Chlorine in PDB 6p1o: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp

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

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 Damp:
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 Damp, PDB code: 6p1o 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) 25.15 / 1.65
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.947, 68.713, 110.724, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 18.7

Other elements in 6p1o:

The structure of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Damp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Manganese (Mn) 1 atom
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 Damp (pdb code 6p1o). 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 Damp, PDB code: 6p1o:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 6p1o

Go back to Chlorine Binding Sites List in 6p1o
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 Damp


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 Damp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:39.3
occ:1.00
 OG A:SER458 2.9 24.9 1.0
N A:SER458 3.1 20.6 1.0
CB A:SER458 3.4 23.5 1.0
C1' T:DA7 3.5 26.8 1.0
O4' T:DA7 3.5 28.5 1.0
CB A:ASN457 3.7 19.4 1.0
C4' T:DA7 3.8 27.1 1.0
CA A:SER458 3.9 16.6 1.0
C2' T:DA7 3.9 26.6 1.0
NH2 A:ARG445 3.9 21.9 1.0
NH2 A:ARG387 3.9 25.6 1.0
NH1 A:ARG445 4.0 23.9 1.0
C A:ASN457 4.2 19.6 1.0
CA A:ASN457 4.2 17.5 1.0
CZ A:ARG445 4.3 22.6 1.0
O2 T:DT6 4.3 23.0 1.0
O2 A:EDO508 4.4 38.8 1.0
C3' T:DA7 4.4 28.9 1.0
CG A:ASN457 4.4 24.7 1.0
C1 A:EDO508 4.6 32.8 1.0
C A:SER458 4.7 19.5 1.0
N9 T:DA7 4.7 25.1 1.0
O1 A:EDO508 4.8 50.7 1.0
O3' T:DA7 4.8 28.4 1.0
N A:HIS459 4.9 19.2 1.0
OD1 A:ASN457 4.9 21.7 1.0

Chlorine binding site 2 out of 3 in 6p1o

Go back to Chlorine Binding Sites List in 6p1o
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 Damp


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

b:47.8
occ:1.00
 O A:HOH811 3.1 38.3 0.5
N A:ARG175 3.3 20.1 0.4
N A:ARG175 3.3 20.5 0.6
N A:GLY174 3.4 24.5 1.0
CB A:SER172 3.4 33.5 1.0
CA A:SER172 3.4 23.8 1.0
C A:SER172 3.4 23.4 1.0
NH1 A:ARG175 3.5 37.8 0.6
CG A:ARG175 3.7 23.1 0.4
CA A:GLY174 3.7 22.5 1.0
CG A:ARG175 3.8 21.6 0.6
O A:SER172 3.8 24.4 1.0
N A:GLU173 3.8 24.9 1.0
CD A:ARG175 4.0 28.3 0.6
C A:GLY174 4.0 21.4 1.0
CB A:ARG175 4.1 22.2 0.6
CB A:ARG175 4.1 21.1 0.4
CD A:ARG175 4.2 24.6 0.4
O6 D:DG1 4.2 25.3 1.0
OG A:SER172 4.3 43.2 1.0
CA A:ARG175 4.3 20.9 0.4
CA A:ARG175 4.3 20.9 0.6
C A:GLU173 4.4 23.0 1.0
O A:HOH811 4.4 31.7 0.5
CZ A:ARG175 4.5 32.5 0.6
C6 D:DG1 4.6 22.9 1.0
CA A:GLU173 4.7 27.4 1.0
NE A:ARG175 4.7 30.6 0.6
C5 D:DG1 4.8 21.6 1.0
N7 D:DG1 4.8 24.5 1.0
N A:SER172 4.9 25.6 1.0

Chlorine binding site 3 out of 3 in 6p1o

Go back to Chlorine Binding Sites List in 6p1o
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 Damp


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

b:62.1
occ:0.98
 O A:HOH820 2.9 38.2 1.0
NH2 A:ARG393 3.1 32.9 1.0
NE A:ARG393 3.4 36.6 1.0
CZ A:ARG393 3.8 26.3 1.0
CD1 A:TRP412 3.8 28.6 1.0
O A:HOH848 4.2 49.1 0.6
CG A:TRP412 4.3 28.3 1.0
CB A:TRP412 4.3 27.9 1.0
O A:SER411 4.5 33.3 1.0
CD A:ARG393 4.6 37.8 1.0
NE1 A:TRP412 4.6 29.3 1.0
CG A:ARG393 4.9 35.5 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: Sat Dec 12 13:28:21 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy