Zinc in PDB 8dw6: T4 Bacteriophage Primosome with Single-Strand Dna, State 3

The structure of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 also contains other interesting chemical elements:

Magnesium

(Mg)

5 atoms

The binding sites of Zinc atom in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3 (pdb code 8dw6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3, PDB code: 8dw6:

Zinc binding site 1 out of 1 in the T4 Bacteriophage Primosome with Single-Strand Dna, State 3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T4 Bacteriophage Primosome with Single-Strand Dna, State 3 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn401 b:30.0 occ:1.00 SG H:CYS65 2.3 349.8 1.0 SG H:CYS37 2.3 334.8 1.0 SG H:CYS68 2.3 342.5 1.0 SG H:CYS40 2.3 325.7 1.0 CB H:CYS65 3.0 349.8 1.0 CB H:CYS37 3.0 334.8 1.0 CB H:CYS40 3.2 325.7 1.0 CB H:CYS68 3.2 342.5 1.0 N H:CYS68 3.4 342.5 1.0 N H:CYS40 3.7 325.7 1.0 CA H:CYS68 3.9 342.5 1.0 CA H:CYS40 4.0 325.7 1.0 CB H:ASN67 4.2 356.3 1.0 ND2 H:ASN67 4.3 356.3 1.0 CA H:CYS37 4.4 334.8 1.0 CA H:CYS65 4.5 349.8 1.0 C H:ASN67 4.5 356.3 1.0 CB H:VAL39 4.6 302.0 1.0 O H:CYS37 4.6 334.8 1.0 N H:ASP42 4.6 369.4 1.0 C H:VAL39 4.7 302.0 1.0 C H:CYS40 4.7 325.7 1.0 CA H:ASN67 4.7 356.3 1.0 N H:ASN67 4.7 356.3 1.0 C H:CYS68 4.7 342.5 1.0 C H:CYS37 4.8 334.8 1.0 CG H:ASN67 4.8 356.3 1.0 CA H:ASP42 4.9 369.4 1.0 N H:GLY41 4.9 345.7 1.0 N H:ASN69 5.0 344.8 1.0 C H:CYS65 5.0 349.8 1.0

X.Feng, M.M.Spiering, R.De Luna Almeida Santos, S.J.Benkovic, H.Li. Structural Basis of the T4 Bacteriophage Primosome Assembly and Primer Synthesis. Biorxiv 2023.
ISSN: ISSN 2692-8205
PubMed: 37205424
DOI: 10.1101/2023.05.03.539249