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Chlorine in PDB 3v7j: Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex

Enzymatic activity of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex

All present enzymatic activity of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex, PDB code: 3v7j was solved by S.Rangarajan, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.02 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.779, 77.114, 116.653, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.3

Other elements in 3v7j:

The structure of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex (pdb code 3v7j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex, PDB code: 3v7j:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3v7j

Go back to Chlorine Binding Sites List in 3v7j
Chlorine binding site 1 out of 4 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl344

b:63.2
occ:1.00
 NH1 A:ARG333 2.6 25.7 1.0
O A:LEU270 2.8 21.2 1.0
O A:GLY274 3.2 27.6 1.0
CD A:ARG333 3.3 28.8 1.0
CD1 A:LEU270 3.4 14.6 1.0
CB A:THR273 3.4 14.0 1.0
C A:LEU270 3.6 21.1 1.0
CZ A:ARG333 3.6 27.4 1.0
CA A:LEU270 3.7 21.1 1.0
CG2 A:THR273 3.8 15.4 1.0
N A:GLY274 3.8 24.3 1.0
CG A:LEU270 3.9 13.5 1.0
NE A:ARG333 3.9 28.8 1.0
OE2 A:GLU316 4.0 25.0 1.0
C A:THR273 4.1 23.9 1.0
C A:GLY274 4.1 27.0 1.0
CE2 A:PHE278 4.1 33.1 1.0
CA A:THR273 4.1 22.7 1.0
CD2 A:PHE278 4.2 33.2 1.0
CB A:LEU270 4.3 12.4 1.0
N A:THR273 4.4 21.8 1.0
CA A:GLY274 4.4 25.6 1.0
OG1 A:THR273 4.4 13.2 1.0
ND2 A:ASN279 4.5 19.3 1.0
O A:VAL269 4.5 10.9 1.0
CG A:ARG333 4.6 30.6 1.0
O A:THR273 4.8 25.1 1.0
O A:HOH382 4.8 12.7 1.0
N A:TYR271 4.8 26.5 1.0
NH2 A:ARG333 4.8 27.8 1.0
CB A:ARG333 4.9 31.2 1.0
N A:LEU270 4.9 20.5 1.0

Chlorine binding site 2 out of 4 in 3v7j

Go back to Chlorine Binding Sites List in 3v7j
Chlorine binding site 2 out of 4 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl345

b:55.6
occ:1.00
 OG A:SER188 3.0 23.6 1.0
O A:ALA185 3.2 25.0 1.0
CA A:ARG152 3.4 39.1 1.0
CD1 A:PHE181 3.4 24.8 1.0
C A:SER187 3.6 27.1 1.0
CG A:MET155 3.6 21.8 1.0
CB A:ARG152 3.7 32.8 1.0
O A:SER187 3.7 26.9 1.0
NH1 A:ARG152 3.8 29.6 1.0
CB A:SER188 3.8 23.0 1.0
CB A:PHE181 3.9 22.6 1.0
N A:ARG152 3.9 39.6 1.0
CA A:SER187 3.9 29.4 1.0
C A:ALA185 3.9 25.7 1.0
CA A:PHE181 4.0 23.7 1.0
N A:SER188 4.0 33.4 1.0
N A:SER187 4.0 30.9 1.0
CB A:MET155 4.1 22.4 1.0
CG A:ARG152 4.1 32.4 1.0
C A:GLU186 4.1 41.2 1.0
CG A:PHE181 4.1 23.1 1.0
O A:GLU186 4.2 41.7 1.0
CB A:ALA185 4.4 23.0 1.0
CA A:SER188 4.4 31.6 1.0
O A:ILE150 4.4 30.6 1.0
CE1 A:PHE181 4.4 25.4 1.0
C A:PRO151 4.6 35.0 1.0
CA A:ALA185 4.6 24.6 1.0
C A:ARG152 4.7 39.7 1.0
CE A:MET155 4.7 19.4 1.0
N A:GLU186 4.7 41.4 1.0
CD A:ARG152 4.7 33.8 1.0
CA A:GLU186 4.8 42.8 1.0
N A:PHE181 4.8 23.1 1.0
O A:ARG152 4.9 39.0 1.0
O A:PRO151 4.9 34.2 1.0
SD A:MET155 4.9 19.6 1.0
CZ A:ARG152 4.9 31.1 1.0
N A:ALA185 5.0 23.9 1.0

Chlorine binding site 3 out of 4 in 3v7j

Go back to Chlorine Binding Sites List in 3v7j
Chlorine binding site 3 out of 4 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl346

b:39.9
occ:1.00
 O A:GLU117 3.2 26.4 1.0
O A:HOH561 3.2 23.1 1.0
O A:HOH535 3.9 23.1 1.0
C A:GLU117 4.4 25.8 1.0
CA A:GLY118 5.0 15.4 1.0

Chlorine binding site 4 out of 4 in 3v7j

Go back to Chlorine Binding Sites List in 3v7j
Chlorine binding site 4 out of 4 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl347

b:46.8
occ:1.00
 O T:HOH73 3.1 8.2 1.0
O A:LEU132 3.4 8.5 1.0
O A:HOH410 3.6 4.8 1.0
C A:LEU132 3.8 8.3 1.0
CA A:ASN133 4.0 8.0 1.0
N A:ASN133 4.1 8.1 1.0
CB A:ASN133 4.4 7.9 1.0
O A:ASP130 4.6 9.8 1.0
OP1 T:DA10 4.7 45.0 1.0
O A:LYS131 4.8 16.1 1.0
N A:LEU132 4.8 8.8 1.0
CA A:LEU132 4.8 8.4 1.0
C A:LYS131 4.9 15.9 1.0
O T:HOH72 5.0 3.5 1.0

Reference:

S.Rangarajan, C.L.Gridley, S.Firbank, S.Dalal, J.B.Sweasy, J.Jaeger. Crystallographic Studies of K72E Mutant Dna Polymerase Explain Loss of Lyase Function and Reveal Changes in the Overall Conformational State of the Polymerase Domain To Be Published.
Page generated: Fri Jul 11 11:35:51 2025

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