Magnesium in PDB 3pzp: Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer

All present enzymatic activity of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer:
2.7.7.7;

The structure of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer, PDB code: 3pzp was solved by R.Vasquez-Del Carpio, T.D.Silverstein, S.Lone, R.E.Johnson, S.Prakash, L.Prakash, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.67 / 3.34
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	117.136, 154.476, 217.854, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 28.8

The binding sites of Magnesium atom in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer (pdb code 3pzp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer, PDB code: 3pzp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg2 b:70.8 occ:1.00 O1B A:DTP1 1.6 76.2 1.0 O A:MET108 2.1 65.0 1.0 OD2 A:ASP198 2.2 77.1 1.0 O1G A:DTP1 2.3 77.8 1.0 O1A A:DTP1 2.3 72.9 1.0 PB A:DTP1 3.0 75.6 1.0 OD2 A:ASP107 3.1 70.6 1.0 C A:MET108 3.1 65.1 1.0 OD1 A:ASP107 3.2 69.4 1.0 CG A:ASP198 3.3 77.8 1.0 CG A:ASP107 3.3 68.1 1.0 PA A:DTP1 3.4 74.3 1.0 PG A:DTP1 3.5 75.8 1.0 O3A A:DTP1 3.5 75.7 1.0 N A:MET108 3.6 66.5 1.0 O3B A:DTP1 3.7 75.3 1.0 OD1 A:ASP198 3.8 81.5 1.0 CA A:MET108 3.8 66.0 1.0 C5' A:DTP1 3.8 75.5 1.0 O5' A:DTP1 4.1 74.3 1.0 O3G A:DTP1 4.1 75.0 1.0 N A:ASP109 4.1 64.6 1.0 C A:ASP107 4.1 66.1 1.0 O2B A:DTP1 4.2 74.4 1.0 CB A:MET108 4.2 67.3 1.0 N A:ALA110 4.4 65.5 1.0 N A:PHE111 4.4 62.8 1.0 CB A:ASP198 4.5 77.6 1.0 CA A:ASP109 4.5 63.9 1.0 CB A:PHE111 4.5 66.8 1.0 CB A:ASP107 4.6 67.6 1.0 NZ A:LYS328 4.6 69.5 1.0 O2G A:DTP1 4.7 76.8 1.0 CE A:LYS328 4.7 70.9 1.0 CA A:ASP107 4.7 67.4 1.0 O A:ASP107 4.7 65.2 1.0 O2A A:DTP1 4.7 75.0 1.0 C A:ASP109 4.8 64.3 1.0 O A:HOH529 4.9 75.1 1.0

Magnesium binding site 2 out of 4 in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3 b:76.4 occ:1.00 O A:VAL354 2.5 77.2 1.0 OP1 P:DC12 2.6 90.4 1.0 O A:ILE357 2.7 76.1 1.0 O A:ARG352 2.8 73.2 1.0 C A:VAL354 3.5 77.9 1.0 P P:DC12 3.8 89.2 1.0 C A:ILE357 3.8 77.8 1.0 C A:ARG352 3.9 73.2 1.0 N A:ILE357 4.0 80.3 1.0 OP2 P:DC12 4.1 88.1 1.0 N A:VAL354 4.1 75.8 1.0 C A:LYS353 4.1 74.4 1.0 CA A:SER355 4.1 81.0 1.0 N A:SER355 4.2 79.5 1.0 N A:GLY356 4.2 82.5 1.0 CA A:VAL354 4.4 77.1 1.0 O A:LYS353 4.4 75.6 1.0 CA A:ILE357 4.5 79.6 1.0 C A:SER355 4.5 82.7 1.0 CA A:LYS353 4.5 72.7 1.0 NE A:ARG352 4.7 80.4 1.0 N A:LYS353 4.7 72.6 1.0 O5' P:DC12 4.8 87.2 1.0 CB A:ILE357 4.8 79.0 1.0 N A:GLY358 4.9 78.5 1.0 O3' P:DC11 4.9 91.0 1.0 CA A:ARG352 5.0 74.2 1.0

