Magnesium in PDB 5w2a: Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp

All present enzymatic activity of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp, PDB code: 5w2a 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)	47.25 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.891, 129.014, 167.346, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 27

The binding sites of Magnesium atom in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp (pdb code 5w2a). 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 Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp, PDB code: 5w2a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:80.0 occ:1.00 O1A A:0KX603 2.2 91.0 1.0 OD2 A:ASP198 2.2 83.3 1.0 O A:MET108 2.2 88.8 1.0 OD1 A:ASP107 2.2 79.9 1.0 O2B A:0KX603 2.2 98.8 1.0 O3G A:0KX603 2.2 97.4 1.0 PB A:0KX603 2.9 0.2 1.0 N3A A:0KX603 3.0 99.9 1.0 PA A:0KX603 3.1 97.7 1.0 PG A:0KX603 3.1 92.0 1.0 CG A:ASP107 3.2 84.2 1.0 O3B A:0KX603 3.2 91.4 1.0 CG A:ASP198 3.3 92.6 1.0 C A:MET108 3.4 91.9 1.0 OD2 A:ASP107 3.5 89.4 1.0 O1G A:0KX603 3.7 89.8 1.0 OD1 A:ASP198 3.9 97.0 1.0 O5' A:0KX603 4.0 97.8 1.0 N A:MET108 4.0 89.0 1.0 C5' A:0KX603 4.0 97.2 1.0 CA A:MET108 4.2 88.8 1.0 NZ A:LYS328 4.3 0.3 1.0 O2A A:0KX603 4.3 100.0 1.0 CB A:ASP198 4.3 96.2 1.0 O1B A:0KX603 4.3 92.1 1.0 C A:ASP107 4.3 83.2 1.0 N A:ASP109 4.4 86.5 1.0 O2G A:0KX603 4.4 0.1 1.0 CB A:ASP107 4.5 80.8 1.0 CA A:ASP109 4.6 78.1 1.0 N A:ALA110 4.6 73.5 1.0 CB A:MET108 4.7 88.8 1.0 N A:PHE111 4.8 85.9 1.0 CA A:ASP107 4.8 81.4 1.0 C A:ASP109 4.8 72.0 1.0 CB A:PHE111 4.8 83.0 1.0 O A:ASP107 4.9 89.5 1.0

Magnesium binding site 2 out of 2 in the Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Human Dna Polymerase Kappa in Complex with Lucidin- Derived Dna Adduct and Incoming Dcmpnpp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:91.8 occ:1.00 O2A B:0KX604 2.2 95.5 1.0 OD2 B:ASP198 2.2 0.1 1.0 O3G B:0KX604 2.2 99.3 1.0 O1B B:0KX604 2.2 98.0 1.0 OD1 B:ASP107 2.2 90.8 1.0 O B:MET108 2.2 0.3 1.0 PB B:0KX604 3.0 0.6 1.0 PG B:0KX604 3.2 0.1 1.0 CG B:ASP198 3.2 0.4 1.0 CG B:ASP107 3.2 0.6 1.0 PA B:0KX604 3.2 0.5 1.0 O3B B:0KX604 3.3 95.3 1.0 N3A B:0KX604 3.4 98.4 1.0 C B:MET108 3.4 98.4 1.0 OD2 B:ASP107 3.6 0.7 1.0 O1G B:0KX604 3.7 1.0 1.0 OD1 B:ASP198 3.8 0.3 1.0 N B:MET108 4.0 0.6 1.0 C5' B:0KX604 4.0 97.1 1.0 O5' B:0KX604 4.1 99.6 1.0 CB B:ASP198 4.1 0.3 1.0 CA B:MET108 4.2 0.4 1.0 C B:ASP107 4.3 98.0 1.0 NZ B:LYS328 4.4 0.6 1.0 N B:ASP109 4.4 93.3 1.0 O1A B:0KX604 4.4 1.0 1.0 O2B B:0KX604 4.4 90.0 1.0 O2G B:0KX604 4.4 0.2 1.0 CB B:ASP107 4.5 0.1 1.0 CA B:ASP109 4.6 97.9 1.0 N B:ALA110 4.6 98.0 1.0 CB B:MET108 4.6 0.7 1.0 N B:PHE111 4.7 98.3 1.0 CB B:PHE111 4.8 94.4 1.0 CA B:ASP107 4.8 94.8 1.0 C B:ASP109 4.8 95.0 1.0 O B:ASP107 4.8 0.8 1.0

O.P.Yockey, V.Jha, P.P.Ghodke, T.Xu, W.Xu, H.Ling, P.I.Pradeepkumar, L.Zhao. Mechanism of Error-Free Dna Replication Past Lucidin-Derived Dna Damage By Human Dna Polymerase Kappa. Chem. Res. Toxicol. V. 30 2023 2017.
ISSN: ISSN 1520-5010
PubMed: 28972744
DOI: 10.1021/ACS.CHEMRESTOX.7B00227