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Chlorine in PDB 6p1n: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dampnpp

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

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 Dampnpp:
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 Dampnpp, PDB code: 6p1n 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) 26.66 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.926, 68.772, 110.609, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.7

Other elements in 6p1n:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dampnpp 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 Dampnpp (pdb code 6p1n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 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 Dampnpp, PDB code: 6p1n:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 6p1n

Go back to Chlorine Binding Sites List in 6p1n
Chlorine binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dampnpp


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

b:42.2
occ:1.00
 OG A:SER458 3.0 25.1 1.0
N A:SER458 3.2 20.9 1.0
O4' T:DA7 3.4 34.1 1.0
C1' T:DA7 3.5 35.0 1.0
CB A:SER458 3.5 24.1 1.0
CB A:ASN457 3.8 20.3 1.0
C4' T:DA7 3.9 31.4 1.0
NH2 A:ARG387 3.9 34.8 1.0
CA A:SER458 3.9 17.9 1.0
NH1 A:ARG445 4.0 32.4 1.0
NH2 A:ARG445 4.0 21.5 1.0
C2' T:DA7 4.1 36.2 1.0
O2 T:DT6 4.2 28.9 1.0
C A:ASN457 4.2 18.6 1.0
CA A:ASN457 4.3 18.6 1.0
CG A:ASN457 4.4 24.8 1.0
O A:HOH840 4.4 34.0 0.6
CZ A:ARG445 4.4 24.1 1.0
C3' T:DA7 4.6 36.7 1.0
N9 T:DA7 4.7 33.6 1.0
C A:SER458 4.8 19.4 1.0
ND2 A:ASN457 4.9 28.3 1.0
O3' T:DA7 4.9 31.6 1.0
N A:HIS459 4.9 20.0 1.0
O3' T:DT6 5.0 28.9 1.0
OD1 A:ASN457 5.0 22.9 1.0

Chlorine binding site 2 out of 2 in 6p1n

Go back to Chlorine Binding Sites List in 6p1n
Chlorine binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dampnpp


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

b:40.0
occ:0.67
 OG A:SER172 2.2 33.2 0.3
O2 A:EDO509 2.5 39.9 0.6
N A:ARG175 3.3 23.1 0.5
CB A:SER172 3.3 32.5 0.3
N A:ARG175 3.3 23.4 0.5
N A:GLY174 3.3 24.4 1.0
CA A:SER172 3.4 27.8 0.3
CB A:SER172 3.4 32.8 0.7
C A:SER172 3.4 24.8 0.7
CA A:SER172 3.4 27.3 0.7
C A:SER172 3.4 25.5 0.3
NH1 A:ARG175 3.6 35.7 0.5
CG A:ARG175 3.6 26.9 0.5
CA A:GLY174 3.7 25.0 1.0
O A:SER172 3.7 26.7 0.7
CG A:ARG175 3.8 25.4 0.5
O A:SER172 3.8 25.4 0.3
N A:GLU173 3.8 25.9 1.0
C2 A:EDO509 3.8 39.2 0.6
C A:GLY174 4.0 24.6 1.0
C1 A:EDO509 4.0 38.0 0.6
CD A:ARG175 4.1 27.8 0.5
CB A:ARG175 4.1 23.4 0.5
CB A:ARG175 4.1 25.2 0.5
CD A:ARG175 4.2 28.6 0.5
O6 D:DG1 4.2 26.8 1.0
CA A:ARG175 4.3 23.3 0.5
C A:GLU173 4.3 23.6 1.0
OG A:SER172 4.3 38.0 0.7
CA A:ARG175 4.3 23.2 0.5
C6 D:DG1 4.6 24.3 1.0
CZ A:ARG175 4.6 34.6 0.5
CA A:GLU173 4.7 27.2 1.0
C5 D:DG1 4.8 23.1 1.0
N A:SER172 4.8 28.2 0.3
NE A:ARG175 4.8 34.3 0.5
N A:SER172 4.8 28.0 0.7
N7 D:DG1 4.8 25.8 1.0
O1 A:EDO509 4.8 41.9 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 12:58:01 2024

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