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Chlorine in PDB 6p1p: Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dcmpnpp

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

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 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 Template 8OG and Bound Incoming Dcmpnpp, PDB code: 6p1p 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) 25.08 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.940, 68.608, 110.282, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.4

Other elements in 6p1p:

The structure of Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG 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 Template 8OG and Bound Incoming Dcmpnpp (pdb code 6p1p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Bound Incoming Dcmpnpp, PDB code: 6p1p:

Chlorine binding site 1 out of 1 in 6p1p

Go back to Chlorine Binding Sites List in 6p1p
Chlorine binding site 1 out of 1 in the Pre-Catalytic Ternary Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG 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 Template 8OG and Bound Incoming Dcmpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:34.6
occ:0.92
 OG A:SER458 3.0 21.2 1.0
N A:SER458 3.2 18.2 1.0
C1' T:DA7 3.4 21.8 1.0
CB A:SER458 3.4 20.1 1.0
NH1 A:ARG445 3.6 18.0 1.0
NH2 A:ARG445 3.6 18.4 1.0
O4' T:DA7 3.7 23.1 1.0
NH2 A:ARG387 3.8 23.2 1.0
O2 A:EDO506 3.8 31.8 1.0
CB A:ASN457 3.8 20.4 1.0
C2' T:DA7 3.9 21.5 1.0
CA A:SER458 3.9 17.7 1.0
O2 T:DT6 4.0 19.1 1.0
CZ A:ARG445 4.0 17.5 1.0
C4' T:DA7 4.1 23.1 1.0
C A:ASN457 4.2 18.1 1.0
CA A:ASN457 4.3 18.3 1.0
CG A:ASN457 4.5 22.2 1.0
O1 A:EDO506 4.6 29.8 1.0
N9 T:DA7 4.6 21.3 1.0
C3' T:DA7 4.6 23.1 1.0
C A:SER458 4.8 17.9 1.0
CZ A:ARG387 4.9 22.1 1.0
ND2 A:ASN457 5.0 26.3 1.0
C2 A:EDO506 5.0 31.0 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 12:58:40 2024

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