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

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

The structure of Human Dna Polymerase Iota Incorporating Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4eyh 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)	32.09 / 2.90
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	98.046, 98.046, 194.649, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 28.1

The binding sites of Magnesium atom in the Human Dna Polymerase Iota Incorporating Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion (pdb code 4eyh). 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 Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion, PDB code: 4eyh:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Human Dna Polymerase Iota Incorporating Dctp 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 Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:76.5 occ:1.00 O3G B:DCP501 2.5 91.8 1.0 OD1 B:ASP34 2.8 67.0 1.0 O B:HOH601 2.8 67.0 1.0 O B:LEU35 2.9 55.9 1.0 O2B B:DCP501 3.0 0.3 1.0 CG B:ASP34 3.0 62.7 1.0 C B:LEU35 3.4 54.2 1.0 OD2 B:ASP34 3.5 63.6 1.0 CB B:ASP34 3.6 60.1 1.0 C B:ASP34 3.7 63.2 1.0 N B:LEU35 3.8 52.0 1.0 PG B:DCP501 3.8 90.9 1.0 O B:ASP34 3.8 63.7 1.0 N B:ASP36 3.9 54.5 1.0 OD1 B:ASP126 3.9 67.8 1.0 MG B:MG504 4.0 0.2 1.0 CA B:ASP36 4.0 56.9 1.0 CA B:ASP34 4.1 50.2 1.0 PB B:DCP501 4.2 0.5 1.0 CA B:LEU35 4.2 53.2 1.0 O1G B:DCP501 4.3 89.7 1.0 O3B B:DCP501 4.4 0.8 1.0 NZ B:LYS214 4.6 85.9 1.0 N B:CYS37 4.6 59.7 1.0 O1A B:DCP501 4.6 0.7 1.0 C B:ASP36 4.7 57.8 1.0 OD1 B:ASP36 4.7 59.5 1.0

Magnesium binding site 2 out of 3 in the Human Dna Polymerase Iota Incorporating Dctp 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 Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg503 b:58.8 occ:1.00 O B:HOH624 2.0 75.9 1.0 OP1 P:DC872 2.6 72.2 1.0 O B:LYS237 2.7 70.5 1.0 O B:ILE242 2.7 68.3 1.0 O P:HOH901 2.8 55.8 1.0 O B:ILE239 2.9 67.8 1.0 C B:LYS237 3.5 70.9 1.0 C B:ILE239 3.6 66.2 1.0 C B:ILE242 3.7 70.2 1.0 P P:DC872 3.7 73.2 1.0 C B:GLU238 4.0 64.9 1.0 OP2 P:DC872 4.0 74.7 1.0 N B:ILE239 4.1 64.7 1.0 CG B:LYS237 4.1 85.0 1.0 N B:PRO240 4.1 64.8 1.0 O B:GLU238 4.2 64.3 1.0 CA B:PRO240 4.2 62.4 1.0 N B:ILE242 4.2 58.6 1.0 NZ B:LYS237 4.3 95.9 1.0 N B:GLU238 4.3 68.1 1.0 N B:GLY241 4.3 61.7 1.0 CA B:GLU238 4.3 66.6 1.0 CA B:LYS237 4.4 75.8 1.0 CA B:ILE239 4.5 65.1 1.0 CA B:ILE242 4.5 60.1 1.0 N B:GLY243 4.6 62.8 1.0 C B:PRO240 4.7 60.7 1.0 CA B:GLY243 4.7 64.3 1.0 O5' P:DC872 4.7 75.8 1.0 CB B:ILE242 4.8 59.8 1.0 CB B:LYS237 4.8 81.1 1.0 O3' P:DC871 4.9 72.1 1.0

Magnesium binding site 3 out of 3 in the Human Dna Polymerase Iota Incorporating Dctp 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 Dctp Opposite N- (Deoxyguanosin-8-Yl)-1-Aminopyrene Lesion within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg504 b:0.2 occ:1.00 OE2 B:GLU127 2.6 63.9 1.0 O1A B:DCP501 2.8 0.7 1.0 OD1 B:ASP34 3.0 67.0 1.0 OD2 B:ASP34 3.1 63.6 1.0 O3' P:DC873 3.2 92.1 1.0 CG B:ASP34 3.4 62.7 1.0 O2A B:DCP501 3.5 0.9 1.0 PA B:DCP501 3.7 0.6 1.0 CD B:GLU127 3.7 61.3 1.0 MG B:MG502 4.0 76.5 1.0 CG B:GLU127 4.1 56.7 1.0 OD1 B:ASP126 4.1 67.8 1.0 O2B B:DCP501 4.2 0.3 1.0 O3G B:DCP501 4.5 91.8 1.0 O3A B:DCP501 4.5 0.5 1.0 C3' P:DC873 4.5 90.7 1.0 OD2 B:ASP126 4.8 64.3 1.0 OE1 B:GLU127 4.8 63.3 1.0 CG B:ASP126 4.9 65.3 1.0 CB B:ASP34 4.9 60.1 1.0 PB B:DCP501 4.9 0.5 1.0 C4' P:DC873 5.0 87.6 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