Zinc in PDB 8p62: S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation

Enzymatic activity of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation

All present enzymatic activity of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation:
2.7.7.7; 3.6.4.12;

Other elements in 8p62:

The structure of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation (pdb code 8p62). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation, PDB code: 8p62:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 1 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Zn902

b:303.6
occ:1.00
 CB 2:CYS367 1.8 297.8 1.0
SG 2:CYS367 2.3 297.8 1.0
SG 2:CYS344 2.3 270.0 1.0
CB 2:CYS344 2.8 270.0 1.0
CA 2:CYS367 3.1 297.8 1.0
OG 2:SER346 3.4 247.8 1.0
N 2:CYS367 3.5 297.8 1.0
OD1 2:ASN366 3.8 296.9 1.0
NZ 2:LYS343 4.1 273.0 1.0
C 2:CYS367 4.3 297.8 1.0
CA 2:CYS344 4.3 270.0 1.0
CB 2:SER346 4.7 247.8 1.0
O 2:CYS344 4.8 270.0 1.0
C 2:ASN366 4.8 296.9 1.0
O 2:CYS364 4.9 285.1 1.0
O 2:CYS367 4.9 297.8 1.0
C 2:CYS344 4.9 270.0 1.0

Zinc binding site 2 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 2 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Zn1002

b:201.1
occ:1.00
 SG 4:CYS349 2.3 152.2 1.0
SG 4:CYS376 2.3 175.3 1.0
SG 4:CYS352 2.3 157.3 1.0
CB 4:CYS352 3.4 157.3 1.0
CB 4:CYS349 3.6 152.2 1.0
SG 4:CYS371 3.6 172.5 1.0
CB 4:CYS376 3.7 175.3 1.0
CB 4:CYS371 4.0 172.5 1.0
N 4:CYS352 4.1 157.3 1.0
CA 4:CYS352 4.4 157.3 1.0
OG 4:SER381 4.4 157.8 1.0
CB 4:ARG373 4.6 170.5 1.0
O 4:CYS349 4.8 152.2 1.0
CD 4:ARG373 4.8 170.5 1.0
O 4:ARG373 4.9 170.5 1.0
CA 4:CYS349 4.9 152.2 1.0
CB 4:VAL351 4.9 154.5 1.0
CA 4:CYS376 5.0 175.3 1.0

Zinc binding site 3 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 3 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
5:Zn1702

b:195.9
occ:1.00
 CB 5:CYS186 2.2 144.2 1.0
SG 5:CYS211 2.3 171.3 1.0
SG 5:CYS186 2.3 144.2 1.0
CB 5:CYS211 3.6 171.3 1.0
CA 5:CYS186 3.7 144.2 1.0
SG 5:CYS236 4.0 167.4 1.0
ND1 5:HIS188 4.1 139.0 1.0
O 5:LEU212 4.1 164.2 1.0
CE1 5:HIS188 4.4 139.0 1.0
N 5:CYS186 4.4 144.2 1.0
C 5:CYS186 4.5 144.2 1.0
N 5:LEU212 4.7 164.2 1.0
N 5:LYS234 4.9 162.3 1.0
CA 5:CYS211 4.9 171.3 1.0
C 5:LEU212 5.0 164.2 1.0

Zinc binding site 4 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 4 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
6:Zn1102

b:178.2
occ:1.00
 SG 6:CYS333 2.3 132.0 1.0
SG 6:CYS311 2.3 140.5 1.0
SG 6:CYS338 2.3 147.7 1.0
SG 6:CYS314 2.3 139.9 1.0
CB 6:CYS333 3.0 132.0 1.0
CB 6:CYS338 3.1 147.7 1.0
CB 6:CYS311 3.2 140.5 1.0
SD 6:MET313 3.6 144.6 1.0
CB 6:CYS314 3.7 139.9 1.0
CB 6:ALA316 4.5 131.6 1.0
O 6:CYS311 4.5 140.5 1.0
CA 6:CYS333 4.5 132.0 1.0
CA 6:CYS311 4.5 140.5 1.0
CA 6:CYS338 4.5 147.7 1.0
CE 6:MET313 4.6 144.6 1.0
CB 6:ASN335 4.6 137.8 1.0
N 6:ASN340 4.7 139.3 1.0
N 6:CYS314 4.7 139.9 1.0
CA 6:CYS314 4.8 139.9 1.0
C 6:CYS311 4.8 140.5 1.0
CA 6:ASN340 4.8 139.3 1.0
CG 6:MET313 4.9 144.6 1.0
CB 6:ASN340 5.0 139.3 1.0
C 6:CYS338 5.0 147.7 1.0