Magnesium binding site 3 out of 4 in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1 b:86.6 occ:1.00 OD1 B:ASP107 2.0 0.2 1.0 O1A B:DTP2 2.1 0.8 1.0 O2B B:DTP2 2.2 0.4 1.0 O1G B:DTP2 2.3 0.9 1.0 OD2 B:ASP198 2.8 0.4 1.0 CG B:ASP107 2.8 1.0 1.0 O B:MET108 2.9 0.5 1.0 OD2 B:ASP107 3.0 0.3 1.0 PB B:DTP2 3.3 0.4 1.0 PA B:DTP2 3.3 1.0 1.0 PG B:DTP2 3.4 1.0 1.0 O3A B:DTP2 3.6 0.2 1.0 O2G B:DTP2 3.7 0.0 1.0 O3B B:DTP2 3.8 0.7 1.0 CE B:LYS328 3.8 0.1 1.0 NZ B:LYS328 3.8 0.5 1.0 C B:MET108 4.0 0.3 1.0 CG B:ASP198 4.0 0.7 1.0 N B:MET108 4.0 0.5 1.0 OE1 B:GLU199 4.2 0.8 1.0 CB B:ASP107 4.3 0.4 1.0 O2A B:DTP2 4.3 0.9 1.0 O B:ASP198 4.4 0.8 1.0 OD1 B:ASP198 4.5 0.1 1.0 CA B:MET108 4.5 1.0 1.0 O5' B:DTP2 4.5 0.5 1.0 CD B:GLU199 4.6 0.4 1.0 C B:ASP107 4.6 0.9 1.0 O1B B:DTP2 4.7 0.2 1.0 C5' B:DTP2 4.7 0.9 1.0 O3G B:DTP2 4.8 0.8 1.0 CA B:ASP107 4.9 0.0 1.0 CD B:LYS328 4.9 1.0 1.0 OE2 B:GLU199 4.9 0.6 1.0 CB B:MET108 5.0 0.4 1.0

Magnesium binding site 4 out of 4 in the Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dna Polymerase Kappa Extending Opposite A Cis-Syn Thymine Dimer within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg4 b:81.8 occ:1.00 O B:ILE357 2.6 91.4 1.0 O B:ARG352 2.7 90.3 1.0 OP1 Q:DC12 2.9 99.1 1.0 O B:VAL354 3.0 92.7 1.0 NH1 B:ARG352 3.3 96.8 1.0 C B:ILE357 3.8 92.0 1.0 C B:ARG352 3.8 88.7 1.0 P Q:DC12 3.9 99.0 1.0 CD B:ARG352 3.9 92.3 1.0 OP2 Q:DC12 4.0 97.5 1.0 CZ B:ARG352 4.1 95.9 1.0 C B:VAL354 4.2 93.2 1.0 NE B:ARG352 4.4 94.2 1.0 N B:ILE357 4.5 93.9 1.0 CG B:ARG352 4.5 89.9 1.0 CA B:ARG352 4.6 87.5 1.0 C B:LYS353 4.6 91.0 1.0 N B:GLY356 4.6 97.1 1.0 CA B:ILE357 4.6 92.1 1.0 NZ B:LYS25 4.7 0.2 1.0 N B:GLY358 4.7 93.1 1.0 N B:LYS353 4.7 88.5 1.0 N B:VAL354 4.8 90.2 1.0 O B:LYS353 4.8 93.0 1.0 CA B:GLY358 4.8 94.4 1.0 CB B:ILE357 4.8 90.1 1.0 CA B:LYS353 4.9 89.9 1.0 O5' Q:DC12 4.9 0.6 1.0 O B:GLY358 4.9 92.1 1.0 CA B:SER355 5.0 97.5 1.0

R.Vasquez-Del Carpio, T.D.Silverstein, S.Lone, R.E.Johnson, L.Prakash, S.Prakash, A.K.Aggarwal. Role of Human Dna Polymerase Kappa in Extension Opposite From A Cis-Syn Thymine Dimer. J.Mol.Biol. V. 408 252 2011.
ISSN: ISSN 0022-2836
PubMed: 21354175
DOI: 10.1016/J.JMB.2011.02.042