Chlorine in PDB 5tws: Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp

The structure of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp, PDB code: 5tws 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)	27.48 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.935, 68.858, 110.319, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 20

The structure of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp also contains other interesting chemical elements:

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

The binding sites of Chlorine atom in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp (pdb code 5tws). 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 Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp, PDB code: 5tws:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:38.0 occ:1.00 OG A:SER458 3.0 16.6 1.0 N A:SER458 3.2 12.4 1.0 O4' T:DA7 3.3 25.1 1.0 C1' T:DA7 3.5 27.2 1.0 CB A:SER458 3.5 17.1 1.0 O1 A:EDO509 3.6 40.8 1.0 NH2 A:ARG445 3.7 12.3 1.0 CB A:ASN457 3.7 14.2 1.0 NH1 A:ARG445 3.8 15.2 1.0 C4' T:DA7 3.8 27.6 1.0 CA A:SER458 4.0 12.9 1.0 O2 T:DT6 4.0 15.6 1.0 CZ A:ARG445 4.1 14.8 1.0 NH2 A:ARG387 4.2 21.9 1.0 C2' T:DA7 4.2 29.2 1.0 C A:ASN457 4.2 12.4 1.0 CA A:ASN457 4.2 13.1 1.0 C1 A:EDO509 4.4 37.6 1.0 CG A:ASN457 4.5 16.8 1.0 C3' T:DA7 4.6 29.5 1.0 N9 T:DA7 4.7 24.1 1.0 C1' T:DT6 4.8 16.6 1.0 C A:SER458 4.9 12.8 1.0 O2 A:EDO509 4.9 35.6 1.0 O3' T:DT6 4.9 18.7 1.0 O3' T:DA7 5.0 28.3 1.0 C5' T:DA7 5.0 28.7 1.0

Chlorine binding site 2 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl505 b:33.8 occ:0.60 N A:PHE469 2.9 19.7 1.0 CA A:THR468 3.6 27.2 1.0 C A:THR468 3.7 23.2 1.0 CB A:THR468 3.9 28.8 1.0 CA A:PHE469 3.9 20.9 1.0 O A:PHE469 3.9 25.8 1.0 CB A:PHE469 3.9 21.1 1.0 CD2 A:PHE469 4.1 28.1 1.0 CG2 A:THR468 4.3 29.7 1.0 C A:PHE469 4.4 24.4 1.0 CG A:PHE469 4.5 25.5 1.0 O A:LYS467 4.7 33.6 1.0 N A:THR468 4.8 31.1 1.0 NE2 A:GLN471 4.8 49.2 1.0 O A:THR468 4.9 21.8 1.0

Chlorine binding site 3 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl506 b:33.9 occ:0.62 N A:ARG233 3.1 25.8 1.0 O A:HOH785 3.2 29.9 1.0 CB A:ARG233 3.3 27.1 1.0 N A:GLU232 3.5 27.3 1.0 CB A:SER231 3.7 28.3 1.0 CA A:ARG233 3.8 26.6 1.0 OH A:TYR255 4.0 32.5 1.0 C A:GLU232 4.1 26.7 1.0 CA A:GLU232 4.1 27.5 1.0 C A:SER231 4.1 25.1 1.0 CB A:GLU232 4.2 30.3 1.0 CA A:SER231 4.2 26.0 1.0 OG A:SER231 4.4 30.4 1.0 CG A:ARG233 4.6 28.8 1.0

Chlorine binding site 4 out of 4 in the Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Post-Catalytic Complex of Human Polymerase Mu (H329A) with Newly Incorporated Utp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl507 b:59.0 occ:1.00 O A:HOH808 3.0 33.9 1.0 NH2 A:ARG393 3.2 24.8 1.0 NE A:ARG393 3.6 28.4 1.0 CZ A:ARG393 3.9 25.2 1.0 CD1 A:TRP412 4.0 23.7 1.0 CB A:TRP412 4.4 21.8 1.0 CG A:TRP412 4.4 24.5 1.0 O A:SER411 4.5 29.4 1.0 CD A:ARG393 4.8 29.4 1.0 NE1 A:TRP412 4.9 21.4 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