Zinc in PDB 8g9f: Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase

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

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

Other elements in 8g9f:

The structure of Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8g9f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8g9f:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8g9f

Go back to Zinc Binding Sites List in 8g9f
Zinc binding site 1 out of 3 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1500

b:175.8
occ:1.00
SG A:CYS1283 2.3 79.6 1.0
SG A:CYS1307 2.3 111.1 1.0
SG A:CYS1312 2.3 108.2 1.0
SG A:CYS1280 2.3 115.6 1.0
HB3 A:CYS1280 2.9 95.3 1.0
HB2 A:CYS1280 2.9 94.5 1.0
CB A:CYS1280 3.0 98.1 1.0
HB2 A:CYS1307 3.1 90.8 1.0
CB A:CYS1307 3.2 89.6 1.0
HB3 A:CYS1312 3.2 102.5 1.0
CB A:CYS1312 3.2 105.5 1.0
H A:CYS1283 3.3 83.8 1.0
HB2 A:CYS1312 3.3 103.0 1.0
HB3 A:ALA1314 3.4 100.7 1.0
HB3 A:CYS1283 3.4 83.4 1.0
HB3 A:CYS1307 3.4 90.5 1.0
CB A:CYS1283 3.5 82.6 1.0
HG22 A:THR1285 3.6 90.4 1.0
HB3 A:LYS1282 4.0 90.9 1.0
HG21 A:THR1285 4.0 90.6 1.0
N A:CYS1283 4.0 80.0 1.0
HB3 A:LYS1309 4.0 96.7 1.0
HB2 A:CYS1283 4.2 83.3 1.0
CG2 A:THR1285 4.3 92.6 1.0
CB A:ALA1314 4.3 102.2 1.0
CA A:CYS1283 4.4 78.9 1.0
H A:THR1285 4.4 90.4 1.0
HD21 A:ASN1287 4.4 79.8 1.0
H A:ALA1314 4.4 101.4 1.0
CA A:CYS1280 4.5 90.6 1.0
H A:LYS1309 4.5 97.1 1.0
H A:GLY1284 4.5 89.5 1.0
HB2 A:ALA1314 4.6 100.8 1.0
CA A:CYS1307 4.6 83.3 1.0
CA A:CYS1312 4.7 103.4 1.0
H A:LYS1282 4.7 90.6 1.0
HB2 A:LYS1309 4.7 96.9 1.0
HA A:CYS1307 4.8 90.2 1.0
HA A:CYS1280 4.8 93.2 1.0
CB A:LYS1309 4.8 96.0 1.0
HB1 A:ALA1314 4.8 100.7 1.0
O A:ALA1314 4.8 99.5 1.0
HD3 A:LYS1309 4.9 97.2 1.0
HG23 A:THR1285 4.9 90.6 1.0
CB A:LYS1282 5.0 88.8 1.0
N A:GLY1284 5.0 88.0 1.0
HA A:CYS1312 5.0 102.9 1.0

Zinc binding site 2 out of 3 in 8g9f

Go back to Zinc Binding Sites List in 8g9f
Zinc binding site 2 out of 3 in the Complete 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 Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:105.5
occ:1.00
SG A:CYS1368 2.2 72.2 1.0
SG A:CYS1350 2.2 63.4 1.0
SG A:CYS1345 2.3 78.4 1.0
SG A:CYS1371 2.3 78.0 1.0
HB3 A:CYS1368 2.8 59.4 1.0
HB2 A:CYS1345 3.0 61.2 1.0
CB A:CYS1368 3.0 60.4 1.0
HB3 A:CYS1350 3.1 62.0 1.0
CB A:CYS1345 3.1 59.8 1.0
CB A:CYS1350 3.2 58.5 1.0
HB2 A:CYS1368 3.2 60.1 1.0
H A:CYS1371 3.2 63.3 1.0
HB2 A:CYS1350 3.4 62.6 1.0
HB3 A:CYS1345 3.4 60.9 1.0
HB3 A:ALA1374 3.5 57.4 1.0
HB3 A:ALA1370 3.5 59.5 1.0
HB3 A:CYS1371 3.5 63.7 1.0
CB A:CYS1371 3.6 62.0 1.0
HB3 A:ASN1352 3.7 60.2 1.0
N A:CYS1371 3.9 59.0 1.0
HB2 A:ASN1352 4.0 60.5 1.0
H A:ASN1352 4.0 62.3 1.0
HB3 A:GLU1347 4.1 68.6 1.0
H A:ALA1370 4.3 59.1 1.0
HB2 A:CYS1371 4.3 63.1 1.0
CB A:ASN1352 4.3 58.3 1.0
CA A:CYS1371 4.3 56.6 1.0
CA A:CYS1368 4.4 53.6 1.0
CB A:ALA1374 4.4 55.4 1.0
CB A:ALA1370 4.5 57.5 1.0
CA A:CYS1345 4.5 49.7 1.0
H A:SER1372 4.6 58.7 1.0
HA A:CYS1345 4.6 59.9 1.0
CA A:CYS1350 4.6 59.5 1.0
H A:ALA1374 4.7 56.6 1.0
HB1 A:ALA1374 4.7 57.4 1.0
C A:CYS1368 4.8 54.5 1.0
N A:ASN1352 4.8 62.9 1.0
H A:GLU1347 4.8 67.3 1.0
C A:ALA1370 4.8 60.8 1.0
H A:GLN1351 4.8 66.5 1.0
H A:LYS1373 4.9 62.6 1.0
O A:CYS1368 4.9 65.4 1.0
HB1 A:ALA1370 4.9 59.1 1.0
HA A:CYS1368 4.9 59.2 1.0
N A:ALA1370 4.9 56.8 1.0
HB2 A:ALA1374 4.9 56.9 1.0
CB A:GLU1347 4.9 65.7 1.0
HB2 A:GLU1347 5.0 68.2 1.0
HB2 A:ALA1370 5.0 59.5 1.0
CA A:ALA1370 5.0 60.4 1.0
C A:CYS1350 5.0 59.4 1.0

