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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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 8w7m

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

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

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

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

Go back to Zinc Binding Sites List in 8w7m
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

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: Thu Dec 28 13:46:56 2023

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