Chlorine in PDB 5vzg: Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp

All present enzymatic activity of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp:
2.7.7.7;

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vzg 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)	34.85 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.668, 68.555, 110.108, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 20.2

The structure of Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp (pdb code 5vzg). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp, PDB code: 5vzg:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:33.7 occ:0.84 O1 A:EDO707 3.1 42.1 1.0 N A:SER458 3.2 13.2 0.6 N A:SER458 3.2 13.4 0.4 OG A:SER458 3.2 9.7 0.6 O4' T:DA7 3.2 32.2 1.0 C4' T:DA7 3.4 32.4 1.0 OG A:SER458 3.5 19.0 0.4 CB A:SER458 3.5 15.2 0.6 CB A:SER458 3.6 15.0 0.4 CB A:ASN457 3.7 10.8 1.0 NH2 A:ARG445 3.8 15.6 1.0 C5' T:DA7 3.8 35.4 1.0 NH1 A:ARG445 3.9 15.3 1.0 O2 T:DT6 4.0 24.3 1.0 CA A:SER458 4.0 11.7 0.6 C1' T:DA7 4.0 36.4 1.0 CA A:SER458 4.0 12.1 0.4 CA A:ASN457 4.1 10.5 1.0 C A:ASN457 4.1 16.2 1.0 NH2 A:ARG387 4.2 44.6 1.0 CZ A:ARG445 4.2 16.9 1.0 C1 A:EDO707 4.4 33.6 1.0 C1' T:DT6 4.5 22.7 1.0 CG A:ASN457 4.6 15.8 1.0 O3' T:DT6 4.7 23.0 1.0 C3' T:DA7 4.8 38.9 1.0 O5' T:DA7 4.9 29.4 1.0 N9 T:DA7 4.9 34.8 1.0 C A:SER458 5.0 14.9 0.4 C A:SER458 5.0 15.3 0.6 O2 A:EDO707 5.0 34.6 1.0 C2 T:DT6 5.0 22.3 1.0

Chlorine binding site 2 out of 2 in the Pre-Catalytic Ternary Complex of Human Polymerase Mu (W434H) 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 (W434H) Mutant with Incoming Nonhydrolyzable Umpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl706 b:34.3 occ:0.88 O A:HOH986 2.8 29.7 1.0 NE2 A:HIS434 2.8 19.1 1.0 OG A:SER458 2.9 9.7 0.6 O A:HOH813 3.0 27.1 1.0 NH2 A:ARG387 3.2 44.6 1.0 CB A:SER458 3.5 15.2 0.6 CB A:SER458 3.6 15.0 0.4 CD2 A:HIS434 3.6 16.3 1.0 NE A:ARG387 3.7 31.1 1.0 CG1 A:VAL420 3.8 14.4 1.0 CZ A:ARG387 3.8 40.9 1.0 CE1 A:HIS434 3.9 23.7 1.0 O A:HOH872 4.2 19.9 1.0 OG A:SER458 4.3 19.0 0.4 O A:SER458 4.4 13.7 0.4 CB A:ALA430 4.4 10.8 1.0 CE1 A:HIS459 4.5 39.8 1.0 O A:SER458 4.5 13.4 0.6 O2 A:EDO707 4.7 34.6 1.0 CA A:SER458 4.8 11.7 0.6 ND1 A:HIS459 4.8 35.8 1.0 C A:SER458 4.8 14.9 0.4 CA A:SER458 4.8 12.1 0.4 C A:SER458 4.8 15.3 0.6 CG A:HIS434 4.8 17.9 1.0 CA A:ALA430 4.9 11.0 1.0 CD A:ARG387 4.9 22.7 1.0 ND1 A:HIS434 4.9 18.7 1.0 NH1 A:ARG387 5.0 39.1 1.0

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