Sodium in PDB 3epg: Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine

All present enzymatic activity of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine, PDB code: 3epg was solved by M.G.Pence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.535, 98.535, 202.354, 90.00, 90.00, 120.00
R / Rfree (%)	23.4 / 28.3

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine (pdb code 3epg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine, PDB code: 3epg:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na421 b:39.4 occ:1.00 O A:ILE239 2.5 30.7 1.0 O A:LYS237 2.6 33.1 1.0 OP1 B:DC12 2.6 28.7 1.0 O A:ILE242 2.7 33.0 1.0 C A:ILE239 3.2 30.9 1.0 C A:LYS237 3.6 33.2 1.0 N A:PRO240 3.7 31.6 1.0 CA A:PRO240 3.8 31.6 1.0 C A:ILE242 3.8 33.6 1.0 P B:DC12 3.9 28.7 1.0 N A:ILE239 3.9 30.2 1.0 C A:GLU238 4.0 31.3 1.0 N A:GLY241 4.1 31.6 1.0 N A:ILE242 4.1 33.1 1.0 CA A:ILE239 4.2 30.3 1.0 O A:GLU238 4.3 31.3 1.0 CA A:GLU238 4.3 31.9 1.0 N A:GLU238 4.3 32.8 1.0 OP2 B:DC12 4.3 30.7 1.0 C A:PRO240 4.4 31.8 1.0 CA A:ILE242 4.5 32.9 1.0 CA A:LYS237 4.5 33.8 1.0 O5' B:DC12 4.8 29.8 1.0 N A:GLY243 4.8 34.7 1.0 O A:ILE236 4.9 34.7 1.0 CD A:PRO240 4.9 31.2 1.0 CB A:ILE242 5.0 32.8 1.0 CD A:LYS237 5.0 34.4 1.0 O3' B:DC11 5.0 28.5 1.0

Sodium binding site 2 out of 4 in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na422 b:48.2 occ:1.00 OE2 A:GLU115 3.6 42.6 1.0 CD A:GLU115 4.0 40.6 1.0 CZ A:PHE116 4.3 38.2 1.0 CE1 A:PHE116 4.3 38.0 1.0 CG A:GLU115 4.5 37.9 1.0 CE2 A:PHE116 4.5 38.5 1.0 OE1 A:GLU115 4.6 39.2 1.0 CD1 A:PHE116 4.6 38.4 1.0 CB A:GLU115 4.7 35.3 1.0 O A:HOH453 4.7 27.5 1.0 CD2 A:PHE116 4.8 37.8 1.0 O A:GLU115 4.8 34.9 1.0 CG A:PHE116 4.8 36.7 1.0 C A:GLU115 4.9 35.4 1.0

Sodium binding site 3 out of 4 in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na423 b:20.0 occ:1.00 O A:HOH470 3.6 30.5 1.0 CB A:PRO240 3.7 31.6 1.0 O A:HOH461 3.8 24.2 1.0 O A:PRO240 4.1 31.9 1.0 C A:PRO240 4.1 31.8 1.0 C5' B:DC12 4.1 30.5 1.0 C4' B:DC12 4.3 31.5 1.0 CA A:PRO240 4.4 31.6 1.0 N A:GLY241 4.5 31.6 1.0 CD2 A:LEU123 4.6 32.7 1.0 NZ A:LYS207 4.9 34.4 1.0 CA A:GLY241 5.0 31.9 1.0

Sodium binding site 4 out of 4 in the Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Human Dna Polymerase Iota Complexed with N2-Ethylguanine within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1 b:20.0 occ:1.00 C5' C:DC845 3.7 37.4 1.0 O5' C:DC845 4.2 39.5 1.0 O3' C:DC845 4.5 33.0 1.0 OP1 C:DC845 4.6 40.3 1.0 C3' C:DC845 4.7 33.5 1.0 C4' C:DC845 4.9 34.2 1.0 P C:DC845 5.0 42.0 1.0

M.G.Pence, P.Blans, C.N.Zink, T.Hollis, J.C.Fishbein, F.W.Perrino. Lesion Bypass of N2-Ethylguanine By Human Dna Polymerase Iota. J.Biol.Chem. V. 284 1732 2009.
ISSN: ISSN 0021-9258
PubMed: 18984581
DOI: 10.1074/JBC.M807296200