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Chlorine in PDB 6p1t: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Cmpcpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Cmpcpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound 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 Template 8OG and Bound Cmpcpp, PDB code: 6p1t 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) 43.04 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.805, 68.715, 110.434, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.1

Other elements in 6p1t:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Cmpcpp also contains other interesting chemical elements:

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

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 Template 8OG and Bound Cmpcpp (pdb code 6p1t). 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 Template 8OG and Bound Cmpcpp, PDB code: 6p1t:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6p1t

Go back to Chlorine Binding Sites List in 6p1t
Chlorine binding site 1 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound 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 Template 8OG and Bound Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:32.2
occ:0.80
 OG A:SER458 3.0 21.3 1.0
N A:SER458 3.2 15.7 1.0
CB A:SER458 3.4 19.7 1.0
C1' T:DA7 3.4 23.4 1.0
O4' T:DA7 3.6 26.5 1.0
NH1 A:ARG445 3.6 16.8 1.0
NH2 A:ARG445 3.6 19.7 1.0
CB A:ASN457 3.8 18.8 1.0
NH2 A:ARG387 3.9 26.4 1.0
CA A:SER458 3.9 14.3 1.0
O2 T:DT6 4.0 20.6 1.0
O2 A:EDO509 4.0 32.0 0.9
C2' T:DA7 4.0 24.9 1.0
CZ A:ARG445 4.0 16.8 1.0
C4' T:DA7 4.1 28.0 1.0
C A:ASN457 4.3 15.6 1.0
CA A:ASN457 4.3 15.9 1.0
O1 A:EDO509 4.6 38.5 0.9
N9 T:DA7 4.6 23.2 1.0
CG A:ASN457 4.6 21.3 1.0
C2 A:EDO509 4.6 36.3 0.9
C3' T:DA7 4.7 27.6 1.0
C A:SER458 4.9 16.0 1.0

Chlorine binding site 2 out of 3 in 6p1t

Go back to Chlorine Binding Sites List in 6p1t
Chlorine binding site 2 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound 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 Template 8OG and Bound Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:39.4
occ:0.67
 OG A:SER172 2.1 28.0 0.3
O A:HOH776 2.9 45.4 1.0
CB A:SER172 3.3 27.2 0.3
N A:ARG175 3.3 18.0 0.4
N A:ARG175 3.3 17.3 0.6
CB A:SER172 3.3 27.3 0.7
N A:GLY174 3.4 19.7 1.0
CA A:SER172 3.4 24.9 0.3
CA A:SER172 3.4 24.8 0.7
C A:SER172 3.4 22.3 0.7
C A:SER172 3.5 22.5 0.3
CG A:ARG175 3.6 23.8 0.4
NH1 A:ARG175 3.7 38.5 0.6
CG A:ARG175 3.7 23.2 0.6
CA A:GLY174 3.8 19.6 1.0
O A:SER172 3.8 21.5 0.7
O A:SER172 3.8 21.6 0.3
N A:GLU173 3.8 20.9 1.0
C A:GLY174 4.0 19.3 1.0
CD A:ARG175 4.1 27.0 0.6
CB A:ARG175 4.1 21.1 0.6
CB A:ARG175 4.1 21.1 0.4
O6 D:DG1 4.1 21.6 1.0
CD A:ARG175 4.2 26.8 0.4
CA A:ARG175 4.3 17.2 0.4
OG A:SER172 4.3 30.4 0.7
CA A:ARG175 4.3 17.2 0.6
C A:GLU173 4.4 19.3 1.0
O A:HOH757 4.4 44.9 1.0
C6 D:DG1 4.5 21.1 1.0
CZ A:ARG175 4.7 39.7 0.6
CA A:GLU173 4.7 23.3 1.0
C5 D:DG1 4.8 20.6 1.0
N7 D:DG1 4.8 20.9 1.0
N A:SER172 4.9 25.0 0.3
NE A:ARG175 4.9 31.0 0.6
N A:SER172 4.9 24.6 0.7

Chlorine binding site 3 out of 3 in 6p1t

Go back to Chlorine Binding Sites List in 6p1t
Chlorine binding site 3 out of 3 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound 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 Template 8OG and Bound Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:22.4
occ:0.55
 O A:HOH810 3.0 34.0 1.0
N A:GLU475 3.1 13.8 1.0
CA A:SER474 3.6 16.5 1.0
O A:HOH812 3.6 16.7 1.0
CG A:GLU475 3.6 12.6 1.0
CD2 A:LEU431 3.8 15.7 1.0
C A:SER474 3.8 13.8 1.0
CB A:SER474 4.0 16.2 1.0
CB A:GLU475 4.0 13.3 1.0
CA A:GLU475 4.2 12.1 1.0
O A:HOH610 4.3 32.3 1.0
O A:HOH856 4.4 42.7 1.0
CD A:GLU475 4.4 13.7 1.0
OE1 A:GLU475 4.6 15.3 1.0
CA A:PRO428 4.6 14.5 1.0
CB A:PRO428 4.7 17.0 1.0
CE2 A:PHE427 4.8 19.1 1.0
O A:ALA473 4.8 18.5 1.0
N A:SER474 4.8 16.4 1.0

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 12:59:34 2024

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