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Chlorine in PDB 6p1r: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp

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

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp:
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 Incoming Ampnpp, PDB code: 6p1r 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) 31.37 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.889, 68.770, 110.489, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 19.4

Other elements in 6p1r:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Ampnpp 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 Template 8OG and Bound Incoming Ampnpp (pdb code 6p1r). 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 Incoming Ampnpp, PDB code: 6p1r:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6p1r

Go back to Chlorine Binding Sites List in 6p1r
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 Incoming Ampnpp


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

b:44.3
occ:1.00
 OG A:SER458 3.1 23.9 1.0
N A:SER458 3.2 19.2 1.0
O4' T:DA7 3.4 38.8 1.0
CB A:SER458 3.5 20.6 1.0
C1' T:DA7 3.6 38.3 1.0
CB A:ASN457 3.7 18.7 1.0
CA A:SER458 3.9 14.7 1.0
C4' T:DA7 3.9 38.5 1.0
NH2 A:ARG387 3.9 32.8 1.0
NH1 A:ARG445 4.0 28.5 1.0
NH2 A:ARG445 4.0 20.9 1.0
C A:ASN457 4.2 18.4 1.0
O2 T:DT6 4.2 36.1 1.0
CA A:ASN457 4.2 17.6 1.0
C2' T:DA7 4.3 38.3 1.0
O A:HOH803 4.3 35.7 1.0
CZ A:ARG445 4.4 23.7 1.0
CG A:ASN457 4.4 22.3 1.0
C3' T:DA7 4.7 39.8 1.0
N9 T:DA7 4.8 37.4 1.0
C A:SER458 4.8 19.5 1.0
O3' T:DT6 4.8 29.7 1.0
OD1 A:ASN457 4.9 21.5 1.0
N A:HIS459 4.9 19.2 1.0
ND2 A:ASN457 4.9 25.5 1.0
C1' T:DT6 4.9 35.1 1.0
O3' T:DA7 5.0 38.4 1.0

Chlorine binding site 2 out of 3 in 6p1r

Go back to Chlorine Binding Sites List in 6p1r
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 Incoming Ampnpp


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

b:47.9
occ:0.86
 OG A:SER425 3.0 23.2 1.0
NE2 A:GLN426 3.0 27.6 1.0
CG A:GLN426 3.4 23.7 1.0
CD A:GLN426 3.7 26.3 1.0
CB A:SER425 4.1 22.7 1.0
OE2 A:GLU340 4.2 26.4 1.0
O A:HOH648 4.5 28.1 1.0
CG A:PRO423 4.7 22.6 1.0
CB A:GLN426 4.8 21.4 1.0
OE1 A:GLN426 4.9 25.7 1.0
N A:GLN426 4.9 20.0 1.0

Chlorine binding site 3 out of 3 in 6p1r

Go back to Chlorine Binding Sites List in 6p1r
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 Incoming Ampnpp


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

b:25.3
occ:0.54
 O A:HOH797 3.0 33.4 1.0
O A:HOH866 3.0 38.2 1.0
N A:GLU475 3.0 16.0 1.0
CA A:SER474 3.5 18.3 1.0
O A:HOH798 3.5 18.2 1.0
CG A:GLU475 3.6 15.0 1.0
C A:SER474 3.7 14.3 1.0
CD2 A:LEU431 3.8 16.1 1.0
CB A:SER474 4.0 18.9 1.0
CB A:GLU475 4.0 15.1 1.0
CA A:GLU475 4.1 14.8 1.0
O A:HOH610 4.2 32.0 1.0
CD A:GLU475 4.4 15.3 1.0
OE1 A:GLU475 4.5 16.4 1.0
CB A:PRO428 4.7 18.9 1.0
CA A:PRO428 4.7 17.3 1.0
N A:SER474 4.7 19.9 1.0
O A:ALA473 4.7 21.5 1.0
CE2 A:PHE427 4.8 22.5 1.0
O A:SER474 4.9 17.6 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 12:58:53 2024

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