Zinc binding site 5 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 5 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
7:Zn903

b:198.6
occ:1.00
 O 7:LYS295 2.1 211.1 1.0
SG 7:CYS289 2.3 214.2 1.0
SG 7:CYS265 2.3 183.2 1.0
O 7:CYS262 2.5 182.2 1.0
CB 7:CYS265 2.9 183.2 1.0
C 7:LYS295 3.3 211.1 1.0
SG 7:CYS262 3.5 182.2 1.0
C 7:CYS262 3.7 182.2 1.0
O 7:GLY296 3.8 194.8 1.0
CB 7:CYS289 4.0 214.2 1.0
CA 7:GLY296 4.1 194.8 1.0
O 7:ASP263 4.1 178.9 1.0
N 7:GLY296 4.2 194.8 1.0
CB 7:LYS295 4.2 211.1 1.0
CG 7:LYS295 4.2 211.1 1.0
CB 7:ASP263 4.3 178.9 1.0
CA 7:CYS265 4.3 183.2 1.0
C 7:GLY296 4.3 194.8 1.0
CA 7:LYS295 4.3 211.1 1.0
CA 7:CYS262 4.5 182.2 1.0
CB 7:CYS262 4.5 182.2 1.0
N 7:CYS265 4.6 183.2 1.0
SG 7:CYS284 4.6 190.6 1.0
C 7:ASP263 4.6 178.9 1.0
N 7:ASP263 4.6 178.9 1.0
CA 7:ASP263 4.7 178.9 1.0
CA 7:CYS289 4.9 214.2 1.0

Zinc binding site 6 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 6 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn4001

b:172.5
occ:1.00
 SG G:CYS2133 2.3 138.3 1.0
SG G:CYS2111 2.3 141.3 1.0
SG G:CYS2108 2.3 139.3 1.0
SG G:CYS2130 2.3 141.1 1.0
CB G:CYS2130 2.9 141.1 1.0
CB G:CYS2108 3.5 139.3 1.0
CB G:CYS2133 3.5 138.3 1.0
CB G:CYS2111 3.6 141.3 1.0
N G:CYS2133 4.0 138.3 1.0
CA G:CYS2133 4.2 138.3 1.0
N G:CYS2111 4.3 141.3 1.0
O G:CYS2133 4.3 138.3 1.0
CA G:CYS2130 4.4 141.1 1.0
CB G:TYR2110 4.5 146.3 1.0
CA G:CYS2111 4.6 141.3 1.0
C G:CYS2133 4.6 138.3 1.0
C G:TYR2110 4.7 146.3 1.0
CA G:CYS2108 4.8 139.3 1.0
CB G:PHE2113 4.9 127.5 1.0
CD2 G:TYR2110 5.0 146.3 1.0

Zinc binding site 7 out of 7 in 8p62

Go back to Zinc Binding Sites List in 8p62
Zinc binding site 7 out of 7 in the S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of S. Cerevisiae Ssdna-Scmge After Dna Replication Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn4002

b:130.6
occ:1.00
 SG G:CYS2167 2.3 109.4 1.0
SG G:CYS2179 2.3 105.0 1.0
SG G:CYS2164 2.3 99.9 1.0
CB G:CYS2179 2.9 105.0 1.0
CB G:CYS2164 3.3 99.9 1.0
O G:ALA2182 3.4 109.4 1.0
NZ G:LYS2169 3.7 101.8 1.0
CB G:CYS2167 3.8 109.4 1.0
N G:CYS2167 4.0 109.4 1.0
CB G:CYS2181 4.1 115.7 1.0
O G:CYS2167 4.3 109.4 1.0
CA G:CYS2179 4.4 105.0 1.0
CA G:CYS2167 4.4 109.4 1.0
C G:ALA2182 4.5 109.4 1.0
C G:CYS2181 4.6 115.7 1.0
N G:CYS2181 4.7 115.7 1.0
C G:CYS2167 4.7 109.4 1.0
CA G:CYS2181 4.7 115.7 1.0
O G:CYS2181 4.7 115.7 1.0
CA G:CYS2164 4.8 99.9 1.0
SG G:CYS2181 4.9 115.7 1.0
N G:ARG2166 4.9 101.9 1.0
N G:ALA2182 4.9 109.4 1.0

Reference:

S.S.Henrikus, M.H.Gross, O.Willhoft, T.Puhringer, J.S.Lewis, A.W.Mcclure, J.F.Greiwe, G.Palm, A.Nans, J.F.X.Diffley, A.Costa. Unwinding of A Eukaryotic Origin of Replication Visualized By Cryo-Em. Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
PubMed: 38760633
DOI: 10.1038/S41594-024-01280-Z
Page generated: Thu Oct 31 09:06:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy