Magnesium in PDB 4fs1: Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota

All present enzymatic activity of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota:
2.7.7.7;

The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota, PDB code: 4fs1 was solved by L.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	84.41 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	97.470, 97.470, 203.541, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 27

The structure of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota (pdb code 4fs1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota, PDB code: 4fs1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:61.9 occ:1.00 O1B A:TTP505 2.2 30.2 0.5 O A:LEU35 2.2 45.0 1.0 OD1 A:ASP34 2.2 44.7 1.0 O1G A:TTP505 2.2 70.3 1.0 O2A A:TTP505 2.2 39.6 0.5 OD2 A:ASP126 2.3 58.6 1.0 CG A:ASP34 3.4 41.5 1.0 C A:LEU35 3.4 38.2 1.0 PB A:TTP505 3.4 46.1 0.5 CG A:ASP126 3.4 47.5 1.0 PA A:TTP505 3.5 39.3 0.5 PG A:TTP505 3.6 57.9 1.0 O3A A:TTP505 3.6 43.5 0.5 N A:LEU35 3.8 36.2 1.0 OD2 A:ASP34 3.9 45.5 1.0 O3B A:TTP505 3.9 47.3 0.5 CB A:ASP126 4.1 42.5 1.0 O A:HOH655 4.1 54.7 1.0 CA A:LEU35 4.2 37.8 1.0 O2G A:TTP505 4.2 67.5 1.0 C A:ASP34 4.2 37.3 1.0 OD1 A:ASP126 4.2 55.5 1.0 C5' A:TTP505 4.2 42.5 1.0 N A:ASP36 4.3 37.6 1.0 O5' A:TTP505 4.4 37.7 1.0 CA A:ASP36 4.5 42.9 1.0 O A:ASP126 4.5 35.9 1.0 CB A:ASP34 4.6 33.1 1.0 CA A:ASP34 4.7 35.6 1.0 N A:CYS37 4.7 36.3 1.0 O1A A:TTP505 4.7 40.6 0.5 C A:ASP36 4.7 42.2 1.0 O2B A:TTP505 4.7 39.2 0.5 O3G A:TTP505 4.7 65.7 1.0 O A:ASP34 4.8 41.8 1.0 CB A:LEU35 4.8 36.1 1.0

Magnesium binding site 2 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.5 occ:1.00 O A:HOH613 2.3 43.0 1.0 O A:LYS237 2.3 50.4 1.0 O A:ILE242 2.5 56.4 1.0 OP1 B:DC12 2.7 42.4 1.0 O A:ILE239 2.9 44.4 1.0 C A:LYS237 3.5 50.7 1.0 C A:ILE239 3.5 45.1 1.0 C A:ILE242 3.6 54.4 1.0 P B:DC12 3.8 35.8 1.0 CA A:PRO240 3.9 48.2 1.0 N A:ILE242 4.0 47.0 1.0 N A:PRO240 4.0 46.5 1.0 CG A:LYS237 4.0 68.8 1.0 OP2 B:DC12 4.0 37.1 1.0 N A:GLY241 4.1 44.0 1.0 N A:ILE239 4.3 34.2 1.0 CA A:LYS237 4.3 52.5 1.0 CA A:ILE242 4.3 49.6 1.0 C A:GLU238 4.3 38.5 1.0 N A:GLU238 4.4 47.0 1.0 C A:PRO240 4.4 46.3 1.0 N A:GLY243 4.5 57.3 1.0 NZ A:LYS237 4.5 75.9 1.0 CA A:GLU238 4.5 40.9 1.0 CA A:ILE239 4.5 40.0 1.0 CB A:ILE242 4.6 44.9 1.0 CA A:GLY243 4.6 54.2 1.0 O A:GLU238 4.7 35.7 1.0 O5' B:DC12 4.7 41.0 1.0 CB A:LYS237 4.8 59.7 1.0 O3' B:DC11 4.8 40.8 1.0 C A:GLY241 5.0 49.0 1.0

Magnesium binding site 3 out of 3 in the Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Base Pairing Mechanism of N2,3-Ethenoguanine with Dttp By Human Polymerase Iota within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:47.4 occ:1.00 O A:HOH634 2.8 35.2 1.0 O A:GLY124 2.8 29.8 1.0 O A:GLU127 3.0 34.2 1.0 NH2 A:ARG122 3.3 29.4 1.0 O A:PHE125 3.3 43.8 1.0 C A:PHE125 3.5 39.4 1.0 CZ A:ARG122 3.5 31.6 1.0 CG A:ARG122 3.5 30.6 1.0 CB A:ARG122 3.6 27.6 1.0 OG A:SER106 3.7 32.1 1.0 ND2 A:ASN128 3.7 29.2 1.0 N A:GLU127 3.8 33.0 1.0 NH1 A:ARG122 3.9 29.4 1.0 C A:GLY124 3.9 27.0 1.0 C A:GLU127 3.9 32.3 1.0 OD1 A:ASN128 3.9 33.9 1.0 CA A:PHE125 3.9 35.0 1.0 N A:ASP126 4.0 40.3 1.0 NE A:ARG122 4.0 30.0 1.0 CG A:ASN128 4.0 31.4 1.0 CA A:ARG122 4.0 28.2 1.0 OG1 A:THR110 4.1 28.4 1.0 N A:LEU123 4.2 27.5 1.0 CD A:ARG122 4.3 31.6 1.0 N A:PHE125 4.4 29.0 1.0 O A:LEU123 4.4 30.4 1.0 CA A:ASP126 4.5 37.5 1.0 C A:ASP126 4.5 33.9 1.0 CA A:GLU127 4.5 31.9 1.0 C A:ARG122 4.6 29.1 1.0 O A:SER106 4.6 40.4 1.0 C A:LEU123 4.7 28.2 1.0 N A:ASN128 4.8 29.9 1.0 CB A:SER106 5.0 31.4 1.0

L.Zhao, M.G.Pence, P.P.Christov, Z.Wawrzak, J.Y.Choi, C.J.Rizzo, M.Egli, F.P.Guengerich. Basis of Miscoding of the Dna Adduct N2,3-Ethenoguanine By Human Y-Family Dna Polymerases. J.Biol.Chem. V. 287 35516 2012.
ISSN: ISSN 0021-9258
PubMed: 22910910
DOI: 10.1074/JBC.M112.403253