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Chlorine in PDB 6p1w: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp, PDB code: 6p1w was solved by A.M.Kaminski, L.C.Pedersen, K.Bebenek, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.802, 68.692, 110.065, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 6p1w:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp (pdb code 6p1w). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp, PDB code: 6p1w:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6p1w

Go back to Chlorine Binding Sites List in 6p1w
Chlorine binding site 1 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:40.7
occ:1.00
 CB A:SER172 3.3 31.1 1.0
N A:ARG175 3.3 18.0 0.4
N A:GLY174 3.4 20.9 1.0
CA A:SER172 3.4 26.3 1.0
N A:ARG175 3.4 17.9 0.6
C A:SER172 3.4 23.2 1.0
CG A:ARG175 3.6 22.0 0.4
NH1 A:ARG175 3.6 38.9 0.6
N A:GLU173 3.8 20.5 1.0
CA A:GLY174 3.8 21.5 1.0
O A:SER172 3.8 24.0 1.0
CG A:ARG175 3.8 20.9 0.6
C A:GLY174 4.0 18.3 1.0
CB A:ARG175 4.1 19.9 0.4
CB A:ARG175 4.1 20.1 0.6
CD A:ARG175 4.1 25.2 0.6
CD A:ARG175 4.2 25.0 0.4
O6 D:DG1 4.2 20.7 1.0
OG A:SER172 4.3 35.8 1.0
CA A:ARG175 4.3 18.8 0.4
C A:GLU173 4.3 20.4 1.0
CA A:ARG175 4.4 18.8 0.6
C6 D:DG1 4.6 19.8 1.0
CA A:GLU173 4.7 22.8 1.0
CZ A:ARG175 4.7 38.0 0.6
N A:SER172 4.8 24.7 1.0
N7 D:DG1 4.8 22.7 1.0
C5 D:DG1 4.8 20.1 1.0
NE A:ARG175 4.9 29.6 0.6

Chlorine binding site 2 out of 4 in 6p1w

Go back to Chlorine Binding Sites List in 6p1w
Chlorine binding site 2 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:35.5
occ:0.91
 OG A:SER458 3.0 20.2 1.0
N A:SER458 3.2 14.4 1.0
CB A:SER458 3.3 19.1 1.0
O4' T:DA7 3.5 23.6 1.0
C1' T:DA7 3.5 22.4 1.0
NH1 A:ARG445 3.6 15.1 1.0
NH2 A:ARG445 3.7 16.8 1.0
O A:HOH831 3.8 26.5 1.0
NH2 A:ARG387 3.9 23.0 1.0
CA A:SER458 3.9 13.3 1.0
CB A:ASN457 3.9 16.1 1.0
O2 T:DT6 4.0 17.7 1.0
CZ A:ARG445 4.1 15.9 1.0
C4' T:DA7 4.1 26.1 1.0
C2' T:DA7 4.2 23.8 1.0
C A:ASN457 4.3 14.3 1.0
CA A:ASN457 4.4 15.5 1.0
O P:HOH114 4.6 18.6 0.6
N9 T:DA7 4.7 20.1 1.0
CG A:ASN457 4.7 17.8 1.0
C3' T:DA7 4.8 23.9 1.0
C A:SER458 4.8 15.2 1.0
CZ2 A:TRP434 4.9 19.6 0.5
CH2 A:TRP434 5.0 25.0 0.5
C1' T:DT6 5.0 17.6 1.0

Chlorine binding site 3 out of 4 in 6p1w

Go back to Chlorine Binding Sites List in 6p1w
Chlorine binding site 3 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:25.6
occ:0.66
 N A:GLU475 3.2 14.5 1.0
O A:HOH755 3.2 34.9 0.9
CA A:SER474 3.6 15.8 1.0
O A:HOH828 3.7 18.0 1.0
CG A:GLU475 3.7 14.2 1.0
O A:HOH607 3.7 38.5 0.9
CD2 A:LEU431 3.8 16.7 1.0
C A:SER474 3.9 14.2 1.0
CB A:SER474 4.1 16.5 1.0
CB A:GLU475 4.1 14.1 1.0
O A:HOH873 4.1 40.9 1.0
CA A:GLU475 4.3 12.5 1.0
CD A:GLU475 4.5 15.2 1.0
CA A:PRO428 4.6 14.9 1.0
OE1 A:GLU475 4.6 16.1 1.0
CB A:PRO428 4.6 17.0 1.0
CE2 A:PHE427 4.7 19.3 1.0
O A:ALA473 4.8 19.0 1.0
N A:SER474 4.8 17.6 1.0
CG A:PRO428 4.9 18.8 1.0
CD2 A:PHE427 4.9 15.7 1.0
CG A:LEU431 5.0 14.7 1.0

Chlorine binding site 4 out of 4 in 6p1w

Go back to Chlorine Binding Sites List in 6p1w
Chlorine binding site 4 out of 4 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl508

b:35.1
occ:0.69
 O A:HOH836 2.7 28.6 1.0
O A:HOH862 2.8 36.9 1.0
NH1 A:ARG393 3.0 21.6 0.7
NH2 A:ARG393 3.0 24.1 0.3
NE A:ARG393 3.3 22.2 0.3
CZ A:ARG393 3.6 22.8 0.3
CD A:ARG393 3.6 23.7 0.7
CD1 A:TRP412 3.7 23.7 1.0
CZ A:ARG393 4.1 22.0 0.7
CG A:TRP412 4.2 23.2 1.0
NE A:ARG393 4.3 22.9 0.7
CB A:TRP412 4.4 22.9 1.0
NE1 A:TRP412 4.4 22.5 1.0
CD A:ARG393 4.5 22.1 0.3
CG A:ARG393 4.6 21.3 0.7
O A:SER411 4.7 24.4 1.0
CG A:ARG393 4.8 21.7 0.3
O A:HOH645 4.9 46.0 1.0
O A:HOH642 4.9 33.8 1.0
NH1 A:ARG393 4.9 23.1 0.3

Reference:

A.M.Kaminski, K.K.Chiruvella, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Unexpected Behavior of Dna Polymerase Mu Opposite Template 8-Oxo-7,8-Dihydro-2'-Guanosine. Nucleic Acids Res. V. 47 9410 2019.
ISSN: ESSN 1362-4962
PubMed: 31435651
DOI: 10.1093/NAR/GKZ680
Page generated: Sat Jul 12 18:08:52 2025

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