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Zinc in PDB 8v6h: Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase

Enzymatic activity of Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase

All present enzymatic activity of Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase:
2.7.7.7;

Other elements in 8v6h:

The structure of Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Iron (Fe) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase (pdb code 8v6h). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase, PDB code: 8v6h:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 8v6h

Go back to Zinc Binding Sites List in 8v6h
Zinc binding site 1 out of 3 in the Dna Initiation Complex (Configuration 2) 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 Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

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:CYS1280 4.8 93.2 1.0
HA A:CYS1307 4.8 90.2 1.0
HB1 A:ALA1314 4.8 100.7 1.0
CB A:LYS1309 4.8 96.0 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 4.9 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 8v6h

Go back to Zinc Binding Sites List in 8v6h
Zinc binding site 2 out of 3 in the Dna Initiation Complex (Configuration 2) 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 Dna Initiation Complex (Configuration 2) of Xenopus Laevis Dna Polymerase Alpha-Primase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

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
HB3 A:CYS1345 3.4 60.9 1.0
HB2 A:CYS1350 3.4 62.6 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 8v6h

Go back to Zinc Binding Sites List in 8v6h
Zinc binding site 3 out of 3 in the Dna Initiation Complex (Configuration 2) 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 Dna Initiation Complex (Configuration 2) 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, N.P.Bradley, 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 To Be Published.
Page generated: Thu Dec 28 13:45:28 2023

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