Zinc in PDB 8qj7: Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1

The structure of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Manganese	(Mn)	2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 (pdb code 8qj7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1, PDB code: 8qj7:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn501 b:308.0 occ:1.00 SG C:CYS128 2.3 270.5 1.0 SG C:CYS122 2.3 266.6 1.0 SG C:CYS121 2.3 264.6 1.0 SG C:CYS131 2.3 266.5 1.0 H C:CYS128 2.9 250.3 1.0 HB3 C:CYS131 2.9 257.7 1.0 HB3 C:CYS128 2.9 256.8 1.0 CB C:CYS128 3.1 257.8 1.0 H C:CYS131 3.1 256.2 1.0 HB2 C:CYS122 3.2 256.9 1.0 CB C:CYS131 3.2 258.3 1.0 H C:CYS122 3.2 257.6 1.0 N C:CYS128 3.3 250.4 1.0 CB C:CYS122 3.4 256.4 1.0 HB2 C:CYS121 3.4 259.2 1.0 CB C:CYS121 3.5 259.8 1.0 N C:CYS122 3.6 259.2 1.0 CA C:CYS128 3.6 250.5 1.0 N C:CYS131 3.8 257.9 1.0 HB2 C:LYS130 3.8 257.2 1.0 HB2 C:CYS131 3.9 255.4 1.0 O C:CYS128 3.9 248.4 1.0 HB2 C:CYS128 4.0 256.9 1.0 HA C:ILE127 4.0 246.1 1.0 C C:CYS128 4.1 247.4 1.0 CA C:CYS122 4.1 256.8 1.0 CA C:CYS131 4.1 255.6 1.0 HB3 C:CYS122 4.1 256.9 1.0 HB3 C:CYS121 4.2 258.8 1.0 C C:ILE127 4.2 246.8 1.0 HE22 C:GLN231 4.3 256.6 1.0 C C:CYS121 4.3 258.4 1.0 HH11 C:ARG119 4.4 250.9 1.0 HE2 C:LYS130 4.4 259.1 1.0 H C:LYS130 4.5 253.2 1.0 CA C:CYS121 4.5 257.7 1.0 HA C:CYS128 4.5 250.7 1.0 CA C:ILE127 4.6 245.7 1.0 HA C:CYS122 4.7 257.4 1.0 HZ3 C:LYS130 4.7 259.1 1.0 HA C:CYS131 4.7 255.6 1.0 CB C:LYS130 4.8 257.4 1.0 HD3 C:LYS130 4.8 259.1 1.0 HD2 C:ARG119 4.8 248.5 1.0 C C:LYS130 4.9 256.2 1.0 N C:LYS130 4.9 255.7 1.0 H C:CYS121 4.9 255.2 1.0

Zinc binding site 2 out of 3 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:224.0 occ:1.00 SG A:CYS1283 2.3 148.3 1.0 SG A:CYS1315 2.3 165.6 1.0 SG A:CYS1286 2.3 161.4 1.0 SG A:CYS1310 2.3 163.2 1.0 HB3 A:CYS1315 2.8 161.8 1.0 CB A:CYS1315 2.9 163.9 1.0 HB3 A:CYS1283 2.9 134.5 1.0 HB2 A:CYS1315 2.9 161.2 1.0 HB2 A:CYS1310 3.0 146.1 1.0 CB A:CYS1283 3.0 136.9 1.0 HB2 A:CYS1283 3.1 135.2 1.0 HG1 A:THR1288 3.1 147.8 1.0 CB A:CYS1310 3.2 147.6 1.0 HB3 A:CYS1310 3.3 145.9 1.0 HG1 A:THR1285 3.5 144.4 1.0 OG1 A:THR1285 3.5 146.7 1.0 H A:CYS1286 3.6 141.1 1.0 OG1 A:THR1288 3.6 151.5 1.0 HB3 A:ASN1312 3.6 159.1 1.0 CB A:CYS1286 3.9 148.2 1.0 HB3 A:CYS1286 3.9 146.2 1.0 HD22 A:ASN1312 4.0 159.7 1.0 HB3 A:ALA1317 4.1 144.6 1.0 N A:CYS1286 4.3 142.8 1.0 CA A:CYS1315 4.4 164.8 1.0 H A:ASN1312 4.4 153.7 1.0 H A:THR1288 4.4 144.1 1.0 CA A:CYS1283 4.5 132.2 1.0 HB2 A:CYS1286 4.5 145.7 1.0 HD21 A:ASN1290 4.5 129.4 1.0 H A:ALA1317 4.6 152.4 1.0 CB A:ASN1312 4.6 163.1 1.0 CA A:CYS1310 4.6 139.8 1.0 CA A:CYS1286 4.7 144.0 1.0 ND2 A:ASN1312 4.7 162.3 1.0 O A:ALA1317 4.7 141.5 1.0 HG21 A:THR1288 4.7 147.2 1.0 HA A:CYS1315 4.8 164.7 1.0 H A:THR1285 4.8 135.5 1.0 H A:GLY1287 4.8 139.4 1.0 HA A:CYS1310 4.8 140.4 1.0 HA A:CYS1283 4.8 132.1 1.0 CB A:THR1285 4.9 143.9 1.0 C A:CYS1315 4.9 161.7 1.0 H A:CYS1315 4.9 165.9 1.0 HB2 A:ASN1312 4.9 159.3 1.0 CB A:THR1288 4.9 146.8 1.0

