.0 28.2 1.0
C A:LEU82 4.3 28.2 1.0
CG A:LEU85 4.4 25.7 1.0
CG A:GLU86 4.7 43.4 1.0
CG A:LYS81 4.7 38.2 1.0
NE A:ARG89 4.8 43.1 1.0
N A:GLU86 4.8 32.3 1.0
OE1 A:GLU86 5.0 49.8 1.0

Chlorine binding site 5 out of 5 in 5j2g

Go back to Chlorine Binding Sites List in 5j2g
Chlorine binding site 5 out of 5 in the Ternary Complex Crystal Structure of Dna Polymerase Beta with G:G 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:G Mismatch at the Primer Terminus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:27.3
occ:1.00
 N A:HIS34 3.3 23.9 1.0
CB A:HIS34 3.4 25.5 1.0
CB A:ALA32 3.4 19.1 1.0
C A:ALA32 3.4 20.9 1.0
CA A:ALA32 3.5 21.8 1.0
N A:LYS35 3.5 21.8 1.0
O A:ALA32 3.7 20.7 1.0
CD2 A:HIS34 3.7 28.9 1.0
CA A:HIS34 3.7 25.3 1.0
N A:ILE33 3.9 21.7 1.0
CG A:HIS34 3.9 28.5 1.0
C A:HIS34 4.1 24.4 1.0
CG A:LYS35 4.1 23.2 1.0
O A:HOH587 4.2 24.1 1.0
C A:ILE33 4.3 25.1 1.0
CB A:LYS35 4.5 20.0 1.0
CA A:LYS35 4.6 21.3 1.0
CA A:ILE33 4.7 24.7 1.0
N A:ALA32 4.9 20.2 1.0
O6 D:DG1 4.9 25.8 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 09:41:46 2024

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