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Zinc in PDB 8kg9: Yeast Replisome in State III

Enzymatic activity of Yeast Replisome in State III

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

Other elements in 8kg9:

The structure of Yeast Replisome in State III 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 III (pdb code 8kg9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Yeast Replisome in State III, PDB code: 8kg9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8kg9

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Zinc binding site 1 out of 7 in the Yeast Replisome in State III


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 III within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Zn901

b:446.8
occ:1.00
 CB 2:CYS344 2.1 359.8 1.0
SG 2:CYS367 2.3 426.6 1.0
SG 2:CYS364 2.3 432.5 1.0
SG 2:CYS341 2.3 361.2 1.0
SG 2:CYS344 2.3 359.8 1.0
CB 2:CYS367 2.6 426.6 1.0
CB 2:CYS364 2.9 432.5 1.0
N 2:CYS367 3.2 426.6 1.0
CA 2:CYS344 3.4 359.8 1.0
CA 2:CYS367 3.5 426.6 1.0
N 2:CYS344 3.6 359.8 1.0
CB 2:CYS341 3.7 361.2 1.0
CG 2:LYS343 4.1 339.2 1.0
N 2:GLY345 4.2 356.7 1.0
C 2:ASN366 4.2 442.2 1.0
C 2:CYS344 4.3 359.8 1.0
O 2:CYS367 4.3 426.6 1.0
CE 2:LYS343 4.3 339.2 1.0
C 2:CYS367 4.4 426.6 1.0
CA 2:CYS364 4.4 432.5 1.0
CB 2:ASN366 4.4 442.2 1.0
CA 2:ASN366 4.7 442.2 1.0
N 2:ASN366 4.7 442.2 1.0
C 2:LYS343 4.8 339.2 1.0
CD 2:LYS343 4.8 339.2 1.0
OD1 2:ASN366 4.9 442.2 1.0
C 2:CYS364 5.0 432.5 1.0
CA 2:CYS341 5.0 361.2 1.0

Zinc binding site 2 out of 7 in 8kg9

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Zinc binding site 2 out of 7 in the Yeast Replisome in State III


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 III within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn1400

b:824.9
occ:1.00
 SG 4:CYS371 2.3 756.3 1.0
SG 4:CYS376 2.3 753.0 1.0
SG 4:CYS349 2.3 753.8 1.0
SG 4:CYS352 2.3 722.6 1.0
CB 4:CYS349 2.9 753.8 1.0
CB 4:CYS371 3.2 756.3 1.0
CB 4:CYS352 3.2 722.6 1.0
CB 4:CYS376 3.3 753.0 1.0
N 4:CYS376 3.6 753.0 1.0
CE 4:MET382 3.7 782.8 1.0
CA 4:CYS376 4.0 753.0 1.0
CA 4:CYS349 4.1 753.8 1.0
CB 4:HIS354 4.2 731.6 1.0
CA 4:CYS371 4.3 756.3 1.0
N 4:HIS354 4.6 731.6 1.0
CB 4:ASP375 4.7 749.7 1.0
C 4:ASP375 4.7 749.7 1.0
CA 4:CYS352 4.7 722.6 1.0
OE1 4:GLU372 4.7 756.3 1.0
N 4:ASP375 4.8 749.7 1.0
OE2 4:GLU372 4.8 756.3 1.0
C 4:CYS349 4.9 753.8 1.0
CA 4:HIS354 4.9 731.6 1.0
N 4:ASP353 4.9 690.4 1.0
N 4:ASN377 4.9 751.6 1.0
O 4:SER381 4.9 756.8 1.0
CA 4:ASP375 5.0 749.7 1.0
C 4:CYS376 5.0 753.0 1.0
SD 4:MET382 5.0 782.8 1.0
O 4:ASN350 5.0 741.8 1.0
CD 4:GLU372 5.0 756.3 1.0

Zinc binding site 3 out of 7 in 8kg9

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Zinc binding site 3 out of 7 in the Yeast Replisome in State III