Zinc binding site 3 out of 3 in the Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Human Dna Polymerase Alpha-Primase in Pre- Initiation Stage 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:144.0 occ:1.00 SG A:CYS1353 2.3 125.7 1.0 SG A:CYS1374 2.3 124.5 1.0 SG A:CYS1348 2.3 112.1 1.0 SG A:CYS1371 2.3 108.2 1.0 HB2 A:CYS1374 2.4 110.9 1.0 H A:CYS1374 2.7 110.1 1.0 HB3 A:CYS1353 2.9 109.8 1.0 CB A:CYS1374 2.9 109.5 1.0 CB A:CYS1353 3.1 108.2 1.0 HB2 A:CYS1348 3.1 99.1 1.0 CB A:CYS1348 3.2 99.2 1.0 HB2 A:CYS1353 3.3 110.8 1.0 HB3 A:CYS1348 3.3 97.7 1.0 N A:CYS1374 3.4 112.0 1.0 CB A:CYS1371 3.4 104.0 1.0 HB2 A:CYS1371 3.4 102.4 1.0 HB3 A:ALA1373 3.5 104.1 1.0 HB3 A:CYS1371 3.5 103.9 1.0 HB3 A:CYS1374 3.7 111.8 1.0 HB3 A:ALA1377 3.7 111.7 1.0 HB3 A:ASN1355 3.7 97.2 1.0 CA A:CYS1374 3.7 110.0 1.0 H A:ASN1355 3.7 97.7 1.0 HB2 A:ASN1355 4.0 98.7 1.0 HB2 A:ALA1377 4.1 112.7 1.0 HB3 A:GLU1350 4.2 112.5 1.0 CB A:ALA1377 4.2 111.8 1.0 HB1 A:ALA1377 4.2 109.8 1.0 CB A:ASN1355 4.3 95.9 1.0 HA A:CYS1374 4.4 110.3 1.0 CB A:ALA1373 4.4 101.5 1.0 H A:ARG1354 4.4 104.2 1.0 CA A:CYS1353 4.5 105.2 1.0 C A:ALA1373 4.5 108.5 1.0 N A:ASN1355 4.6 94.1 1.0 HB1 A:ALA1373 4.6 103.3 1.0 CA A:CYS1348 4.6 92.9 1.0 H A:ALA1373 4.7 103.3 1.0 O A:CYS1374 4.7 122.2 1.0 C A:CYS1374 4.7 117.2 1.0 HD22 A:ASN1355 4.7 103.5 1.0 N A:ARG1354 4.7 102.9 1.0 HD11 A:LEU1379 4.8 95.6 1.0 CA A:CYS1371 4.9 94.6 1.0 HA A:CYS1348 4.9 92.2 1.0 OE1 A:GLU1350 4.9 127.6 1.0 C A:CYS1353 4.9 103.8 1.0 H A:GLU1350 4.9 107.9 1.0 HD12 A:LEU1379 4.9 94.6 1.0 CA A:ALA1373 4.9 101.9 1.0 HA A:CYS1353 5.0 107.6 1.0

Z.Yin, M.L.Kilkenny, D.S.Ker, L.Pellegrini. Cryoem Insights Into Rna Primer Synthesis By the Human Primosome. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 38335062
DOI: 10.1111/FEBS.17082