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

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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

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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

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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

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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

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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

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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

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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

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