Magnesium in PDB 8p62: S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation

All present enzymatic activity of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation:
2.7.7.7; 3.6.4.12;

The structure of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Magnesium atom in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation (pdb code 8p62). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation, PDB code: 8p62:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg1001 b:83.6 occ:1.00 O3B 3:ATP1002 1.9 79.3 1.0 O1A 3:ATP1002 2.0 79.3 1.0 O2G 3:ATP1002 2.1 79.3 1.0 O2B 3:ATP1002 2.2 79.3 1.0 PB 3:ATP1002 2.3 79.3 1.0 O3A 3:ATP1002 2.4 79.3 1.0 PA 3:ATP1002 2.4 79.3 1.0 PG 3:ATP1002 2.4 79.3 1.0 O2A 3:ATP1002 2.8 79.3 1.0 OG 3:SER416 2.9 80.0 1.0 O3G 3:ATP1002 3.1 79.3 1.0 OE2 5:GLU498 3.2 82.0 1.0 CB 3:SER416 3.6 80.0 1.0 O1B 3:ATP1002 3.7 79.3 1.0 O1G 3:ATP1002 3.8 79.3 1.0 CD 5:GLU498 3.9 82.0 1.0 O5' 3:ATP1002 3.9 79.3 1.0 NH2 5:ARG651 4.0 76.3 1.0 NH1 5:ARG651 4.1 76.3 1.0 N 3:SER416 4.1 80.0 1.0 OE1 5:GLU498 4.3 82.0 1.0 NH2 5:ARG549 4.5 73.0 1.0 CA 3:SER416 4.5 80.0 1.0 CZ 5:ARG651 4.5 76.3 1.0 NZ 3:LYS415 4.6 80.6 1.0 C5' 3:ATP1002 4.6 79.3 1.0 CG 5:GLU498 4.7 82.0 1.0 N 3:LYS415 4.9 80.6 1.0 CB 5:GLU498 4.9 82.0 1.0

Magnesium binding site 2 out of 3 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg1703 b:75.5 occ:1.00 O1G 5:ATP1701 2.3 82.7 1.0 CB 5:SER423 3.1 82.0 1.0 OG 5:SER423 3.5 82.0 1.0 O2B 5:ATP1701 3.6 82.7 1.0 OE1 2:GLN626 3.6 75.0 1.0 PG 5:ATP1701 3.7 82.7 1.0 O3B 5:ATP1701 4.1 82.7 1.0 CD 2:GLN626 4.3 75.0 1.0 CA 5:SER423 4.4 82.0 1.0 PB 5:ATP1701 4.6 82.7 1.0 N 5:SER423 4.6 82.0 1.0 O3G 5:ATP1701 4.6 82.7 1.0 O1A 5:ATP1701 4.7 82.7 1.0 CG 2:GLN626 4.7 75.0 1.0 O2G 5:ATP1701 4.7 82.7 1.0 NH1 2:ARG676 4.8 63.9 1.0 NH2 2:ARG676 5.0 63.9 1.0

Magnesium binding site 3 out of 3 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range: probe atom residue distance (Å) B Occ 7:Mg902 b:134.4 occ:1.00 O1G 7:ATP901 2.0 132.5 1.0 O1B 7:ATP901 2.0 132.5 1.0 PG 7:ATP901 2.3 132.5 1.0 O2G 7:ATP901 2.4 132.5 1.0 O3B 7:ATP901 2.6 132.5 1.0 PB 7:ATP901 2.8 132.5 1.0 OD2 7:ASP524 3.3 154.5 1.0 O3A 7:ATP901 3.7 132.5 1.0 O3G 7:ATP901 3.9 132.5 1.0 OD1 7:ASP524 3.9 154.5 1.0 CB 7:SER467 3.9 132.6 1.0 OG 7:SER467 3.9 132.6 1.0 CG 7:ASP524 4.0 154.5 1.0 O2B 7:ATP901 4.1 132.5 1.0 O2A 7:ATP901 4.5 132.5 1.0 CE 7:LYS466 4.6 133.2 1.0 PA 7:ATP901 4.6 132.5 1.0 N 7:SER467 4.9 132.6 1.0 CG 7:LYS466 4.9 133.2 1.0 CA 7:SER467 4.9 132.6 1.0 O1A 7:ATP901 5.0 132.5 1.0

S.S.Henrikus, M.H.Gross, O.Willhoft, T.Puhringer, J.S.Lewis, A.W.Mcclure, J.F.Greiwe, G.Palm, A.Nans, J.F.X.Diffley, A.Costa. Unwinding of A Eukaryotic Origin of Replication Visualized By Cryo-Em. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 38760633
DOI: 10.1038/S41594-024-01280-Z