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 III within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Zn802

b:408.3
occ:1.00
 CB 5:CYS186 2.1 313.6 1.0
SG 5:CYS211 2.3 293.9 1.0
SG 5:CYS186 2.3 313.6 1.0
SG 5:CYS236 2.3 331.3 1.0
SG 5:CYS183 2.3 293.2 1.0
CB 5:CYS211 3.1 293.9 1.0
CB 5:CYS236 3.3 331.3 1.0
CA 5:CYS211 3.5 293.9 1.0
CB 5:CYS183 3.6 293.2 1.0
CA 5:CYS186 3.6 313.6 1.0
O 5:CYS211 3.7 293.9 1.0
O 5:SER213 3.8 271.7 1.0
C 5:CYS211 4.0 293.9 1.0
N 5:CYS186 4.2 313.6 1.0
O 5:CYS183 4.3 293.2 1.0
C 5:CYS186 4.5 313.6 1.0
CB 5:HIS188 4.6 291.0 1.0
C 5:SER213 4.7 271.7 1.0
CA 5:CYS236 4.8 331.3 1.0
OD1 5:ASN185 4.8 309.9 1.0
N 5:CYS211 4.8 293.9 1.0
CA 5:CYS183 4.8 293.2 1.0
O 5:CYS186 4.9 313.6 1.0

Zinc binding site 4 out of 7 in 8kg9

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Zinc binding site 4 out of 7 in the Yeast Replisome in State III


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 III within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn1400

b:521.9
occ:1.00
 ND2 6:ASN340 2.1 510.7 1.0
O 6:CYS338 2.2 520.3 1.0
SG 6:CYS333 2.3 484.7 1.0
SG 6:CYS338 2.3 520.3 1.0
CB 6:CYS314 2.6 439.7 1.0
CB 6:CYS333 3.0 484.7 1.0
CB 6:CYS338 3.1 520.3 1.0
N 6:CYS314 3.1 439.7 1.0
CA 6:CYS314 3.2 439.7 1.0
C 6:CYS338 3.2 520.3 1.0
CG 6:ASN340 3.3 510.7 1.0
SG 6:CYS314 3.6 439.7 1.0
C 6:MET313 3.7 425.5 1.0
CA 6:CYS338 3.7 520.3 1.0
CG 6:MET313 3.8 425.5 1.0
O 6:MET313 4.0 425.5 1.0
OD1 6:ASN340 4.0 510.7 1.0
CB 6:ASN340 4.1 510.7 1.0
N 6:GLU339 4.4 541.5 1.0
CA 6:CYS333 4.5 484.7 1.0
O 6:SER337 4.5 498.8 1.0
N 6:ASN340 4.6 510.7 1.0
CA 6:MET313 4.6 425.5 1.0
C 6:CYS314 4.7 439.7 1.0
CB 6:MET313 4.7 425.5 1.0
O 6:CYS311 4.7 392.6 1.0
CA 6:GLU339 4.8 541.5 1.0
CE 6:MET313 4.8 425.5 1.0
C 6:GLU339 4.8 541.5 1.0
N 6:CYS338 5.0 520.3 1.0

Zinc binding site 5 out of 7 in 8kg9

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Zinc binding site 5 out of 7 in the Yeast Replisome in State III


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 III within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Zn901

b:676.5
occ:1.00
 SG 7:CYS265 2.3 624.9 1.0
SG 7:CYS284 2.3 625.9 1.0
SG 7:CYS262 2.3 646.0 1.0
SG 7:CYS289 2.3 570.5 1.0
CB 7:CYS265 2.9 624.9 1.0
CB 7:CYS262 2.9 646.0 1.0
CB 7:CYS289 3.4 570.5 1.0
CB 7:CYS284 3.6 625.9 1.0
CA 7:GLY296 3.9 625.3 1.0
N 7:CYS265 3.9 624.9 1.0
CB 7:SER286 3.9 573.8 1.0
CA 7:CYS265 4.0 624.9 1.0
NE2 7:GLN264 4.3 591.8 1.0
CD2 7:LEU298 4.4 670.6 1.0
CA 7:CYS262 4.4 646.0 1.0
C 7:GLY296 4.5 625.3 1.0
OG 7:SER286 4.6 573.8 1.0
CD 7:GLN264 4.6 591.8 1.0
OE2 7:GLU288 4.6 567.8 1.0
CG 7:GLN264 4.7 591.8 1.0
CA 7:CYS289 4.8 570.5 1.0
N 7:GLY266 4.8 634.8 1.0
CA 7:CYS284 4.9 625.9 1.0
C 7:CYS265 4.9 624.9 1.0
C 7:CYS262 4.9 646.0 1.0
OD1 7:ASP263 4.9 608.2 1.0
N 7:GLN297 5.0 647.6 1.0

