Zinc in PDB 8g99: Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase

Enzymatic activity of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase

All present enzymatic activity of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase:
2.7.7.7;

Other elements in 8g99:

The structure of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g99). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g99:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 8g99

Go back to Zinc Binding Sites List in 8g99
Zinc binding site 1 out of 2 in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1500

b:103.0
occ:1.00
SG A:CYS1283 2.2 63.5 1.0
SG A:CYS1312 2.3 90.9 1.0
SG A:CYS1307 2.3 75.1 1.0
SG A:CYS1280 2.3 79.9 1.0
HB2 A:CYS1280 2.9 64.6 1.0
HB3 A:CYS1280 2.9 65.1 1.0
CB A:CYS1280 3.0 65.9 1.0
HB2 A:CYS1307 3.1 61.5 1.0
HB3 A:CYS1312 3.2 74.3 1.0
CB A:CYS1312 3.2 76.5 1.0
CB A:CYS1307 3.2 59.7 1.0
H A:CYS1283 3.3 63.3 1.0
HB2 A:CYS1312 3.3 74.7 1.0
HB3 A:CYS1283 3.4 63.2 1.0
HB3 A:ALA1314 3.4 67.8 1.0
HB3 A:CYS1307 3.4 61.0 1.0
CB A:CYS1283 3.5 63.2 1.0
HG22 A:THR1285 3.6 60.8 1.0
HG21 A:THR1285 4.0 60.5 1.0
HB3 A:LYS1309 4.0 69.4 1.0
HB3 A:LYS1282 4.0 67.2 1.0
N A:CYS1283 4.0 59.5 1.0
HB2 A:CYS1283 4.2 63.0 1.0
CG2 A:THR1285 4.2 62.3 1.0
CB A:ALA1314 4.3 67.7 1.0
H A:THR1285 4.3 61.0 1.0
CA A:CYS1283 4.3 61.5 1.0
H A:ALA1314 4.4 69.1 1.0
CA A:CYS1280 4.5 63.9 1.0
H A:LYS1309 4.5 69.2 1.0
HD21 A:ASN1287 4.5 54.2 1.0
H A:GLY1284 4.5 62.5 1.0
HB2 A:ALA1314 4.6 68.2 1.0
CA A:CYS1307 4.6 54.5 1.0
CA A:CYS1312 4.6 73.3 1.0
HB2 A:LYS1309 4.7 69.5 1.0
H A:LYS1282 4.7 67.3 1.0
HA A:CYS1280 4.7 64.1 1.0
HA A:CYS1307 4.8 61.0 1.0
CB A:LYS1309 4.8 70.2 1.0
HD3 A:LYS1309 4.8 69.5 1.0
HB1 A:ALA1314 4.8 67.9 1.0
HG23 A:THR1285 4.8 60.6 1.0
O A:ALA1314 4.9 67.4 1.0
HA A:CYS1312 5.0 74.8 1.0
N A:GLY1284 5.0 61.0 1.0
CB A:LYS1282 5.0 66.6 1.0

Zinc binding site 2 out of 2 in 8g99

Go back to Zinc Binding Sites List in 8g99
Zinc binding site 2 out of 2 in the Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Partial Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:83.8
occ:1.00
SG A:CYS1371 2.3 49.4 1.0
SG A:CYS1368 2.3 43.0 1.0
SG A:CYS1350 2.3 35.9 1.0
SG A:CYS1345 2.3 46.6 1.0
HB3 A:CYS1368 2.9 33.9 1.0
HB2 A:CYS1345 3.0 35.8 1.0
CB A:CYS1368 3.1 34.7 1.0
HB3 A:CYS1350 3.1 40.6 1.0
CB A:CYS1345 3.2 30.9 1.0
H A:CYS1371 3.2 40.5 1.0
CB A:CYS1350 3.2 39.5 1.0
HB2 A:CYS1368 3.3 34.0 1.0
HB2 A:CYS1350 3.4 40.8 1.0
HB3 A:CYS1345 3.5 35.1 1.0
HB3 A:ALA1370 3.5 35.1 1.0
HB3 A:ALA1374 3.5 36.8 1.0
HB3 A:CYS1371 3.5 41.5 1.0
CB A:CYS1371 3.5 43.0 1.0
HB3 A:ASN1352 3.8 36.5 1.0
N A:CYS1371 3.9 36.5 1.0
H A:ASN1352 4.0 37.9 1.0
HB2 A:ASN1352 4.0 36.9 1.0
HB3 A:GLU1347 4.1 42.1 1.0
HB2 A:CYS1371 4.3 41.2 1.0
H A:ALA1370 4.3 35.3 1.0
CA A:CYS1371 4.3 38.1 1.0
CB A:ASN1352 4.4 34.1 1.0
CB A:ALA1370 4.4 31.9 1.0
CB A:ALA1374 4.5 39.1 1.0
CA A:CYS1368 4.5 31.3 1.0
H A:SER1372 4.6 38.3 1.0
CA A:CYS1345 4.6 23.4 1.0
CA A:CYS1350 4.6 41.4 1.0
HA A:CYS1345 4.7 34.5 1.0
H A:ALA1374 4.7 36.3 1.0
HB1 A:ALA1374 4.8 36.6 1.0
H A:GLN1351 4.8 41.6 1.0
C A:ALA1370 4.8 34.7 1.0
N A:ASN1352 4.8 34.3 1.0
H A:GLU1347 4.8 42.3 1.0
C A:CYS1368 4.8 28.4 1.0
HB1 A:ALA1370 4.9 35.4 1.0
H A:LYS1373 4.9 39.9 1.0
O A:CYS1368 4.9 38.7 1.0
N A:ALA1370 4.9 36.0 1.0
HB2 A:ALA1374 4.9 36.2 1.0
CB A:GLU1347 4.9 39.3 1.0
HB2 A:GLU1347 5.0 42.1 1.0
HB2 A:ALA1370 5.0 35.0 1.0
CA A:ALA1370 5.0 32.3 1.0
C A:CYS1350 5.0 40.8 1.0
HA A:CYS1368 5.0 33.8 1.0
N A:GLN1351 5.0 39.1 1.0

Reference:

E.A.Mullins, L.E.Salay, C.L.Durie, J.E.Jackman, M.D.Ohi, W.J.Chazin, B.F.Eichman. A Mechanistic Model of Primer Synthesis From Catalytic Structures of Dna Polymerase Alpha-Primase. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 36993335
DOI: 10.1101/2023.03.16.533013
Page generated: Wed Apr 26 00:45:17 2023

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