Magnesium in PDB 8kg9: Yeast Replisome in State III

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

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

Zinc

(Zn)

7 atoms

The binding sites of Magnesium atom in the Yeast Replisome in State III (pdb code 8kg9). 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 III, PDB code: 8kg9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

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


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 III within 5.0Å range: probe atom residue distance (Å) B Occ 2:Mg903 b:475.8 occ:1.00 O1A 2:ADP902 2.1 432.6 1.0 O3B 2:ADP902 2.5 432.6 1.0 CB 2:SER550 2.6 465.4 1.0 N 2:SER550 2.6 465.4 1.0 O2A 2:ADP902 2.7 432.6 1.0 PA 2:ADP902 2.7 432.6 1.0 CA 2:SER550 3.1 465.4 1.0 O3A 2:ADP902 3.4 432.6 1.0 PB 2:ADP902 3.6 432.6 1.0 C 2:LYS549 3.7 437.8 1.0 OD1 2:ASP607 3.7 492.7 1.0 OG 2:SER550 3.9 465.4 1.0 CB 2:LYS549 3.9 437.8 1.0 N 2:LYS549 4.1 437.8 1.0 CA 2:LYS549 4.1 437.8 1.0 OE1 6:GLU657 4.2 601.6 1.0 O5' 2:ADP902 4.2 432.6 1.0 C 2:SER550 4.4 465.4 1.0 OD2 2:ASP607 4.4 492.7 1.0 NH2 6:ARG798 4.4 553.9 1.0 CG 2:ASP607 4.5 492.7 1.0 CE 2:LYS549 4.5 437.8 1.0 O2B 2:ADP902 4.6 432.6 1.0 O1B 2:ADP902 4.6 432.6 1.0 N 2:GLN551 4.6 469.9 1.0 CD 6:GLU657 4.7 601.6 1.0 NE2 6:GLN658 4.7 609.3 1.0 O 2:LYS549 4.8 437.8 1.0 C 2:ALA548 4.8 406.5 1.0 OE2 6:GLU657 5.0 601.6 1.0 CG 2:LYS549 5.0 437.8 1.0

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


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 III within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg801 b:671.9 occ:1.00 NH2 5:ARG549 2.1 732.3 1.0 OG 3:SER416 2.1 543.5 1.0 NH1 5:ARG549 2.3 732.3 1.0 CZ 5:ARG549 2.3 732.3 1.0 O2B 3:ADP1001 2.8 596.9 1.0 NE 5:ARG549 3.4 732.3 1.0 CB 3:SER416 3.4 543.5 1.0 OE2 3:GLU474 3.6 518.4 1.0 OD2 3:ASP473 3.8 494.9 1.0 NZ 3:LYS415 3.8 557.4 1.0 PB 3:ADP1001 3.8 596.9 1.0 O1B 3:ADP1001 3.9 596.9 1.0 O1A 3:ADP1001 4.1 596.9 1.0 O3A 3:ADP1001 4.4 596.9 1.0 OD1 3:ASP473 4.4 494.9 1.0 CD 5:ARG549 4.4 732.3 1.0 CA 3:SER416 4.4 543.5 1.0 CG 3:ASP473 4.5 494.9 1.0 N 3:SER416 4.6 543.5 1.0 CD 3:GLU474 4.6 518.4 1.0 PA 3:ADP1001 4.7 596.9 1.0 CG 3:GLU474 4.9 518.4 1.0 OD1 3:ASN517 4.9 565.6 1.0 CD 3:LYS415 4.9 557.4 1.0 CE 3:LYS415 4.9 557.4 1.0

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


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 III within 5.0Å range: probe atom residue distance (Å) B Occ 5:Mg804 b:624.3 occ:1.00 OG 5:SER423 2.0 479.9 1.0 O3G 5:AGS803 2.1 456.1 1.0 OD1 5:ASP480 2.7 631.7 1.0 OD2 5:ASP480 3.1 631.7 1.0 CG 5:ASP480 3.3 631.7 1.0 CB 5:SER423 3.3 479.9 1.0 O1B 5:AGS803 3.5 456.1 1.0 PG 5:AGS803 3.6 456.1 1.0 O2G 5:AGS803 4.1 456.1 1.0 O3B 5:AGS803 4.3 456.1 1.0 PB 5:AGS803 4.3 456.1 1.0 CA 5:SER423 4.4 479.9 1.0 O3A 5:AGS803 4.4 456.1 1.0 N 5:SER423 4.6 479.9 1.0 ND2 5:ASN524 4.7 720.3 1.0 N 5:GLU481 4.7 635.5 1.0 CB 5:ASP480 4.7 631.7 1.0 CB 5:ALA522 4.9 731.0 1.0 S1G 5:AGS803 4.9 456.1 1.0

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


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 III within 5.0Å range: probe atom residue distance (Å) B Occ 7:Mg902 b:495.3 occ:1.00 O 7:LYS466 2.4 381.7 1.0 OG 7:SER467 2.6 403.8 1.0 CA 7:SER467 2.8 403.8 1.0 CB 7:SER467 2.9 403.8 1.0 CD2 7:LEU470 3.1 383.5 1.0 C 7:LYS466 3.2 381.7 1.0 N 7:SER467 3.3 403.8 1.0 OD1 7:ASP524 3.3 443.6 1.0 OH 7:TYR482 3.6 410.6 1.0 CB 7:LEU470 3.8 383.5 1.0 CG 7:ASP524 4.0 443.6 1.0 CG 7:LEU470 4.1 383.5 1.0 CE1 7:TYR482 4.1 410.6 1.0 C 7:SER467 4.1 403.8 1.0 CB 7:ALA566 4.3 417.5 1.0 CZ 7:TYR482 4.3 410.6 1.0 O2B 7:AGS903 4.4 404.5 1.0 O 7:SER467 4.5 403.8 1.0 CA 7:LYS466 4.6 381.7 1.0 OD2 7:ASP524 4.6 443.6 1.0 CA 7:ASP524 4.6 443.6 1.0 CB 7:ASP524 4.6 443.6 1.0 CB 7:LYS466 4.8 381.7 1.0 O 7:ILE523 4.9 433.8 1.0 N 7:GLU525 4.9 463.2 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