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Chlorine in PDB 3c2k: Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site

Enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site

All present enzymatic activity of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k was solved by V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.39 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.790, 80.680, 55.060, 90.00, 108.38, 90.00
R / Rfree (%) 21 / 27.8

Other elements in 3c2k:

The structure of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site also contains other interesting chemical elements:

Manganese (Mn) 5 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site (pdb code 3c2k). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site, PDB code: 3c2k:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 3c2k

Go back to Chlorine Binding Sites List in 3c2k
Chlorine binding site 1 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl347

b:40.6
occ:1.00
 ND2 A:ASN294 3.2 24.7 1.0
OG1 A:THR297 3.6 27.2 1.0
CZ A:ARG299 3.9 37.0 1.0
NH2 A:ARG299 4.1 37.5 1.0
CG A:ASN294 4.1 23.2 1.0
NH1 A:ARG299 4.1 38.2 1.0
NE A:ARG299 4.2 37.6 1.0
CD2 A:TYR296 4.2 24.4 1.0
CB A:TYR296 4.2 26.7 1.0
OD1 A:ASN294 4.2 22.8 1.0
CG2 A:THR297 4.4 29.1 1.0
CB A:THR297 4.6 28.7 1.0
CG A:TYR296 4.7 25.6 1.0
CD A:ARG299 4.7 35.0 1.0
O A:HOH423 4.7 24.9 1.0
N A:THR297 4.9 29.1 1.0

Chlorine binding site 2 out of 4 in 3c2k

Go back to Chlorine Binding Sites List in 3c2k
Chlorine binding site 2 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl348

b:44.9
occ:1.00
 N A:HIS34 3.4 30.2 1.0
CB A:ALA32 3.4 28.1 1.0
C A:ALA32 3.4 30.4 1.0
CB A:HIS34 3.5 31.9 1.0
CA A:ALA32 3.5 31.0 1.0
N A:LYS35 3.6 27.4 1.0
O A:ALA32 3.7 30.9 1.0
CA A:HIS34 3.9 30.2 1.0
N A:ILE33 3.9 30.8 1.0
CD2 A:HIS34 3.9 35.5 1.0
CG A:LYS35 3.9 27.0 1.0
CG A:HIS34 4.0 34.5 1.0
C A:HIS34 4.2 29.4 1.0
C A:ILE33 4.4 30.7 1.0
CB A:LYS35 4.5 25.4 1.0
CA A:LYS35 4.6 25.3 1.0
CA A:ILE33 4.7 31.0 1.0
O A:HOH401 4.7 37.7 1.0
CD A:LYS35 4.8 26.8 1.0
O D:HOH175 4.9 37.7 1.0
N A:ALA32 4.9 28.9 1.0

Chlorine binding site 3 out of 4 in 3c2k

Go back to Chlorine Binding Sites List in 3c2k
Chlorine binding site 3 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl349

b:43.8
occ:1.00
 NH2 A:ARG89 3.2 42.4 1.0
NH1 A:ARG89 3.3 40.9 1.0
N A:LEU82 3.4 35.9 1.0
CZ A:ARG89 3.7 42.1 1.0
CB A:LEU85 4.0 39.7 1.0
O A:LEU82 4.0 35.5 1.0
CA A:LYS81 4.1 37.9 1.0
CD1 A:LEU85 4.1 38.7 1.0
CB A:LEU82 4.2 36.1 1.0
C A:LYS81 4.2 36.9 1.0
CA A:LEU82 4.3 36.0 1.0
OE2 A:GLU86 4.3 60.3 1.0
CB A:LYS81 4.4 41.2 1.0
C A:LEU82 4.6 36.0 1.0
CG A:LEU85 4.7 40.0 1.0
CG A:GLU86 4.7 53.4 1.0
N A:GLU86 4.9 44.7 1.0
CG A:LYS81 4.9 45.7 1.0
CD A:GLU86 5.0 58.3 1.0

Chlorine binding site 4 out of 4 in 3c2k

Go back to Chlorine Binding Sites List in 3c2k
Chlorine binding site 4 out of 4 in the Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta with A Gapped Dna Substrate and Dumpnpp with Manganese in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl350

b:72.2
occ:1.00
 O A:HOH421 3.1 22.0 1.0
CA A:GLN264 3.3 29.7 1.0
N A:CYS267 3.3 28.1 1.0
C A:GLN264 3.4 29.1 1.0
O A:GLN264 3.5 29.8 1.0
CB A:CYS267 3.7 26.8 1.0
N A:TYR266 3.7 30.2 1.0
CG1 A:VAL313 3.8 39.9 1.0
SG A:CYS267 3.8 27.9 1.0
CB A:VAL313 3.8 39.2 1.0
O A:ASP263 3.9 28.7 1.0
CB A:TYR266 3.9 34.9 1.0
CB A:GLN264 4.0 29.3 1.0
N A:TYR265 4.1 28.9 1.0
O A:TYR296 4.1 28.2 1.0
CA A:CYS267 4.1 25.9 1.0
CA A:TYR266 4.1 31.9 1.0
C A:TYR266 4.1 29.9 1.0
N A:GLN264 4.3 29.3 1.0
C A:ASP263 4.5 29.8 1.0
CG2 A:VAL313 4.5 39.5 1.0
C A:TYR265 4.6 29.6 1.0
CG A:GLN264 4.7 29.9 1.0
CD2 A:TYR266 4.7 41.8 1.0
CG A:TYR266 4.9 38.8 1.0
CA A:TYR265 4.9 29.0 1.0
O A:VAL313 4.9 41.6 1.0

Reference:

V.K.Batra, W.A.Beard, D.D.Shock, L.C.Pedersen, S.H.Wilson. Structures of Dna Polymerase Beta with Active-Site Mismatches Suggest A Transient Abasic Site Intermediate During Misincorporation. Mol.Cell V. 30 315 2008.
ISSN: ISSN 1097-2765
PubMed: 18471977
DOI: 10.1016/J.MOLCEL.2008.02.025
Page generated: Fri Jul 11 03:33:52 2025

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