Magnesium in PDB 4u7c: Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna

All present enzymatic activity of Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna:
2.7.7.7;

The structure of Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna, PDB code: 4u7c was solved by V.K.Jha, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.11 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.640, 130.170, 166.300, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.2

The binding sites of Magnesium atom in the Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna (pdb code 4u7c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna, PDB code: 4u7c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:31.1 occ:1.00 O A:MET108 2.1 34.6 1.0 OD1 A:ASP107 2.1 41.3 1.0 O2G A:0KX602 2.2 39.9 1.0 O2A A:0KX602 2.2 44.9 1.0 OD1 A:ASP198 2.3 37.8 1.0 O1B A:0KX602 2.3 39.8 1.0 C A:MET108 3.2 32.2 1.0 PB A:0KX602 3.3 45.9 1.0 PA A:0KX602 3.3 44.0 1.0 CG A:ASP107 3.3 38.2 1.0 CG A:ASP198 3.5 37.8 1.0 PG A:0KX602 3.5 36.0 1.0 N3A A:0KX602 3.7 43.5 1.0 O3B A:0KX602 3.7 36.4 1.0 N A:MET108 3.8 29.6 1.0 O5' A:0KX602 3.9 45.7 1.0 CA A:MET108 4.0 29.6 1.0 OD2 A:ASP198 4.0 49.1 1.0 C A:ASP107 4.0 32.5 1.0 OD2 A:ASP107 4.0 48.5 1.0 N A:ASP109 4.3 30.0 1.0 NZ A:LYS328 4.3 35.2 1.0 O A:ASP107 4.4 39.3 1.0 O3G A:0KX602 4.4 41.5 1.0 O1G A:0KX602 4.4 45.4 1.0 CB A:ASP107 4.4 32.0 1.0 CB A:MET108 4.4 27.3 1.0 N A:ALA110 4.5 28.9 1.0 CA A:ASP109 4.5 31.2 1.0 CA A:ASP107 4.5 29.0 1.0 O1A A:0KX602 4.6 46.4 1.0 O2B A:0KX602 4.6 33.4 1.0 CB A:ASP198 4.6 36.7 1.0 N A:PHE111 4.6 29.5 1.0 O A:ASP198 4.7 39.5 1.0 C A:ASP109 4.7 33.2 1.0 CB A:PHE111 4.8 31.0 1.0 CE A:LYS328 5.0 49.9 1.0

Magnesium binding site 2 out of 2 in the Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Dna Polymerase Kappa in Complex with Benzopyrene Adducted Dna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:51.3 occ:1.00 OD1 B:ASP107 2.0 51.0 1.0 O2G B:0KX603 2.1 52.4 1.0 O2B B:0KX603 2.3 54.7 1.0 O1A B:0KX603 2.3 56.2 1.0 OD2 B:ASP198 2.7 52.6 1.0 O B:MET108 2.7 51.8 1.0 CG B:ASP107 3.1 54.3 1.0 PB B:0KX603 3.2 58.3 1.0 PA B:0KX603 3.2 61.1 1.0 PG B:0KX603 3.3 56.1 1.0 O3B B:0KX603 3.4 45.7 1.0 N3A B:0KX603 3.5 61.2 1.0 O5' B:0KX603 3.6 56.2 1.0 CG B:ASP198 3.6 54.3 1.0 OD2 B:ASP107 3.7 59.4 1.0 NZ B:LYS328 3.8 51.6 1.0 C B:MET108 3.9 44.7 1.0 OD1 B:ASP198 3.9 59.7 1.0 O3G B:0KX603 4.2 56.0 1.0 N B:MET108 4.2 43.3 1.0 CB B:ASP107 4.3 54.1 1.0 C B:ASP107 4.3 46.6 1.0 O1G B:0KX603 4.3 65.0 1.0 O1B B:0KX603 4.5 53.8 1.0 O2A B:0KX603 4.5 62.9 1.0 CA B:MET108 4.6 40.0 1.0 CA B:ASP107 4.6 42.0 1.0 CE B:LYS328 4.7 65.3 1.0 O B:ASP107 4.7 49.7 1.0 O B:ASP198 4.8 50.9 1.0 CB B:ASP198 4.8 50.3 1.0 N B:ASP109 4.9 44.3 1.0 N B:ALA110 5.0 49.7 1.0 C5' B:0KX603 5.0 54.1 1.0 OE2 B:GLU199 5.0 61.7 1.0

V.Jha, C.Bian, G.Xing, H.Ling. Structure and Mechanism of Error-Free Replication Past the Major Benzo[A]Pyrene Adduct By Human Dna Polymerase Kappa. Nucleic Acids Res. V. 44 4957 2016.
ISSN: ESSN 1362-4962
PubMed: 27034468
DOI: 10.1093/NAR/GKW204