Zinc in PDB 8d9d: Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template

All present enzymatic activity of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template:
2.7.7.102; 2.7.7.7;

The structure of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template also contains other interesting chemical elements:

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

The binding sites of Zinc atom in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template (pdb code 8d9d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template, PDB code: 8d9d:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:149.6 occ:1.00 SG A:CYS128 2.3 110.6 1.0 SG A:CYS121 2.3 129.1 1.0 SG A:CYS122 2.3 129.5 1.0 SG A:CYS131 2.3 107.8 1.0 NH2 A:ARG119 2.8 124.6 1.0 CB A:CYS131 3.2 107.8 1.0 CB A:CYS128 3.3 110.6 1.0 NE A:ARG119 3.5 124.6 1.0 N A:CYS128 3.5 110.6 1.0 CZ A:ARG119 3.6 124.6 1.0 CB A:CYS121 3.6 129.1 1.0 CB A:CYS122 3.7 129.5 1.0 CA A:CYS128 3.9 110.6 1.0 N A:CYS122 3.9 129.5 1.0 O A:CYS128 4.1 110.6 1.0 N A:CYS131 4.3 107.8 1.0 CA A:CYS131 4.3 107.8 1.0 C A:CYS128 4.3 110.6 1.0 CA A:CYS122 4.4 129.5 1.0 C A:ILE127 4.5 113.4 1.0 C A:CYS121 4.5 129.1 1.0 CA A:CYS121 4.6 129.1 1.0 CD A:ARG119 4.8 124.6 1.0 NH1 A:ARG119 4.8 124.6 1.0 CA A:ILE127 4.8 113.4 1.0

Zinc binding site 2 out of 3 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1502 b:229.0 occ:1.00 SG C:CYS1310 2.3 163.3 1.0 SG C:CYS1283 2.3 160.1 1.0 SG C:CYS1315 2.3 157.6 1.0 SG C:CYS1286 2.3 163.1 1.0 CB C:CYS1283 3.1 160.1 1.0 CB C:CYS1315 3.1 157.6 1.0 CB C:CYS1310 3.2 163.3 1.0 CB C:CYS1286 3.6 163.1 1.0 N C:CYS1286 4.0 163.1 1.0 CA C:CYS1286 4.4 163.1 1.0 CB C:ASN1312 4.5 161.9 1.0 CA C:CYS1283 4.6 160.1 1.0 CA C:CYS1315 4.6 157.6 1.0 CA C:CYS1310 4.6 163.3 1.0 N C:GLY1287 4.8 161.4 1.0 OG1 C:THR1288 4.9 161.6 1.0 CB C:THR1288 5.0 161.6 1.0 CB C:THR1285 5.0 159.6 1.0 C C:CYS1286 5.0 163.1 1.0 N C:THR1288 5.0 161.6 1.0

Zinc binding site 3 out of 3 in the Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Dna Polymerase-Alpha/Primase Elongation Complex II Bound to Primer/Template within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1503 b:193.6 occ:1.00 SG C:CYS1374 2.3 145.4 1.0 SG C:CYS1353 2.3 157.7 1.0 SG C:CYS1348 2.3 152.8 1.0 SG C:CYS1371 2.3 149.5 1.0 CB C:CYS1353 3.1 157.7 1.0 CB C:CYS1371 3.2 149.5 1.0 CB C:CYS1374 3.4 145.4 1.0 CB C:CYS1348 3.6 152.8 1.0 N C:CYS1374 3.6 145.4 1.0 CA C:CYS1374 4.0 145.4 1.0 O C:CYS1374 4.1 145.4 1.0 CB C:ASN1355 4.1 149.4 1.0 CB C:ALA1377 4.2 145.0 1.0 C C:CYS1374 4.5 145.4 1.0 CB C:ALA1373 4.5 144.7 1.0 CA C:CYS1353 4.6 157.7 1.0 CA C:CYS1371 4.6 149.5 1.0 C C:ALA1373 4.7 144.7 1.0 N C:ASN1355 4.9 149.4 1.0 CA C:CYS1348 4.9 152.8 1.0 CG C:ASN1355 5.0 149.4 1.0 N C:ALA1373 5.0 144.7 1.0

Q.He, A.G.Baranovskiy, L.M.Morstadt, A.E.Lisova, N.D.Babayeva, B.L.Lusk, C.Lim, T.H.Tahirov. Structures of Human Primosome Elongation Complexes Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00971-3