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Chlorine in PDB 4r65: Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta

Enzymatic activity of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta

All present enzymatic activity of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r65 was solved by V.K.Batra, W.A.Beard, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.74 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.810, 79.940, 55.480, 90.00, 107.30, 90.00
R / Rfree (%) 18.7 / 22.2

Other elements in 4r65:

The structure of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta 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 R258A Mutant of Dna Polymerase Beta (pdb code 4r65). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta, PDB code: 4r65:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4r65

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Chlorine binding site 1 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


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 R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:39.2
occ:1.00
 N A:LYS331 3.1 22.9 1.0
CG A:LYS331 3.4 30.7 1.0
CD A:PRO330 3.4 22.6 1.0
CB A:LYS331 3.5 27.1 1.0
N A:PRO330 3.6 24.0 1.0
CB A:GLU329 3.7 29.5 1.0
CB A:PRO330 3.8 18.5 1.0
CG A:PRO330 3.9 22.4 1.0
CA A:LYS331 3.9 25.0 1.0
CD A:LYS331 3.9 37.1 1.0
C A:PRO330 4.0 20.7 1.0
CA A:PRO330 4.1 17.8 1.0
C A:GLU329 4.1 23.6 1.0
OE1 A:GLU329 4.2 37.4 1.0
CA A:GLU329 4.4 26.1 1.0
CE A:LYS331 4.5 39.5 1.0
CG A:GLU329 4.7 32.1 1.0
O A:ARG182 4.7 16.3 1.0
O A:GLU329 4.9 24.6 1.0
CD A:GLU329 4.9 37.6 1.0

Chlorine binding site 2 out of 6 in 4r65

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Chlorine binding site 2 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


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 R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:33.3
occ:1.00
 N A:HIS34 3.2 22.0 1.0
CB A:HIS34 3.5 25.0 1.0
CB A:ALA32 3.5 23.1 1.0
C A:ALA32 3.5 23.3 1.0
CA A:ALA32 3.6 25.8 1.0
N A:LYS35 3.6 20.9 1.0
CA A:HIS34 3.7 25.2 1.0
N A:ILE33 3.8 23.9 1.0
CD2 A:HIS34 3.8 30.8 1.0
O D:HOH109 3.8 35.5 1.0
O A:ALA32 3.9 26.3 1.0
CG A:HIS34 4.0 27.6 1.0
C A:HIS34 4.1 21.2 1.0
CG A:LYS35 4.2 21.4 1.0
C A:ILE33 4.3 23.6 1.0
CB A:LYS35 4.6 21.4 1.0
CA A:ILE33 4.6 26.0 1.0
CA A:LYS35 4.7 21.6 1.0
O6 D:DG1 4.8 27.1 1.0

Chlorine binding site 3 out of 6 in 4r65

Go back to Chlorine Binding Sites List in 4r65
Chlorine binding site 3 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


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 R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:33.0
occ:1.00
 NE2 A:GLN159 2.7 19.9 1.0
O A:HOH554 3.0 21.7 1.0
O A:HOH793 3.0 29.4 1.0
N A:VAL177 3.0 15.6 1.0
CA A:THR176 3.8 17.4 1.0
CB A:VAL177 3.8 14.9 1.0
CG2 A:VAL177 3.8 15.4 1.0
CD A:GLN159 3.9 20.5 1.0
C A:THR176 3.9 17.9 1.0
CA A:VAL177 3.9 15.4 1.0
O A:VAL177 4.2 17.5 1.0
O A:ALA175 4.3 16.5 1.0
CG2 A:THR176 4.3 20.3 1.0
CG A:GLN159 4.3 14.8 1.0
CD2 A:LEU163 4.3 21.6 1.0
C A:VAL177 4.5 17.4 1.0
O A:HOH740 4.6 34.3 1.0
O A:HOH782 4.7 33.9 1.0
CB A:THR176 4.7 19.0 1.0
CD1 A:LEU163 4.7 17.6 1.0
N A:THR176 4.8 17.2 1.0
OE1 A:GLN159 4.9 21.8 1.0
CE2 A:PHE181 4.9 19.8 1.0
O A:HOH602 4.9 29.6 1.0
C A:ALA175 4.9 17.8 1.0