Zinc binding site 6 out of 7 in 8kg9

Go back to Zinc Binding Sites List in 8kg9
Zinc binding site 6 out of 7 in the Yeast Replisome in State III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Yeast Replisome in State III within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn3000

b:1000.0
occ:1.00
 CB M:CYS2181 1.7 889.3 1.0
SG M:CYS2164 2.3 903.1 1.0
SG M:CYS2167 2.3 961.3 1.0
SG M:CYS2179 2.4 879.6 1.0
SG M:CYS2181 2.4 889.3 1.0
CB M:CYS2167 3.1 961.3 1.0
CA M:CYS2181 3.1 889.3 1.0
CB M:CYS2164 3.2 903.1 1.0
CB M:CYS2179 3.4 879.6 1.0
N M:CYS2167 3.6 961.3 1.0
N M:CYS2181 3.6 889.3 1.0
NZ M:LYS2169 3.8 950.7 1.0
C M:CYS2181 3.8 889.3 1.0
CA M:CYS2167 3.9 961.3 1.0
O M:GLY2183 3.9 877.6 1.0
N M:HIS2168 4.3 932.3 1.0
O M:CYS2181 4.3 889.3 1.0
N M:ALA2182 4.4 806.5 1.0
N M:GLY2183 4.4 877.6 1.0
C M:CYS2167 4.5 961.3 1.0
CA M:CYS2164 4.6 903.1 1.0
C M:GLY2183 4.6 877.6 1.0
N M:ARG2166 4.7 907.4 1.0
C M:ARG2166 4.7 907.4 1.0
CA M:GLY2183 4.7 877.6 1.0
CA M:CYS2179 4.8 879.6 1.0
N M:SER2165 4.9 907.4 1.0
CE M:LYS2169 4.9 950.7 1.0
C M:PRO2180 4.9 901.1 1.0
N M:LYS2169 4.9 950.7 1.0

Zinc binding site 7 out of 7 in 8kg9

Go back to Zinc Binding Sites List in 8kg9
Zinc binding site 7 out of 7 in the Yeast Replisome in State III


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Yeast Replisome in State III within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn3001

b:1000.0
occ:1.00
 SG M:CYS2130 2.3 1000.0 1.0
SG M:CYS2133 2.3 1000.0 1.0
SG M:CYS2108 2.3 1000.0 1.0
SG M:CYS2111 2.3 1000.0 1.0
CB M:CYS2108 2.5 1000.0 1.0
CB M:CYS2111 2.6 1000.0 1.0
N M:CYS2111 3.6 1000.0 1.0
CA M:CYS2111 3.7 1000.0 1.0
CB M:CYS2133 3.9 1000.0 1.0
CB M:CYS2130 3.9 1000.0 1.0
CA M:CYS2108 4.0 1000.0 1.0
O M:LYS2135 4.2 1000.0 1.0
O M:CYS2133 4.2 1000.0 1.0
N M:CYS2133 4.2 1000.0 1.0
CB M:LYS2135 4.4 1000.0 1.0
O M:CYS2108 4.4 1000.0 1.0
C M:CYS2108 4.4 1000.0 1.0
CA M:CYS2133 4.4 1000.0 1.0
C M:CYS2133 4.6 1000.0 1.0
C M:CYS2111 4.7 1000.0 1.0
C M:TYR2110 4.8 1000.0 1.0
N M:CYS2108 4.8 1000.0 1.0
C M:LYS2135 4.9 1000.0 1.0
N M:LYS2135 5.0 1000.0 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 Oct 31 08:43:19 2024

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