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Chlorine in PDB 4yd1: Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

Enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp

All present enzymatic activity of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1 was solved by A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.97 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.259, 69.042, 116.988, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19

Other elements in 4yd1:

The structure of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp (pdb code 4yd1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp, PDB code: 4yd1:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 4yd1

Go back to Chlorine Binding Sites List in 4yd1
Chlorine binding site 1 out of 4 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl608

b:30.8
occ:1.00
 O A:HOH984 3.2 41.9 1.0
N A:GLY174 3.3 19.3 1.0
NH1 A:ARG175 3.3 37.0 1.0
N A:ARG175 3.3 17.2 1.0
CA A:SER172 3.4 22.6 1.0
C A:SER172 3.4 20.5 1.0
CB A:SER172 3.5 25.2 1.0
CA A:GLY174 3.7 17.8 1.0
O D:HOH107 3.7 46.0 1.0
N A:GLU173 3.7 19.5 1.0
CG A:ARG175 3.9 18.5 1.0
O A:SER172 3.9 19.0 1.0
C A:GLY174 4.0 17.9 1.0
O6 D:DG1 4.1 20.7 1.0
O A:HOH940 4.2 36.3 1.0
CB A:ARG175 4.2 16.9 1.0
OG A:SER172 4.3 27.7 1.0
CD A:ARG175 4.3 22.8 1.0
C A:GLU173 4.3 17.3 1.0
CA A:ARG175 4.4 16.5 1.0
C6 D:DG1 4.4 21.4 1.0
CZ A:ARG175 4.5 36.0 1.0
CA A:GLU173 4.6 20.1 1.0
N7 D:DG1 4.7 20.8 1.0
C5 D:DG1 4.7 19.9 1.0
N A:SER172 4.8 21.8 1.0
NE A:ARG175 4.9 32.8 1.0

Chlorine binding site 2 out of 4 in 4yd1

Go back to Chlorine Binding Sites List in 4yd1
Chlorine binding site 2 out of 4 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl609

b:26.4
occ:1.00
 O A:HOH963 2.4 45.1 1.0
O A:HOH926 3.0 25.1 1.0
O A:HOH1051 3.1 30.5 1.0
N A:GLU475 3.2 10.0 1.0
CA A:SER474 3.5 13.7 1.0
O A:HOH953 3.7 12.1 1.0
C A:SER474 3.8 12.5 1.0
CD2 A:LEU431 3.8 11.7 1.0
CG A:GLU475 3.8 11.9 1.0
CB A:SER474 4.1 14.0 1.0
CB A:GLU475 4.2 9.7 1.0
CA A:GLU475 4.2 10.1 1.0
CE1 A:PHE427 4.4 15.9 1.0
O A:HOH719 4.4 24.5 1.0
CD A:GLU475 4.5 12.4 1.0
CB A:PRO428 4.6 10.6 1.0
OE1 A:GLU475 4.6 13.8 1.0
CA A:PRO428 4.7 10.4 1.0
N A:SER474 4.7 13.7 1.0
O A:ALA473 4.7 15.4 1.0
CD1 A:PHE427 4.8 12.4 1.0
CG A:PRO428 4.8 12.9 1.0
O A:SER474 4.9 11.7 1.0

Chlorine binding site 3 out of 4 in 4yd1

Go back to Chlorine Binding Sites List in 4yd1
Chlorine binding site 3 out of 4 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl610

b:20.0
occ:0.73
 O A:HOH1074 3.1 48.0 1.0
N A:LEU326 3.2 14.6 1.0
O A:HOH1067 3.6 37.9 1.0
N A:GLN327 3.8 15.6 1.0
CA A:LYS325 3.8 12.6 1.0
CB A:LYS325 3.9 12.5 1.0
C A:LYS325 3.9 16.1 1.0
CD2 A:LEU149 4.0 19.6 1.0
CA A:LEU326 4.1 17.1 1.0
CB A:LEU326 4.1 22.6 1.0
O A:GLN327 4.2 20.1 1.0
CG A:LYS325 4.2 14.7 1.0
CE A:LYS325 4.3 23.5 1.0
CG A:GLN327 4.3 30.6 1.0
C A:LEU326 4.4 17.9 1.0
CD1 A:LEU149 4.5 15.6 1.0
CG A:LEU149 4.6 15.4 1.0
CG A:LEU326 4.7 26.0 1.0
CA A:GLN327 4.7 16.8 1.0
CD A:LYS325 4.8 20.4 1.0
C A:GLN327 4.9 17.5 1.0
CB A:GLN327 5.0 21.4 1.0

Chlorine binding site 4 out of 4 in 4yd1

Go back to Chlorine Binding Sites List in 4yd1
Chlorine binding site 4 out of 4 in the Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ternary Complex of Human Dna Polymerase Mu with 2-Nt Gapped Dna Substrate and An Incoming Nonhydrolyzable Dumpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl611

b:22.0
occ:1.00
 O A:HOH759 2.9 22.7 1.0
NE1 A:TRP434 3.1 11.7 1.0
NH1 A:ARG387 3.3 19.0 1.0
CD A:ARG387 3.7 22.9 1.0
CD2 A:PHE385 3.7 16.7 1.0
CE2 A:TRP434 3.9 11.9 1.0
CZ2 A:TRP434 4.0 12.8 1.0
CG2 A:VAL420 4.0 11.1 1.0
CD1 A:TRP434 4.2 11.4 1.0
CZ A:ARG387 4.2 22.2 1.0
O T:HOH245 4.3 43.7 1.0
CB A:PHE385 4.3 13.1 1.0
CG A:ARG387 4.4 23.2 1.0
NE A:ARG387 4.4 22.2 1.0
NE2 A:HIS459 4.4 24.5 1.0
CG A:PHE385 4.4 16.6 1.0
CB A:SER458 4.5 21.3 1.0
CE2 A:PHE385 4.5 18.1 1.0
O T:HOH204 4.7 45.7 1.0
CE1 A:HIS459 4.8 24.5 1.0
OG A:SER458 4.8 28.1 1.0

Reference:

A.F.Moon, R.A.Gosavi, T.A.Kunkel, L.C.Pedersen, K.Bebenek. Creative Template-Dependent Synthesis By Human Polymerase Mu. Proc.Natl.Acad.Sci.Usa V. 112 E4530 2015.
ISSN: ESSN 1091-6490
PubMed: 26240373
DOI: 10.1073/PNAS.1505798112
Page generated: Fri Jul 11 23:18:48 2025

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