Chlorine binding site 4 out of 6 in 4r65

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Chlorine binding site 4 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


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 R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:29.9
occ:1.00
 OG1 A:THR297 3.1 20.9 1.0
ND2 A:ASN294 3.2 20.0 1.0
O A:HOH703 3.2 38.1 1.0
O A:HOH748 3.4 35.0 1.0
CG2 A:THR297 3.7 21.6 1.0
CZ A:ARG299 3.9 39.7 1.0
CB A:TYR296 3.9 23.3 1.0
OD1 A:ASN294 3.9 20.6 1.0
CB A:THR297 4.0 22.6 1.0
CG A:ASN294 4.0 21.3 1.0
CD2 A:TYR296 4.1 22.6 1.0
NH2 A:ARG299 4.1 35.4 1.0
NH1 A:ARG299 4.1 39.0 1.0
NE A:ARG299 4.2 32.3 1.0
O A:HOH806 4.4 36.5 1.0
CG A:TYR296 4.4 22.3 1.0
N A:THR297 4.6 20.4 1.0
CD A:ARG299 4.7 28.0 1.0
O A:HOH522 4.7 22.2 1.0
O T:HOH136 4.9 33.0 1.0
CA A:THR297 4.9 22.2 1.0

Chlorine binding site 5 out of 6 in 4r65

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Chlorine binding site 5 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


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 R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:40.0
occ:1.00
 NH2 A:ARG89 2.9 40.5 1.0
N A:LEU82 3.3 19.4 1.0
O A:HOH795 3.5 33.2 1.0
NH1 A:ARG89 3.5 34.5 1.0
CZ A:ARG89 3.6 37.9 1.0
CB A:LEU85 3.8 19.6 1.0
CD1 A:LEU85 3.9 23.4 1.0
CA A:LYS81 3.9 23.9 1.0
CB A:LYS81 4.0 32.4 1.0
CB A:LEU82 4.0 24.7 1.0
C A:LYS81 4.0 23.6 1.0
O A:LEU82 4.0 25.1 1.0
O A:HOH800 4.1 35.0 1.0
CA A:LEU82 4.1 25.5 1.0
CG A:LEU85 4.4 19.1 1.0
C A:LEU82 4.5 25.4 1.0
NE A:ARG89 4.9 32.1 1.0
CE1 A:PHE76 4.9 26.6 1.0
CD1 A:PHE76 4.9 23.1 1.0
O A:GLY80 5.0 27.5 1.0

Chlorine binding site 6 out of 6 in 4r65

Go back to Chlorine Binding Sites List in 4r65
Chlorine binding site 6 out of 6 in the Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ternary Complex Crystal Structure of R258A Mutant of Dna Polymerase Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl411

b:50.5
occ:1.00
 O A:HOH581 3.0 25.1 1.0
NZ A:LYS84 3.3 35.3 1.0
CZ A:PHE25 4.0 22.9 1.0
CD1 A:ILE88 4.1 19.2 1.0
CG1 A:ILE88 4.1 22.7 1.0
CE1 A:PHE25 4.1 23.6 1.0
O A:HOH531 4.2 21.1 1.0
CE A:LYS84 4.2 28.4 1.0
CG A:LYS84 4.2 29.3 1.0
O A:HOH773 4.4 38.9 1.0
CD A:LYS84 4.8 25.0 1.0
O A:HOH732 4.8 36.4 1.0
CE2 A:PHE25 4.8 20.6 1.0
O A:LYS84 4.9 22.7 1.0

Reference:

W.A.Beard, D.D.Shock, V.K.Batra, R.Prasad, S.H.Wilson. Substrate-Induced Dna Polymerase Beta Activation. J.Biol.Chem. 2014.
ISSN: ESSN 1083-351X
PubMed: 25261471
DOI: 10.1074/JBC.M114.607432
Page generated: Fri Jul 26 01:06:52 2024

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