Magnesium in PDB 4eyi: Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion

All present enzymatic activity of Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion:
2.7.7.7;

The structure of Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4eyi was solved by K.Kirouac, H.Ling, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.36 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.850, 98.850, 194.203, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 26.4

The binding sites of Magnesium atom in the Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion (pdb code 4eyi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4eyi:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


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 Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:80.2 occ:1.00 O1A B:DTP501 2.4 0.4 1.0 OE2 B:GLU127 2.7 72.5 1.0 OD1 B:ASP126 2.9 68.0 1.0 OD2 B:ASP34 3.1 69.3 1.0 O3' P:DC873 3.2 85.0 1.0 OD1 B:ASP34 3.3 67.4 1.0 O B:HOH601 3.3 63.4 1.0 CG B:GLU127 3.3 66.2 1.0 OD2 B:ASP126 3.3 68.9 1.0 MG B:MG503 3.4 92.2 1.0 CD B:GLU127 3.4 69.7 1.0 CG B:ASP126 3.5 65.0 1.0 CG B:ASP34 3.5 67.2 1.0 PA B:DTP501 3.8 0.7 1.0 C5' B:DTP501 3.9 1.0 1.0 C4' P:DC873 4.2 82.4 1.0 C3' P:DC873 4.3 84.1 1.0 O5' B:DTP501 4.3 0.8 1.0 O3A B:DTP501 4.3 0.5 1.0 C5' P:DC873 4.4 82.0 1.0 OE1 B:GLU127 4.6 70.8 1.0 CB B:GLU127 4.8 60.0 1.0 CB B:ASP34 4.9 64.1 1.0 CB B:ASP126 4.9 58.7 1.0 O B:ASP126 4.9 56.8 1.0 O1B B:DTP501 5.0 0.0 1.0

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


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 Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:92.2 occ:1.00 O1G B:DTP501 2.4 95.1 1.0 OD1 B:ASP34 2.4 67.4 1.0 OD1 B:ASP126 2.6 68.0 1.0 O B:LEU35 2.7 66.0 1.0 O1B B:DTP501 2.7 0.0 1.0 O3A B:DTP501 2.9 0.5 1.0 PB B:DTP501 3.2 0.8 1.0 O3B B:DTP501 3.4 92.4 1.0 MG B:MG502 3.4 80.2 1.0 PG B:DTP501 3.5 95.5 1.0 O1A B:DTP501 3.6 0.4 1.0 CG B:ASP34 3.6 67.2 1.0 C B:LEU35 3.8 59.6 1.0 PA B:DTP501 3.8 0.7 1.0 CG B:ASP126 3.9 65.0 1.0 OD2 B:ASP34 4.0 69.3 1.0 C5' B:DTP501 4.1 1.0 1.0 O2G B:DTP501 4.3 96.4 1.0 O5' B:DTP501 4.3 0.8 1.0 N B:CYS37 4.3 62.5 1.0 N B:LEU35 4.4 55.3 1.0 CA B:ASP36 4.6 58.5 1.0 N B:ASP36 4.6 55.1 1.0 O3G B:DTP501 4.7 94.6 1.0 O2B B:DTP501 4.7 0.5 1.0 C B:ASP34 4.7 58.5 1.0 CA B:LEU35 4.7 56.5 1.0 OD2 B:ASP126 4.7 68.9 1.0 C B:ASP36 4.8 60.2 1.0 CB B:ASP126 4.8 58.7 1.0 CB B:ASP34 4.8 64.1 1.0 O B:HOH601 4.9 63.4 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion


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 Iota Incorporating Datp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:76.0 occ:1.00 O B:LYS237 2.6 77.7 1.0 OP1 P:DC872 2.7 64.8 1.0 O B:HOH602 2.9 60.0 1.0 O B:ILE242 2.9 71.4 1.0 O B:ILE239 3.2 64.7 1.0 P P:DC872 3.6 63.9 1.0 OP2 P:DC872 3.6 59.4 1.0 NZ B:LYS237 3.7 94.9 1.0 C B:LYS237 3.8 72.7 1.0 CG B:LYS237 4.0 86.0 1.0 C B:ILE239 4.0 62.7 1.0 C B:ILE242 4.1 70.6 1.0 C B:GLU238 4.4 66.7 1.0 CA B:PRO240 4.4 60.1 1.0 O B:GLU238 4.4 69.1 1.0 O5' P:DC872 4.5 66.4 1.0 N B:PRO240 4.5 63.1 1.0 CA B:GLY243 4.6 74.8 1.0 N B:ILE239 4.6 61.3 1.0 CA B:LYS237 4.7 75.9 1.0 CA B:GLU238 4.7 67.9 1.0 N B:GLY241 4.7 63.8 1.0 N B:GLU238 4.7 68.4 1.0 CE B:LYS237 4.7 94.5 1.0 N B:GLY243 4.8 71.7 1.0 O3' P:DC871 4.9 68.2 1.0 N B:ILE242 4.9 67.7 1.0 CB B:LYS237 4.9 82.8 1.0 CD B:LYS237 5.0 89.9 1.0 CA B:ILE239 5.0 60.5 1.0 OP2 P:DC873 5.0 79.6 1.0

K.N.Kirouac, A.K.Basu, H.Ling. Replication of A Carcinogenic Nitropyrene Dna Lesion By Human Y-Family Dna Polymerase. Nucleic Acids Res. V. 41 2060 2013.
ISSN: ISSN 0305-1048
PubMed: 23268450
DOI: 10.1093/NAR/GKS1296