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Chlorine in PDB 6p1q: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp

Enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp

All present enzymatic activity of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp:
2.7.7.7;

Protein crystallography data

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp, PDB code: 6p1q was solved by L.C.Pedersen, A.M.Kaminski, 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) 25.07 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.768, 68.740, 110.479, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.6

Other elements in 6p1q:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp 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 Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp (pdb code 6p1q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp, PDB code: 6p1q:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6p1q

Go back to Chlorine Binding Sites List in 6p1q
Chlorine binding site 1 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:57.1
occ:0.81
 O A:HOH796 2.8 40.3 1.0
NH2 A:ARG393 3.2 33.4 1.0
NE A:ARG393 3.4 36.5 1.0
CD1 A:TRP412 3.8 28.5 1.0
CZ A:ARG393 3.8 29.2 1.0
CB A:TRP412 4.2 23.8 1.0
CG A:TRP412 4.3 28.1 1.0
O A:HOH825 4.3 54.1 1.0
O A:SER411 4.4 28.9 1.0
CD A:ARG393 4.6 38.0 1.0
NE1 A:TRP412 4.7 26.2 1.0
CG A:ARG393 4.9 34.1 1.0

Chlorine binding site 2 out of 3 in 6p1q

Go back to Chlorine Binding Sites List in 6p1q
Chlorine binding site 2 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:40.5
occ:0.88
 N A:GLY174 3.3 19.7 1.0
N A:ARG175 3.3 21.0 0.3
N A:ARG175 3.3 21.1 0.7
CB A:SER172 3.3 38.9 1.0
CA A:SER172 3.4 27.3 1.0
C A:SER172 3.4 24.0 1.0
CG A:ARG175 3.6 23.0 0.3
NH1 A:ARG175 3.7 36.9 0.7
CA A:GLY174 3.7 18.7 1.0
N A:GLU173 3.7 23.7 1.0
O A:SER172 3.8 21.2 1.0
CG A:ARG175 3.8 22.5 0.7
C A:GLY174 4.0 22.3 1.0
CB A:ARG175 4.2 21.2 0.7
CD A:ARG175 4.2 25.4 0.3
CD A:ARG175 4.2 25.8 0.7
CB A:ARG175 4.2 21.1 0.3
O6 D:DG1 4.2 22.6 1.0
C A:GLU173 4.3 18.9 1.0
O A:HOH785 4.3 47.1 1.0
OG A:SER172 4.3 45.3 1.0
CA A:ARG175 4.4 20.1 0.3
CA A:ARG175 4.4 20.3 0.7
C6 D:DG1 4.6 21.9 1.0
CA A:GLU173 4.6 26.0 1.0
CZ A:ARG175 4.7 33.9 0.7
C5 D:DG1 4.8 23.3 1.0
N A:SER172 4.9 25.6 1.0
N7 D:DG1 4.9 26.2 1.0
NE A:ARG175 4.9 29.6 0.7

Chlorine binding site 3 out of 3 in 6p1q

Go back to Chlorine Binding Sites List in 6p1q
Chlorine binding site 3 out of 3 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Dcmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:50.0
occ:1.00
 OG A:SER458 2.8 27.1 1.0
N A:SER458 3.2 17.0 1.0
C1' T:DA7 3.3 35.3 1.0
O4' T:DA7 3.3 33.5 1.0
CB A:SER458 3.5 23.8 1.0
CB A:ASN457 3.6 19.4 1.0
C4' T:DA7 3.7 36.4 1.0
C2' T:DA7 3.8 36.8 1.0
CA A:SER458 3.9 16.2 1.0
NH2 A:ARG387 3.9 33.8 1.0
NH2 A:ARG445 3.9 21.1 1.0
NH1 A:ARG445 4.0 20.8 1.0
C A:ASN457 4.2 16.6 1.0
CA A:ASN457 4.3 16.1 1.0
C3' T:DA7 4.3 37.7 1.0
CG A:ASN457 4.3 24.8 1.0
O2 T:DT6 4.4 27.1 1.0
CZ A:ARG445 4.4 21.9 1.0
O A:HOH808 4.6 36.9 1.0
N9 T:DA7 4.6 38.1 1.0
C A:SER458 4.7 20.6 1.0
O3' T:DA7 4.7 39.3 1.0
N A:HIS459 4.7 19.2 1.0
OD1 A:ASN457 4.8 20.5 1.0
ND2 A:ASN457 4.9 30.1 1.0
NE2 A:HIS459 4.9 43.0 1.0
CD2 A:HIS459 5.0 37.7 1.0
O3' T:DT6 5.0 34.0 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 12:58:52 2024

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