Magnesium in PDB 8w7m: Yeast Replisome in State V

All present enzymatic activity of Yeast Replisome in State V:
3.6.4.12;

The structure of Yeast Replisome in State V also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Magnesium atom in the Yeast Replisome in State V (pdb code 8w7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Yeast Replisome in State V, PDB code: 8w7m:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg902 b:285.0 occ:1.00 O2A 2:ADP901 2.0 289.4 1.0 O1B 2:ADP901 2.1 289.4 1.0 O2B 2:ADP901 2.1 289.4 1.0 PB 2:ADP901 2.3 289.4 1.0 PA 2:ADP901 2.3 289.4 1.0 O1A 2:ADP901 2.6 289.4 1.0 O3A 2:ADP901 2.6 289.4 1.0 CB 2:SER550 2.7 285.3 1.0 NH2 6:ARG798 3.5 291.9 1.0 OG 2:SER550 3.6 285.3 1.0 O3B 2:ADP901 3.8 289.4 1.0 N 2:SER550 3.8 285.3 1.0 CA 2:SER550 3.8 285.3 1.0 O5' 2:ADP901 3.9 289.4 1.0 NH1 6:ARG798 4.4 291.9 1.0 CZ 6:ARG798 4.4 291.9 1.0 C5' 2:ADP901 4.6 289.4 1.0 NH2 6:ARG708 4.7 298.2 1.0 C 2:SER550 4.7 285.3 1.0 N 2:GLN551 4.7 283.2 1.0 OE2 6:GLU657 4.8 310.2 1.0 N 2:GLY546 4.9 302.3 1.0 CG 2:LYS549 4.9 301.6 1.0 N 2:LYS549 5.0 301.6 1.0

Magnesium binding site 2 out of 4 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 3:Mg1002 b:295.6 occ:1.00 O3B 3:ADP1001 1.9 282.8 1.0 O1A 3:ADP1001 2.1 282.8 1.0 PB 3:ADP1001 2.3 282.8 1.0 PA 3:ADP1001 2.3 282.8 1.0 O1B 3:ADP1001 2.3 282.8 1.0 O2A 3:ADP1001 2.5 282.8 1.0 O3A 3:ADP1001 2.6 282.8 1.0 CB 3:SER416 2.9 271.7 1.0 OG 3:SER416 3.6 271.7 1.0 O2B 3:ADP1001 3.8 282.8 1.0 O5' 3:ADP1001 3.9 282.8 1.0 N 3:SER416 3.9 271.7 1.0 CA 3:SER416 4.0 271.7 1.0 NH2 5:ARG651 4.4 288.0 1.0 OE2 5:GLU498 4.5 295.9 1.0 N 3:SER412 4.6 287.7 1.0 C5' 3:ADP1001 4.7 282.8 1.0 CA 3:SER412 4.7 287.7 1.0 N 3:GLN417 4.7 266.7 1.0 C 3:SER416 4.8 271.7 1.0 N 3:ALA414 4.9 267.6 1.0 CG 3:LYS415 4.9 269.1 1.0 CG 5:GLU498 5.0 295.9 1.0 OD2 3:ASP473 5.0 277.8 1.0

Magnesium binding site 3 out of 4 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 4:Mg1002 b:339.4 occ:1.00 O1B 4:AGS1001 1.8 310.6 1.0 O2A 4:AGS1001 1.8 310.6 1.0 O3G 4:AGS1001 1.9 310.6 1.0 CB 4:SER575 2.3 316.1 1.0 PA 4:AGS1001 2.4 310.6 1.0 O1A 4:AGS1001 2.4 310.6 1.0 PB 4:AGS1001 2.8 310.6 1.0 N 4:SER575 2.9 316.1 1.0 O3A 4:AGS1001 3.0 310.6 1.0 CA 4:SER575 3.1 316.1 1.0 PG 4:AGS1001 3.2 310.6 1.0 OG 4:SER575 3.5 316.1 1.0 O3B 4:AGS1001 3.5 310.6 1.0 OE1 7:GLU542 3.8 286.8 1.0 O5' 4:AGS1001 3.9 310.6 1.0 O2G 4:AGS1001 4.0 310.6 1.0 C 4:LYS574 4.1 302.0 1.0 O2B 4:AGS1001 4.2 310.6 1.0 OE2 7:GLU542 4.2 286.8 1.0 C 4:SER575 4.2 316.1 1.0 NH2 7:ARG593 4.3 285.0 1.0 CD 7:GLU542 4.3 286.8 1.0 N 4:LYS574 4.3 302.0 1.0 N 4:GLN576 4.4 296.8 1.0 C 4:SER573 4.6 299.0 1.0 CA 4:LYS574 4.6 302.0 1.0 S1G 4:AGS1001 4.7 310.6 1.0 CB 4:LYS574 4.7 302.0 1.0 C5' 4:AGS1001 4.9 310.6 1.0 CA 4:SER573 4.9 299.0 1.0

Magnesium binding site 4 out of 4 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 7:Mg901 b:306.3 occ:1.00 O3B 7:AGS902 1.9 285.8 1.0 O3A 7:AGS902 1.9 285.8 1.0 OG 7:SER467 2.0 287.6 1.0 CB 7:SER467 2.2 287.6 1.0 PB 7:AGS902 2.3 285.8 1.0 N 7:SER467 2.4 287.6 1.0 PG 7:AGS902 2.4 285.8 1.0 S1G 7:AGS902 2.4 285.8 1.0 CA 7:SER467 2.8 287.6 1.0 O3G 7:AGS902 3.1 285.8 1.0 PA 7:AGS902 3.2 285.8 1.0 O2B 7:AGS902 3.3 285.8 1.0 O1B 7:AGS902 3.4 285.8 1.0 O1A 7:AGS902 3.6 285.8 1.0 C 7:LYS466 3.6 279.1 1.0 O2G 7:AGS902 3.8 285.8 1.0 C 7:SER467 3.9 287.6 1.0 N 7:LYS466 3.9 279.1 1.0 N 7:GLN468 3.9 280.2 1.0 O2A 7:AGS902 3.9 285.8 1.0 CA 7:LYS466 4.2 279.1 1.0 CB 7:LYS466 4.3 279.1 1.0 O5' 7:AGS902 4.3 285.8 1.0 C 7:ALA465 4.4 271.2 1.0 OE1 3:GLN492 4.5 310.9 1.0 O 7:LYS466 4.7 279.1 1.0 NH2 3:ARG700 4.8 278.1 1.0 CA 7:ALA465 4.9 271.2 1.0 O 7:ALA465 4.9 271.2 1.0 O 7:SER467 5.0 287.6 1.0

Z.Xu, J.Feng, D.Yu, Y.Huo, X.Ma, W.H.Lam, Z.Liu, X.D.Li, T.Ishibashi, S.Dang, Y.Zhai. Synergism Between Cmg Helicase and Leading Strand Dna Polymerase at Replication Fork. Nat Commun V. 14 5849 2023.
ISSN: ESSN 2041-1723
PubMed: 37730685
DOI: 10.1038/S41467-023-41506-0