Zinc binding site 3 out of 3 in 8g9f

Go back to Zinc Binding Sites List in 8g9f
Zinc binding site 3 out of 3 in the Complete 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 3 of Complete Auto-Inhibitory Complex of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:176.6
occ:1.00
SG D:CYS130 2.1 110.1 1.0
SG D:CYS133 2.3 122.9 1.0
SG D:CYS123 2.3 149.9 1.0
SG D:CYS124 2.3 124.5 1.0
HB2 D:CYS123 2.9 139.7 1.0
HB3 D:CYS133 3.0 111.8 1.0
H D:CYS130 3.0 104.6 1.0
HB3 D:CYS130 3.1 104.7 1.0
CB D:CYS130 3.1 103.7 1.0
CB D:CYS123 3.2 140.3 1.0
CB D:CYS133 3.2 110.5 1.0
H D:CYS133 3.2 111.1 1.0
N D:CYS130 3.4 102.0 1.0
HB2 D:CYS124 3.4 126.8 1.0
CB D:CYS124 3.5 128.2 1.0
CA D:CYS130 3.7 102.1 1.0
N D:CYS133 3.7 108.6 1.0
HB2 D:LYS132 3.8 110.8 1.0
H D:CYS124 3.8 126.9 1.0
HA D:ILE129 3.8 95.3 1.0
N D:CYS124 3.8 126.3 1.0
HB3 D:CYS123 3.8 139.6 1.0
HB2 D:CYS133 4.0 111.3 1.0
HB2 D:CYS130 4.0 104.8 1.0
C D:CYS123 4.0 137.7 1.0
O D:CYS130 4.0 107.0 1.0
CA D:CYS133 4.1 109.8 1.0
C D:CYS130 4.1 101.9 1.0
C D:ILE129 4.1 91.4 1.0
CA D:CYS123 4.2 138.7 1.0
H D:LYS132 4.2 109.9 1.0
HH11 D:ARG121 4.2 114.5 1.0
HB3 D:CYS124 4.3 126.8 1.0
CA D:CYS124 4.3 126.0 1.0
HE22 D:GLN233 4.4 127.3 1.0
CA D:ILE129 4.5 91.0 1.0
H D:CYS123 4.5 138.8 1.0
C D:LYS132 4.6 108.1 1.0
O D:CYS123 4.6 137.8 1.0
HA D:CYS130 4.6 104.5 1.0
HA D:CYS133 4.6 111.8 1.0
CB D:LYS132 4.7 113.1 1.0
HD2 D:ARG121 4.7 114.7 1.0
N D:LYS132 4.7 109.2 1.0
HA D:CYS124 4.8 126.4 1.0
N D:CYS123 4.9 138.5 1.0
CA D:LYS132 4.9 111.4 1.0
HA D:CYS123 4.9 139.1 1.0
NH1 D:ARG121 4.9 113.6 1.0
O D:ILE129 5.0 93.0 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 00:45:18 2023

Last articles

Cl in 4NHT
Cl in 4NO7
Cl in 4NML
Cl in 4NN3
Cl in 4NMW
Cl in 4NM7
Cl in 4NM5
Cl in 4NM3
Cl in 4NM0
Cl in 4NHQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy