Magnesium in PDB 8w7m: Yeast Replisome in State V

Enzymatic activity of Yeast Replisome in State V

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

Other elements in 8w7m:

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

Zinc (Zn) 5 atoms

Magnesium Binding Sites:

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 8w7m

Go back to Magnesium Binding Sites List in 8w7m
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 8w7m

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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 8w7m

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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 8w7m

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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

Reference:

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
Page generated: Fri Oct 4 22:39:08 2024

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