Atomistry » Chlorine » PDB 3bpr-3c4c » 3c2k
Atomistry »
  Chlorine »
    PDB 3bpr-3c4c »
      3c2k »

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: Sat Jul 20 16:46:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy