Zinc 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:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Yeast Replisome in State V (pdb code 8w7m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Yeast Replisome in State V, PDB code: 8w7m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 2:Zn903 b:407.1 occ:1.00 SG 2:CYS364 2.3 327.7 1.0 SG 2:CYS367 2.3 331.7 1.0 SG 2:CYS344 2.3 328.6 1.0 SG 2:CYS341 2.3 326.8 1.0 CB 2:CYS341 3.1 326.8 1.0 CB 2:CYS364 3.2 327.7 1.0 CB 2:CYS367 3.4 331.7 1.0 N 2:CYS367 3.4 331.7 1.0 N 2:CYS344 3.6 328.6 1.0 O 2:CYS367 3.7 331.7 1.0 N 2:GLY345 3.8 319.2 1.0 CA 2:CYS367 3.8 331.7 1.0 CB 2:CYS344 3.9 328.6 1.0 CB 2:LYS343 4.0 322.4 1.0 CB 2:ASN366 4.2 317.9 1.0 CA 2:CYS344 4.2 328.6 1.0 C 2:CYS367 4.3 331.7 1.0 C 2:ASN366 4.3 317.9 1.0 CG 2:LYS343 4.5 322.4 1.0 CA 2:CYS341 4.5 326.8 1.0 C 2:CYS344 4.6 328.6 1.0 C 2:LYS343 4.6 322.4 1.0 CA 2:GLY345 4.6 319.2 1.0 CA 2:CYS364 4.7 327.7 1.0 CA 2:ASN366 4.7 317.9 1.0 CA 2:LYS343 4.7 322.4 1.0 N 2:ASN366 4.8 317.9 1.0 N 2:LYS343 4.9 322.4 1.0 C 2:CYS341 4.9 326.8 1.0

Zinc binding site 2 out of 5 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 4:Zn1003 b:418.6 occ:1.00 SG 4:CYS352 2.3 369.1 1.0 SG 4:CYS349 2.3 375.2 1.0 SG 4:CYS376 2.3 360.2 1.0 SG 4:CYS371 2.3 367.1 1.0 CB 4:CYS376 3.0 360.2 1.0 CB 4:CYS349 3.1 375.2 1.0 CB 4:CYS371 3.1 367.1 1.0 CB 4:CYS352 3.6 369.1 1.0 CG1 4:VAL351 3.8 357.3 1.0 CE 4:MET382 3.9 372.2 1.0 N 4:CYS352 3.9 369.1 1.0 CA 4:CYS352 4.3 369.1 1.0 CA 4:CYS376 4.4 360.2 1.0 CA 4:CYS349 4.5 375.2 1.0 CB 4:HIS354 4.5 356.7 1.0 CA 4:CYS371 4.5 367.1 1.0 CB 4:GLU378 4.6 359.7 1.0 N 4:GLU378 4.7 359.7 1.0 N 4:ASN377 4.7 357.8 1.0 C 4:CYS376 4.7 360.2 1.0 SD 4:MET382 4.7 372.2 1.0 NH1 4:ARG373 4.7 359.4 1.0 N 4:HIS354 4.8 356.7 1.0 C 4:CYS352 4.8 369.1 1.0 N 4:ASP353 4.9 365.0 1.0 OG 4:SER381 4.9 365.2 1.0 C 4:VAL351 5.0 357.3 1.0

Zinc binding site 3 out of 5 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 5:Zn1600 b:306.2 occ:1.00 SG 5:CYS186 2.3 253.4 1.0 SG 5:CYS183 2.3 243.3 1.0 SG 5:CYS211 2.3 256.6 1.0 SG 5:CYS236 2.3 265.2 1.0 CB 5:CYS236 3.2 265.2 1.0 CB 5:CYS186 3.3 253.4 1.0 CB 5:CYS211 3.6 256.6 1.0 CB 5:CYS183 3.8 243.3 1.0 N 5:CYS186 3.8 253.4 1.0 O 5:SER213 4.0 252.9 1.0 CA 5:CYS211 4.1 256.6 1.0 CA 5:CYS186 4.1 253.4 1.0 CG 5:PRO240 4.3 252.7 1.0 O 5:CYS211 4.5 256.6 1.0 CB 5:PRO240 4.5 252.7 1.0 C 5:CYS211 4.6 256.6 1.0 CA 5:CYS236 4.7 265.2 1.0 C 5:SER213 4.8 252.9 1.0 C 5:CYS186 4.9 253.4 1.0 N 5:ARG187 4.9 229.5 1.0 C 5:ASN185 4.9 240.3 1.0 CA 5:CYS183 5.0 243.3 1.0 N 5:ASN185 5.0 240.3 1.0

Zinc binding site 4 out of 5 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 6:Zn1600 b:319.7 occ:1.00 SG 6:CYS314 2.3 270.0 1.0 SG 6:CYS311 2.3 273.3 1.0 SG 6:CYS338 2.3 285.9 1.0 SG 6:CYS333 2.3 270.2 1.0 CB 6:CYS338 2.9 285.9 1.0 CB 6:CYS311 3.2 273.3 1.0 CB 6:CYS333 3.4 270.2 1.0 CB 6:CYS314 3.5 270.0 1.0 CB 6:ASN340 3.9 270.3 1.0 CB 6:ALA316 3.9 270.5 1.0 N 6:CYS314 4.1 270.0 1.0 CA 6:CYS314 4.3 270.0 1.0 CA 6:CYS338 4.4 285.9 1.0 N 6:ASN340 4.5 270.3 1.0 N 6:ALA316 4.6 270.5 1.0 CH2 6:TRP344 4.6 263.0 1.0 CA 6:CYS311 4.7 273.3 1.0 CA 6:CYS333 4.8 270.2 1.0 CB 6:ASN335 4.8 287.9 1.0 C 6:CYS338 4.8 285.9 1.0 ND2 6:ASN340 4.8 270.3 1.0 CG 6:ASN340 4.8 270.3 1.0 ND2 6:ASN335 4.8 287.9 1.0 CA 6:ASN340 4.8 270.3 1.0 CA 6:ALA316 4.9 270.5 1.0 C 6:CYS314 4.9 270.0 1.0 N 6:GLU339 4.9 275.4 1.0

Zinc binding site 5 out of 5 in the Yeast Replisome in State V


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Yeast Replisome in State V within 5.0Å range: probe atom residue distance (Å) B Occ 7:Zn903 b:419.4 occ:1.00 SG 7:CYS284 2.3 375.9 1.0 SG 7:CYS265 2.3 387.8 1.0 SG 7:CYS289 2.3 384.2 1.0 SG 7:CYS262 2.3 393.2 1.0 CB 7:CYS262 2.7 393.2 1.0 CB 7:CYS265 3.1 387.8 1.0 N 7:CYS265 3.2 387.8 1.0 CB 7:CYS284 3.4 375.9 1.0 OG 7:SER286 3.7 371.6 1.0 CA 7:CYS265 3.7 387.8 1.0 CA 7:GLY296 3.8 381.2 1.0 CB 7:CYS289 3.9 384.2 1.0 CA 7:CYS262 3.9 393.2 1.0 O 7:CYS262 4.0 393.2 1.0 C 7:CYS262 4.1 393.2 1.0 CB 7:GLN264 4.2 381.0 1.0 C 7:GLN264 4.2 381.0 1.0 N 7:GLN264 4.4 381.0 1.0 CA 7:GLN264 4.5 381.0 1.0 C 7:GLY296 4.6 381.2 1.0 N 7:CYS262 4.7 393.2 1.0 N 7:GLY296 4.7 381.2 1.0 CA 7:CYS284 4.8 375.9 1.0 C 7:CYS265 4.8 387.8 1.0 N 7:GLY266 4.8 377.3 1.0 N 7:GLN297 4.9 387.1 1.0 CD2 7:LEU298 4.9 375.3 1.0 N 7:ASP263 4.9 394.6 1.0 CB 7:SER286 5.0 371.6 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