Zinc in PDB 9k2v: Cyanophage A4 Pre-Ejectosome

The binding sites of Zinc atom in the Cyanophage A4 Pre-Ejectosome (pdb code 9k2v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cyanophage A4 Pre-Ejectosome, PDB code: 9k2v:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Cyanophage A4 Pre-Ejectosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cyanophage A4 Pre-Ejectosome within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn1101 b:70.0 occ:1.00 NE2 E:HIS665 2.3 54.7 1.0 OD1 E:ASP669 2.4 46.3 1.0 OD2 E:ASP669 2.5 46.3 1.0 CD2 E:HIS748 2.6 40.2 1.0 CG E:ASP669 2.8 46.3 1.0 CE1 E:HIS665 3.0 54.7 1.0 NE2 E:HIS748 3.2 40.2 1.0 CD2 E:HIS665 3.2 54.7 1.0 CG E:HIS748 3.5 40.2 1.0 ND1 E:HIS665 4.1 54.7 1.0 CG E:HIS665 4.2 54.7 1.0 CB E:HIS748 4.2 40.2 1.0 CE1 E:HIS748 4.2 40.2 1.0 CE1 E:HIS715 4.3 38.8 1.0 CB E:ASP669 4.3 46.3 1.0 ND1 E:HIS748 4.4 40.2 1.0 O E:GLY667 4.4 47.2 1.0 ND1 E:HIS715 4.6 38.8 1.0 CA E:HIS748 4.7 40.2 1.0

Zinc binding site 2 out of 5 in the Cyanophage A4 Pre-Ejectosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cyanophage A4 Pre-Ejectosome within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:66.0 occ:1.00 NE2 A:HIS665 2.3 57.1 1.0 OD2 A:ASP669 2.4 46.6 1.0 CD2 A:HIS748 2.6 40.4 1.0 OD1 A:ASP669 2.7 46.6 1.0 CG A:ASP669 2.8 46.6 1.0 CE1 A:HIS665 3.0 57.1 1.0 CD2 A:HIS665 3.2 57.1 1.0 NE2 A:HIS748 3.3 40.4 1.0 CG A:HIS748 3.5 40.4 1.0 ND1 A:HIS665 4.0 57.1 1.0 CG A:HIS665 4.1 57.1 1.0 CB A:HIS748 4.2 40.4 1.0 CE1 A:HIS748 4.3 40.4 1.0 CE1 A:HIS715 4.3 39.2 1.0 CB A:ASP669 4.3 46.6 1.0 O A:GLY667 4.4 47.9 1.0 ND1 A:HIS748 4.4 40.4 1.0 ND1 A:HIS715 4.6 39.2 1.0 CA A:HIS748 4.7 40.4 1.0

Zinc binding site 3 out of 5 in the Cyanophage A4 Pre-Ejectosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cyanophage A4 Pre-Ejectosome within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:67.0 occ:1.00 NE2 B:HIS665 2.3 56.3 1.0 OD1 B:ASP669 2.4 46.7 1.0 OD2 B:ASP669 2.4 46.7 1.0 CD2 B:HIS748 2.6 40.9 1.0 CG B:ASP669 2.7 46.7 1.0 CE1 B:HIS665 3.0 56.3 1.0 CD2 B:HIS665 3.2 56.3 1.0 NE2 B:HIS748 3.2 40.9 1.0 CG B:HIS748 3.5 40.9 1.0 ND1 B:HIS665 4.0 56.3 1.0 CG B:HIS665 4.1 56.3 1.0 CB B:HIS748 4.2 40.9 1.0 CE1 B:HIS748 4.2 40.9 1.0 CB B:ASP669 4.3 46.7 1.0 CE1 B:HIS715 4.3 40.2 1.0 ND1 B:HIS748 4.4 40.9 1.0 O B:GLY667 4.4 48.3 1.0 ND1 B:HIS715 4.6 40.2 1.0 CA B:HIS748 4.7 40.9 1.0

Zinc binding site 4 out of 5 in the Cyanophage A4 Pre-Ejectosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cyanophage A4 Pre-Ejectosome within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:74.0 occ:1.00 CE1 C:HIS665 2.0 58.0 1.0 NE2 C:HIS665 2.3 58.0 1.0 OD2 C:ASP669 2.5 46.9 1.0 OD1 C:ASP669 2.5 46.9 1.0 CD2 C:HIS748 2.8 40.1 1.0 CG C:ASP669 2.8 46.9 1.0 ND1 C:HIS665 3.1 58.0 1.0 NE2 C:HIS748 3.4 40.1 1.0 CD2 C:HIS665 3.5 58.0 1.0 CG C:HIS748 3.8 40.1 1.0 CG C:HIS665 3.9 58.0 1.0 O C:GLY667 4.3 49.1 1.0 CB C:ASP669 4.4 46.9 1.0 CE1 C:HIS748 4.5 40.1 1.0 CB C:HIS748 4.5 40.1 1.0 CE1 C:HIS715 4.6 38.2 1.0 ND1 C:HIS748 4.7 40.1 1.0 ND1 C:HIS715 4.9 38.2 1.0

Zinc binding site 5 out of 5 in the Cyanophage A4 Pre-Ejectosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cyanophage A4 Pre-Ejectosome within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1101 b:71.6 occ:1.00 CE1 D:HIS665 1.9 57.4 1.0 NE2 D:HIS665 2.3 57.4 1.0 OD1 D:ASP669 2.7 48.2 1.0 OD2 D:ASP669 2.8 48.2 1.0 CD2 D:HIS748 2.8 41.8 1.0 ND1 D:HIS665 3.0 57.4 1.0 CG D:ASP669 3.0 48.2 1.0 NE2 D:HIS748 3.4 41.8 1.0 CD2 D:HIS665 3.4 57.4 1.0 CG D:HIS665 3.7 57.4 1.0 CG D:HIS748 3.8 41.8 1.0 CB D:ASP669 4.2 48.2 1.0 O D:GLY667 4.4 48.6 1.0 CE1 D:HIS748 4.4 41.8 1.0 CE1 D:HIS715 4.5 39.6 1.0 CB D:HIS748 4.6 41.8 1.0 ND1 D:HIS748 4.7 41.8 1.0 ND1 D:HIS715 4.8 39.6 1.0

P.Hou, R.Q.Zhou, Y.L.Jiang, R.C.Yu, K.Du, N.Gan, F.Ke, Q.Y.Zhang, Q.Li, C.Z.Zhou. Cryo-Em Structure of Cyanopodophage A4 Reveals A Pentameric Pre-Ejectosome in the Double-Stabilized Capsid. Proc.Natl.Acad.Sci.Usa V. 122 03122 2025.
ISSN: ESSN 1091-6490
PubMed: 40163721
DOI: 10.1073/PNAS.2423403122