Magnesium in PDB 3v6h: Replication of N2,3-Ethenoguanine By Dna Polymerases

All present enzymatic activity of Replication of N2,3-Ethenoguanine By Dna Polymerases:
2.7.7.7;

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6h was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.80 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.532, 111.267, 98.942, 90.00, 102.68, 90.00
R / Rfree (%)	21.5 / 26.7

The structure of Replication of N2,3-Ethenoguanine By Dna Polymerases also contains other interesting chemical elements:

Fluorine	(F)	2 atoms
Calcium	(Ca)	3 atoms

The binding sites of Magnesium atom in the Replication of N2,3-Ethenoguanine By Dna Polymerases (pdb code 3v6h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Replication of N2,3-Ethenoguanine By Dna Polymerases, PDB code: 3v6h:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:19.3 occ:1.00 OD1 A:ASP7 2.0 34.5 1.0 O1A A:DCP401 2.1 38.3 1.0 OD2 A:ASP105 2.1 37.9 1.0 O A:PHE8 2.1 31.5 1.0 O1G A:DCP401 2.2 46.3 1.0 O2B A:DCP401 2.2 32.0 1.0 CG A:ASP7 3.2 34.4 1.0 CG A:ASP105 3.3 34.9 1.0 C A:PHE8 3.3 31.7 1.0 PB A:DCP401 3.3 36.8 1.0 PA A:DCP401 3.4 42.7 1.0 MG A:MG403 3.4 29.6 1.0 O A:HOH529 3.4 51.9 1.0 PG A:DCP401 3.5 45.8 1.0 O3A A:DCP401 3.6 38.0 1.0 OD2 A:ASP7 3.7 34.2 1.0 O3B A:DCP401 3.9 40.4 1.0 OD1 A:ASP105 3.9 40.3 1.0 N A:PHE8 3.9 29.9 1.0 C5' A:DCP401 4.0 46.1 1.0 NZ A:LYS159 4.1 46.4 1.0 O5' A:DCP401 4.2 46.8 1.0 CA A:PHE8 4.2 31.0 1.0 C A:ASP7 4.2 30.2 1.0 N A:ASP9 4.3 33.3 1.0 N A:TYR10 4.3 31.4 1.0 O3G A:DCP401 4.4 44.8 1.0 CA A:ASP9 4.4 31.7 1.0 CB A:ASP105 4.4 34.4 1.0 CB A:ASP7 4.4 31.6 1.0 O2G A:DCP401 4.6 47.4 1.0 O2A A:DCP401 4.6 44.5 1.0 C A:ASP9 4.6 31.9 1.0 O A:ASP7 4.6 28.9 1.0 N A:PHE11 4.7 28.2 1.0 O1B A:DCP401 4.7 41.3 1.0 CA A:ASP7 4.8 30.4 1.0 CB A:PHE11 4.9 28.0 1.0 O A:ASP105 4.9 35.4 1.0 CB A:PHE8 5.0 29.1 1.0

Magnesium binding site 2 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:29.6 occ:1.00 O A:HOH604 2.2 48.0 1.0 O1A A:DCP401 2.4 38.3 1.0 OE1 A:GLU106 2.4 41.9 1.0 OD2 A:ASP7 2.4 34.2 1.0 OD1 A:ASP105 2.5 40.3 1.0 CG A:ASP7 3.0 34.4 1.0 OD1 A:ASP7 3.1 34.5 1.0 OD2 A:ASP105 3.1 37.9 1.0 CG A:ASP105 3.2 34.9 1.0 MG A:MG402 3.4 19.3 1.0 PA A:DCP401 3.5 42.7 1.0 O A:HOH614 3.5 46.3 1.0 CD A:GLU106 3.6 41.8 1.0 O2A A:DCP401 3.9 44.5 1.0 O5' A:DCP401 4.0 46.8 1.0 OP2 D:DOC13 4.1 74.7 0.8 C5' A:DCP401 4.1 46.1 1.0 CB A:GLU106 4.3 38.8 1.0 CB A:ASP7 4.4 31.6 1.0 CG A:GLU106 4.4 39.4 1.0 NZ A:LYS159 4.5 46.4 1.0 OE2 A:GLU106 4.5 45.9 1.0 CB A:ASP105 4.7 34.4 1.0 NZ A:LYS152 4.7 43.5 1.0 O1G A:DCP401 4.7 46.3 1.0 O2B A:DCP401 4.8 32.0 1.0 O3A A:DCP401 4.9 38.0 1.0 O A:ASP105 4.9 35.4 1.0 C A:ASP105 4.9 34.4 1.0

