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Chlorine in PDB 6p1v: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp

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

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 Dcmpnpp:
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 Dcmpnpp, PDB code: 6p1v 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) 31.30 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.902, 68.606, 110.125, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.4

Other elements in 6p1v:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp 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 Dcmpnpp (pdb code 6p1v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 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 Dcmpnpp, PDB code: 6p1v:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6p1v

Go back to Chlorine Binding Sites List in 6p1v
Chlorine binding site 1 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp


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 Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:42.8
occ:1.00
 OG A:SER458 2.8 20.2 1.0
N A:SER458 3.2 17.7 1.0
CB A:SER458 3.3 19.9 1.0
NH2 A:ARG445 3.4 18.5 1.0
C1' T:DA7 3.5 23.0 1.0
NH1 A:ARG445 3.6 16.4 1.0
O1 A:EDO509 3.6 30.4 1.0
NH2 A:ARG387 3.7 21.0 1.0
CB A:ASN457 3.8 20.4 1.0
O4' T:DA7 3.8 24.9 1.0
CA A:SER458 3.8 18.6 1.0
CZ A:ARG445 3.9 17.1 1.0
C2' T:DA7 4.0 23.4 1.0
O2 T:DT6 4.0 21.2 1.0
C A:ASN457 4.2 18.9 1.0
CA A:ASN457 4.3 19.7 1.0
C4' T:DA7 4.3 24.6 1.0
O2 A:EDO509 4.5 28.1 1.0
CG A:ASN457 4.6 23.4 1.0
N9 T:DA7 4.6 23.1 1.0
C1 A:EDO509 4.7 29.2 1.0
C3' T:DA7 4.8 24.7 1.0
C A:SER458 4.8 18.7 1.0
CZ A:ARG387 4.8 20.5 1.0
N A:HIS459 5.0 18.3 1.0

Chlorine binding site 2 out of 3 in 6p1v

Go back to Chlorine Binding Sites List in 6p1v
Chlorine binding site 2 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp


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 Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:46.2
occ:0.74
 N A:PHE469 3.0 29.0 1.0
O A:HOH609 3.5 49.4 1.0
CA A:THR468 3.5 32.6 1.0
C A:THR468 3.7 30.6 1.0
CB A:THR468 3.8 33.0 1.0
CA A:PHE469 3.9 28.3 1.0
CB A:PHE469 3.9 28.4 1.0
O A:PHE469 4.0 27.9 1.0
CD2 A:PHE469 4.1 31.5 1.0
CG2 A:THR468 4.4 34.0 1.0
C A:PHE469 4.5 27.0 1.0
CG A:PHE469 4.5 30.4 1.0
O A:LYS467 4.6 37.4 0.6
O A:LYS467 4.6 37.4 0.4
N A:THR468 4.8 35.4 1.0
O A:THR468 5.0 29.3 1.0

Chlorine binding site 3 out of 3 in 6p1v

Go back to Chlorine Binding Sites List in 6p1v
Chlorine binding site 3 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Undamaged Template Dg and Bound Incoming Dcmpnpp


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 Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:48.2
occ:0.76
 CB A:SER172 3.2 32.3 1.0
CA A:SER172 3.4 28.3 1.0
O A:HOH837 3.4 49.7 1.0
N A:GLY174 3.5 21.9 1.0
N A:ARG175 3.5 22.9 0.4
NH1 A:ARG175 3.5 37.1 0.6
N A:ARG175 3.5 22.8 0.6
C A:SER172 3.5 25.7 1.0
CG A:ARG175 3.6 28.4 0.4
CG A:ARG175 3.8 28.3 0.6
CA A:GLY174 3.8 21.8 1.0
N A:GLU173 3.9 24.9 1.0
O A:SER172 4.0 23.6 1.0
OG A:SER172 4.1 36.1 1.0
CD A:ARG175 4.1 30.9 0.4
C A:GLY174 4.2 22.3 1.0
O6 D:DG1 4.2 24.8 1.0
CD A:ARG175 4.3 31.0 0.6
CB A:ARG175 4.3 26.0 0.4
CB A:ARG175 4.3 26.1 0.6
C A:GLU173 4.5 22.6 1.0
CA A:ARG175 4.5 23.9 0.4
CA A:ARG175 4.5 23.9 0.6
C6 D:DG1 4.6 24.1 1.0
CZ A:ARG175 4.6 37.2 0.6
N A:SER172 4.8 27.8 1.0
N7 D:DG1 4.8 25.1 1.0
CA A:GLU173 4.8 26.0 1.0
C5 D:DG1 4.8 24.8 1.0
O A:HOH679 4.9 49.5 1.0
NE A:ARG175 4.9 33.6 0.6

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: Mon Jul 29 13:00:41 2024

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