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Chlorine in PDB 5twr: Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp

Enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

Protein crystallography data

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5twr was solved by A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.71 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.703, 68.606, 109.767, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.4

Other elements in 5twr:

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp 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 Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5twr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5twr:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5twr

Go back to Chlorine Binding Sites List in 5twr
Chlorine binding site 1 out of 3 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp


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 Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:21.9
occ:0.27
 OG A:SER172 1.5 35.2 0.7
O A:HOH997 1.9 41.1 0.7
CB A:SER172 2.6 31.4 0.7
CB A:SER172 2.7 31.7 0.3
CA A:SER172 2.8 26.9 0.7
CA A:SER172 2.9 27.4 0.3
C A:SER172 2.9 24.3 0.7
C A:SER172 3.0 24.2 0.3
O A:HOH1020 3.0 46.3 1.0
N A:ARG175 3.2 18.2 0.6
N A:ARG175 3.2 18.2 0.4
O A:SER172 3.2 23.2 0.7
O A:SER172 3.3 23.5 0.3
N A:GLY174 3.4 18.6 1.0
OG A:SER172 3.4 32.0 0.3
CG A:ARG175 3.5 21.2 0.6
N A:GLU173 3.5 20.6 1.0
CG A:ARG175 3.6 20.7 0.4
CB A:ARG175 3.8 20.1 0.6
CB A:ARG175 3.8 19.9 0.4
CA A:GLY174 3.8 18.3 1.0
CD A:ARG175 4.0 23.5 0.6
C A:GLY174 4.0 18.7 1.0
CA A:ARG175 4.1 18.0 0.6
CA A:ARG175 4.1 18.1 0.4
CD A:ARG175 4.2 22.9 0.4
C A:GLU173 4.2 18.0 1.0
N A:SER172 4.3 25.9 0.7
N A:SER172 4.3 26.6 0.3
CA A:GLU173 4.5 20.8 1.0
O6 D:DG1 4.7 23.4 1.0
O A:HOH994 4.7 41.9 1.0
NE A:ARG175 4.8 22.6 0.4
O A:GLY171 4.9 29.4 1.0
C6 D:DG1 5.0 21.8 1.0

Chlorine binding site 2 out of 3 in 5twr

Go back to Chlorine Binding Sites List in 5twr
Chlorine binding site 2 out of 3 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl707

b:75.9
occ:1.00
 OG A:SER458 2.9 18.0 1.0
N A:SER458 3.2 13.1 1.0
C4' T:DA7 3.3 24.0 1.0
O4' T:DA7 3.3 24.2 1.0
CB A:SER458 3.4 17.0 1.0
CB A:ASN457 3.8 15.0 1.0
C1' T:DA7 3.8 25.5 1.0
NH2 A:ARG387 3.9 23.1 1.0
CA A:SER458 3.9 14.9 1.0
C5' T:DA7 3.9 30.6 1.0
NH2 A:ARG445 4.0 16.1 1.0
O A:HOH1019 4.0 34.7 1.0
O2 T:DT6 4.1 17.2 1.0
NH1 A:ARG445 4.1 13.7 1.0
C A:ASN457 4.2 15.8 1.0
CA A:ASN457 4.3 13.3 1.0
CZ A:ARG445 4.4 16.1 1.0
C3' T:DA7 4.5 26.9 1.0
CG A:ASN457 4.6 18.8 1.0
C2' T:DA7 4.7 28.6 1.0
C A:SER458 4.8 16.3 1.0
O3' T:DA7 4.8 26.8 1.0
N9 T:DA7 4.9 24.7 1.0
N A:HIS459 4.9 14.9 1.0
C1' T:DT6 4.9 19.2 1.0

Chlorine binding site 3 out of 3 in 5twr

Go back to Chlorine Binding Sites List in 5twr
Chlorine binding site 3 out of 3 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pre-Catalytic Ternary Complex of Human Polymerase Mu (H329A) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl710

b:70.0
occ:1.00
 O A:HOH935 2.5 42.6 1.0
O A:HOH1063 2.5 40.2 1.0
N A:SER293 3.0 24.9 1.0
N A:ARG292 3.2 20.5 1.0
OG A:SER293 3.4 27.2 1.0
CB A:ARG292 3.5 27.0 1.0
CB A:SER293 3.6 27.6 1.0
CA A:ARG292 3.7 24.4 1.0
O A:HOH840 3.7 44.1 1.0
O A:LEU326 3.7 18.6 1.0
C A:ARG292 3.8 23.7 1.0
CB A:LEU291 3.9 19.6 1.0
CA A:SER293 3.9 23.9 1.0
C A:LEU291 4.0 21.2 1.0
CA A:LEU291 4.3 20.3 1.0
CG A:ARG292 4.7 32.7 1.0
C A:LEU326 4.8 21.0 1.0
CG A:LEU291 4.9 20.0 1.0
O A:LEU291 4.9 20.9 1.0
O A:ARG292 4.9 25.1 1.0

Reference:

A.F.Moon, J.M.Pryor, D.A.Ramsden, T.A.Kunkel, K.Bebenek, L.C.Pedersen. Structural Accommodation of Ribonucleotide Incorporation By the Dna Repair Enzyme Polymerase Mu. Nucleic Acids Res. V. 45 9138 2017.
ISSN: ESSN 1362-4962
PubMed: 28911097
DOI: 10.1093/NAR/GKX527
Page generated: Fri Jul 26 17:47:39 2024

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