Magnesium binding site 3 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:40.3 occ:1.00 O1G B:DCP401 2.0 65.4 1.0 OD1 B:ASP7 2.1 66.7 1.0 O B:PHE8 2.1 57.2 1.0 O2B B:DCP401 2.3 70.1 1.0 OD2 B:ASP105 2.3 62.6 1.0 O1A B:DCP401 2.4 59.8 1.0 CG B:ASP7 3.1 65.1 1.0 MG B:MG404 3.2 53.0 1.0 C B:PHE8 3.3 58.5 1.0 PG B:DCP401 3.4 63.6 1.0 OD2 B:ASP7 3.5 66.3 1.0 PB B:DCP401 3.5 73.8 1.0 CG B:ASP105 3.5 62.1 1.0 PA B:DCP401 3.7 72.6 1.0 O3B B:DCP401 3.8 69.0 1.0 O B:HOH526 3.8 67.9 1.0 O3A B:DCP401 3.9 72.2 1.0 N B:PHE8 4.0 60.7 1.0 N B:TYR10 4.1 54.3 1.0 O2G B:DCP401 4.2 64.8 1.0 N B:ASP9 4.2 57.8 1.0 CA B:PHE8 4.2 60.6 1.0 CA B:ASP9 4.3 56.0 1.0 OD1 B:ASP105 4.3 63.4 1.0 CB B:ASP105 4.3 62.1 1.0 C B:ASP7 4.4 61.7 1.0 C B:ASP9 4.4 55.0 1.0 CB B:ASP7 4.5 65.0 1.0 O3G B:DCP401 4.5 69.2 1.0 N B:PHE11 4.6 50.0 1.0 O2A B:DCP401 4.7 65.6 1.0 O5' B:DCP401 4.7 74.9 1.0 C5' B:DCP401 4.8 73.1 1.0 O1B B:DCP401 4.8 77.6 1.0 CA B:ASP7 4.8 63.2 1.0 CA B:TYR10 4.9 52.1 1.0 O B:ASP7 4.9 61.8 1.0 CB B:PHE8 4.9 63.3 1.0 CB B:PHE11 5.0 51.7 1.0

Magnesium binding site 4 out of 4 in the Replication of N2,3-Ethenoguanine By Dna Polymerases


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Replication of N2,3-Ethenoguanine By Dna Polymerases within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg404 b:53.0 occ:1.00 OE2 B:GLU106 2.1 73.3 1.0 OD2 B:ASP105 2.4 62.6 1.0 OD2 B:ASP7 2.4 66.3 1.0 OD1 B:ASP105 2.4 63.4 1.0 O1A B:DCP401 2.4 59.8 1.0 CG B:ASP7 2.7 65.1 1.0 CG B:ASP105 2.7 62.1 1.0 OD1 B:ASP7 2.7 66.7 1.0 CD B:GLU106 3.0 68.5 1.0 CG B:GLU106 3.1 68.3 1.0 MG B:MG402 3.2 40.3 1.0 PA B:DCP401 3.7 72.6 1.0 CB B:ASP7 3.9 65.0 1.0 OP2 P:DOC13 3.9 86.1 1.0 OE1 B:GLU106 4.1 64.9 1.0 CB B:ASP105 4.1 62.1 1.0 O5' B:DCP401 4.2 74.9 1.0 C5' B:DCP401 4.3 73.1 1.0 O B:ASP105 4.3 68.6 1.0 CB B:GLU106 4.4 65.4 1.0 C B:ASP105 4.4 65.4 1.0 O2A B:DCP401 4.5 65.6 1.0 CA B:ASP7 4.5 63.2 1.0 O2B B:DCP401 4.6 70.1 1.0 OG B:SER103 4.6 52.1 1.0 O1G B:DCP401 4.6 65.4 1.0 O B:PHE8 4.7 57.2 1.0 N B:GLU106 4.8 65.3 1.0 CA B:ASP105 4.9 62.3 1.0 N B:PHE8 4.9 60.7 1.0 NZ B:LYS152 5.0 61.0 1.0 CA B:GLU106 5.0 65.7 1.0

L.Zhao, P.P.Christov, I.D.Kozekov, M.G.Pence, P.S.Pallan, C.J.Rizzo, M.Egli, F.P.Guengerich. Replication of N(2) ,3-Ethenoguanine By Dna Polymerases. Angew.Chem.Int.Ed.Engl. V. 51 5466 2012.
ISSN: ISSN 1433-7851
PubMed: 22488769
DOI: 10.1002/ANIE.201109004