Magnesium in PDB 8s0f: H. Sapiens OC1M Bound to Double Stranded Dna

All present enzymatic activity of H. Sapiens OC1M Bound to Double Stranded Dna:
3.6.4.12;

The structure of H. Sapiens OC1M Bound to Double Stranded Dna also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the H. Sapiens OC1M Bound to Double Stranded Dna (pdb code 8s0f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the H. Sapiens OC1M Bound to Double Stranded Dna, PDB code: 8s0f:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the H. Sapiens OC1M Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of H. Sapiens OC1M Bound to Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg1001 b:131.3 occ:1.00 O1B 6:AGS901 2.0 148.9 1.0 OG 2:SER530 2.1 153.8 1.0 O3G 6:AGS901 2.3 148.9 1.0 CB 2:SER530 2.9 153.8 1.0 PG 6:AGS901 3.2 148.9 1.0 N 2:SER530 3.3 153.8 1.0 PB 6:AGS901 3.3 148.9 1.0 O2G 6:AGS901 3.4 148.9 1.0 O1A 6:AGS901 3.6 148.9 1.0 O3B 6:AGS901 3.6 148.9 1.0 CA 2:SER530 3.6 153.8 1.0 PA 6:AGS901 4.1 148.9 1.0 O3A 6:AGS901 4.1 148.9 1.0 O2A 6:AGS901 4.2 148.9 1.0 C 2:LYS529 4.4 167.1 1.0 O2B 6:AGS901 4.4 148.9 1.0 N 2:LYS529 4.5 167.1 1.0 CB 2:LYS529 4.6 167.1 1.0 CA 2:LYS529 4.7 167.1 1.0 C 2:SER530 4.9 153.8 1.0 NE2 6:GLN479 4.9 161.6 1.0

Magnesium binding site 2 out of 5 in the H. Sapiens OC1M Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of H. Sapiens OC1M Bound to Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ 6:Mg903 b:155.6 occ:1.00 O1B 6:AGS902 1.9 161.7 1.0 O2G 6:AGS902 2.0 161.7 1.0 OG 6:SER403 2.1 153.9 1.0 O3G 6:AGS902 2.6 161.7 1.0 PG 6:AGS902 2.7 161.7 1.0 PB 6:AGS902 3.0 161.7 1.0 CB 6:SER403 3.1 153.9 1.0 O3B 6:AGS902 3.3 161.7 1.0 O2A 6:AGS902 3.5 161.7 1.0 N 6:SER403 3.5 153.9 1.0 CA 6:SER403 3.9 153.9 1.0 O1A 6:AGS902 3.9 161.7 1.0 O3A 6:AGS902 3.9 161.7 1.0 PA 6:AGS902 4.0 161.7 1.0 OD2 6:ASP460 4.1 159.7 1.0 OD1 6:ASP460 4.2 159.7 1.0 O2B 6:AGS902 4.2 161.7 1.0 NH2 4:ARG732 4.4 169.1 1.0 CB 6:LYS402 4.5 145.5 1.0 S1G 6:AGS902 4.5 161.7 1.0 C 6:LYS402 4.5 145.5 1.0 CG 6:ASP460 4.6 159.7 1.0 CA 6:LYS402 4.9 145.5 1.0 N 6:LYS402 4.9 145.5 1.0

Magnesium binding site 3 out of 5 in the H. Sapiens OC1M Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of H. Sapiens OC1M Bound to Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:347.9 occ:1.00 O2G A:AGS901 2.0 360.9 1.0 OG1 A:THR541 2.0 344.1 1.0 O1B A:AGS901 2.2 360.9 1.0 PG A:AGS901 3.0 360.9 1.0 CB A:THR541 3.1 344.1 1.0 S1G A:AGS901 3.3 360.9 1.0 PB A:AGS901 3.3 360.9 1.0 O3B A:AGS901 3.5 360.9 1.0 O2A A:AGS901 3.8 360.9 1.0 O3A A:AGS901 3.9 360.9 1.0 O1A A:AGS901 4.0 360.9 1.0 N A:THR541 4.0 344.1 1.0 PA A:AGS901 4.1 360.9 1.0 CG2 A:THR541 4.1 344.1 1.0 CA A:THR541 4.2 344.1 1.0 NH2 D:ARG209 4.2 240.1 1.0 OD2 A:ASP620 4.2 341.0 1.0 O3G A:AGS901 4.3 360.9 1.0 OD1 A:ASP620 4.4 341.0 1.0 O2B A:AGS901 4.6 360.9 1.0 CG A:ASP620 4.8 341.0 1.0

Magnesium binding site 4 out of 5 in the H. Sapiens OC1M Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of H. Sapiens OC1M Bound to Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg902 b:170.7 occ:1.00 OG1 D:THR74 2.1 161.3 1.0 O1B D:AGS901 2.2 170.0 1.0 O2G D:AGS901 2.3 170.0 1.0 PB D:AGS901 3.3 170.0 1.0 CB D:THR74 3.3 161.3 1.0 PG D:AGS901 3.4 170.0 1.0 O3B D:AGS901 3.6 170.0 1.0 O2B D:AGS901 3.8 170.0 1.0 CG2 D:THR74 4.0 161.3 1.0 S1G D:AGS901 4.2 170.0 1.0 OD2 D:ASP159 4.4 201.7 1.0 CA D:THR74 4.5 161.3 1.0 OE1 E:GLU146 4.5 138.8 1.0 N D:THR74 4.5 161.3 1.0 O3A D:AGS901 4.7 170.0 1.0 O3G D:AGS901 4.7 170.0 1.0 O1A D:AGS901 4.9 170.0 1.0 CD2 D:LEU192 4.9 201.1 1.0

Magnesium binding site 5 out of 5 in the H. Sapiens OC1M Bound to Double Stranded Dna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of H. Sapiens OC1M Bound to Double Stranded Dna within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg502 b:156.2 occ:1.00 O1B E:AGS501 2.0 143.3 1.0 OG1 E:THR44 2.1 154.1 1.0 O2G E:AGS501 2.2 143.3 1.0 O3G E:AGS501 2.3 143.3 1.0 PG E:AGS501 2.6 143.3 1.0 CB E:THR44 3.0 154.1 1.0 PB E:AGS501 3.1 143.3 1.0 O3B E:AGS501 3.3 143.3 1.0 N E:THR44 3.8 154.1 1.0 O1A E:AGS501 3.9 143.3 1.0 CA E:THR44 4.0 154.1 1.0 O2A E:AGS501 4.0 143.3 1.0 CG2 E:THR44 4.0 154.1 1.0 O3A E:AGS501 4.1 143.3 1.0 PA E:AGS501 4.2 143.3 1.0 O2B E:AGS501 4.3 143.3 1.0 S1G E:AGS501 4.4 143.3 1.0

F.Weissmann, J.F.Greiwe, T.Puehringer, E.L.Eastwood, E.C.Couves, T.C.R.Miller, J.F.X.Diffley, A.Costa. Mcm Double Hexamer Loading Visualised with Human Proteins Nature 2024.
ISSN: ESSN 1476-4687