Chlorine in PDB 6p1u: Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp

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

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 Cmp:
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 Cmp, PDB code: 6p1u 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) 34.98 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.864, 68.825, 110.594, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 19.3

Other elements in 6p1u:

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

Manganese (Mn) 1 atom
Sodium (Na) 3 atoms

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 Cmp (pdb code 6p1u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 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 Cmp, PDB code: 6p1u:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6p1u

Go back to Chlorine Binding Sites List in 6p1u
Chlorine binding site 1 out of 4 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


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

b:35.3
occ:0.84
 OG A:SER458 3.1 25.4 1.0
N A:SER458 3.2 20.5 1.0
C1' T:DA7 3.4 27.4 1.0
O2 P:EDO101 3.5 46.9 1.0
CB A:SER458 3.5 22.7 1.0
NH2 A:ARG445 3.5 20.9 1.0
NH1 A:ARG445 3.6 22.2 1.0
O4' T:DA7 3.6 27.5 1.0
CB A:ASN457 3.7 21.5 1.0
C2' T:DA7 3.8 26.7 1.0
NH2 A:ARG387 3.8 26.2 1.0
O1 P:EDO101 4.0 32.9 1.0
CA A:SER458 4.0 17.8 1.0
CZ A:ARG445 4.0 21.3 1.0
C4' T:DA7 4.0 29.5 1.0
O2 T:DT6 4.1 22.4 1.0
C A:ASN457 4.2 19.7 1.0
CA A:ASN457 4.2 19.2 1.0
CG A:ASN457 4.5 26.9 1.0
C3' T:DA7 4.6 30.5 1.0
N9 T:DA7 4.6 25.3 1.0
C2 P:EDO101 4.7 38.6 1.0
C A:SER458 4.9 18.9 1.0
C1 P:EDO101 4.9 37.1 1.0

Chlorine binding site 2 out of 4 in 6p1u

Go back to Chlorine Binding Sites List in 6p1u
Chlorine binding site 2 out of 4 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


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

b:34.2
occ:0.40
 OG A:SER172 2.1 40.4 0.6
O A:HOH737 2.6 43.6 1.0
CB A:SER172 3.3 35.5 0.6
N A:GLY174 3.3 25.9 1.0
N A:ARG175 3.3 23.1 0.5
N A:ARG175 3.4 23.0 0.5
CB A:SER172 3.4 35.2 0.4
CA A:SER172 3.4 31.4 0.6
CA A:SER172 3.4 31.6 0.4
C A:SER172 3.5 29.0 0.6
NH1 A:ARG175 3.5 50.9 0.5
C A:SER172 3.5 28.9 0.4
CA A:GLY174 3.7 26.2 1.0
CG A:ARG175 3.8 26.4 0.5
N A:GLU173 3.8 26.8 1.0
O A:SER172 3.9 28.7 0.6
CG A:ARG175 3.9 25.1 0.5
O A:SER172 3.9 28.6 0.4
C A:GLY174 4.0 24.6 1.0
OG A:SER172 4.0 37.9 0.4
O6 D:DG1 4.1 28.2 1.0
CD A:ARG175 4.2 29.8 0.5
CB A:ARG175 4.2 24.7 0.5
CB A:ARG175 4.3 25.1 0.5
O A:HOH768 4.3 43.6 0.8
C A:GLU173 4.3 25.4 1.0
CD A:ARG175 4.3 29.4 0.5
CA A:ARG175 4.4 23.2 0.5
CA A:ARG175 4.4 23.1 0.5
O D:HOH110 4.4 32.9 0.5
C6 D:DG1 4.5 28.2 1.0
CZ A:ARG175 4.6 49.0 0.5
CA A:GLU173 4.7 28.8 1.0
C5 D:DG1 4.8 27.4 1.0
N7 D:DG1 4.8 29.6 1.0
N A:SER172 4.9 32.5 0.6
N A:SER172 4.9 32.3 0.4
NE A:ARG175 4.9 35.7 0.5

Chlorine binding site 3 out of 4 in 6p1u

Go back to Chlorine Binding Sites List in 6p1u
Chlorine binding site 3 out of 4 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


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

b:26.6
occ:0.56
 N A:GLU475 3.0 17.3 1.0
O A:HOH752 3.2 25.1 0.6
O A:HOH787 3.5 20.4 1.0
CA A:SER474 3.5 19.2 1.0
CG A:GLU475 3.6 18.1 1.0
C A:SER474 3.7 17.5 1.0
CD2 A:LEU431 3.8 18.0 1.0
CB A:GLU475 4.0 17.1 1.0
CB A:SER474 4.0 21.1 1.0
CA A:GLU475 4.1 15.5 1.0
O A:HOH607 4.1 35.9 1.0
CD A:GLU475 4.4 17.7 1.0
OE1 A:GLU475 4.5 20.4 1.0
N A:SER474 4.7 21.1 1.0
CB A:PRO428 4.8 20.0 1.0
CA A:PRO428 4.8 18.3 1.0
O A:ALA473 4.8 24.2 1.0
CE2 A:PHE427 4.8 23.6 1.0
O A:SER474 4.9 18.7 1.0

Chlorine binding site 4 out of 4 in 6p1u

Go back to Chlorine Binding Sites List in 6p1u
Chlorine binding site 4 out of 4 in the Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Post-Catalytic Nicked Complex of Human Dna Polymerase Mu with 1-Nt Gapped Substrate Containing Template 8OG and Newly Incorporated Cmp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:61.2
occ:0.82
 O A:HOH783 2.9 40.3 1.0
NH2 A:ARG393 3.2 37.5 1.0
NE A:ARG393 3.6 36.4 1.0
CD1 A:TRP412 3.8 33.1 1.0
CZ A:ARG393 3.9 33.0 1.0
CG A:TRP412 4.3 32.1 1.0
CB A:TRP412 4.3 31.9 1.0
O A:SER411 4.3 35.3 1.0
NE1 A:TRP412 4.7 33.2 1.0
CD A:ARG393 4.8 36.7 1.0
C A:SER411 4.9 35.8 1.0
CG A:PRO395 5.0 56.7 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 13:28:27 2020

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