Zinc in PDB 9dih: Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand

The structure of Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand, PDB code: 9dih was solved by O.Rechkoblit, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.88 / 1.94
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.697, 191.527, 118.435, 90, 90, 90
R / Rfree (%)	17.1 / 21.8

The binding sites of Zinc atom in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand (pdb code 9dih). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand, PDB code: 9dih:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:33.8 occ:1.00 SG A:CYS32 2.3 30.7 1.0 SG A:CYS35 2.3 32.0 1.0 SG A:CYS90 2.3 37.3 1.0 SG A:CYS87 2.4 33.9 1.0 HB2 A:CYS90 2.9 41.5 1.0 HB3 A:CYS35 2.9 32.0 1.0 H A:CYS87 3.1 36.9 1.0 CB A:CYS35 3.2 26.4 1.0 CB A:CYS90 3.2 34.4 1.0 HB3 A:CYS87 3.3 46.1 1.0 HB3 A:CYS32 3.3 36.5 1.0 CB A:CYS32 3.3 30.2 1.0 H A:CYS35 3.4 35.7 1.0 HB2 A:CYS32 3.4 36.5 1.0 CB A:CYS87 3.4 38.1 1.0 H A:CYS90 3.7 39.4 1.0 HB3 A:CYS90 3.7 41.5 1.0 N A:CYS35 3.8 29.5 1.0 N A:CYS87 3.9 30.5 1.0 HB2 A:CYS35 4.0 32.0 1.0 HB2 A:LEU34 4.0 28.1 1.0 CA A:CYS35 4.0 25.1 1.0 HG21 A:THR37 4.1 42.4 1.0 HG22 A:THR37 4.1 42.4 1.0 HB2 A:CYS87 4.2 46.1 1.0 CA A:CYS87 4.2 32.5 1.0 N A:CYS90 4.4 32.6 1.0 CA A:CYS90 4.4 32.4 1.0 H A:LEU34 4.4 40.8 1.0 H A:THR37 4.6 33.9 1.0 CG2 A:THR37 4.6 35.1 1.0 O A:HOH655 4.6 39.8 1.0 C A:LEU34 4.6 34.5 1.0 H A:GLY36 4.6 32.6 1.0 CA A:CYS32 4.7 28.4 1.0 HA A:LEU86 4.7 43.5 1.0 HA A:CYS35 4.8 30.5 1.0 HA A:CYS90 4.8 39.2 1.0 C A:CYS35 4.8 29.6 1.0 CB A:LEU34 4.8 23.1 1.0 O A:CYS87 4.9 35.3 1.0 HB3 A:LEU86 4.9 43.6 1.0 HD22 A:LEU86 4.9 38.7 1.0 C A:CYS87 4.9 35.2 1.0

Zinc binding site 2 out of 2 in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Diamp Cyclic Dinucleotide Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:44.0 occ:1.00 SG B:CYS87 2.2 40.7 1.0 SG B:CYS32 2.2 39.5 1.0 SG B:CYS90 2.3 45.8 1.0 SG B:CYS35 2.3 46.4 1.0 HB2 B:CYS90 2.9 60.9 1.0 HB3 B:CYS35 3.2 57.9 1.0 CB B:CYS90 3.2 50.5 1.0 H B:CYS35 3.2 55.6 1.0 CB B:CYS32 3.2 41.7 1.0 H B:CYS87 3.2 45.9 1.0 HB3 B:CYS32 3.2 50.3 1.0 HB2 B:CYS32 3.3 50.3 1.0 CB B:CYS35 3.4 48.0 1.0 HB3 B:CYS87 3.4 53.0 1.0 CB B:CYS87 3.5 44.0 1.0 H B:CYS90 3.6 62.2 1.0 HB3 B:CYS90 3.8 60.9 1.0 N B:CYS35 3.8 46.1 1.0 N B:CYS87 3.9 38.0 1.0 HB2 B:LEU34 4.0 47.6 1.0 HB2 B:CYS35 4.1 57.9 1.0 CA B:CYS35 4.2 41.4 1.0 N B:CYS90 4.2 51.6 1.0 CA B:CYS87 4.2 37.9 1.0 HB2 B:CYS87 4.2 53.0 1.0 CA B:CYS90 4.3 48.9 1.0 H B:LEU34 4.3 49.7 1.0 HG1 B:THR37 4.3 72.2 1.0 H B:THR37 4.5 47.1 1.0 H B:GLY36 4.6 50.1 1.0 CA B:CYS32 4.6 35.1 1.0 O B:CYS87 4.6 45.6 1.0 HB B:THR37 4.6 51.1 1.0 HA B:CYS90 4.7 59.0 1.0 C B:CYS87 4.8 42.1 1.0 HA B:LEU86 4.8 40.9 1.0 HB3 B:LEU86 4.8 45.3 1.0 C B:LEU34 4.8 52.6 1.0 OG1 B:THR37 4.9 59.9 1.0 CB B:LEU34 4.9 39.5 1.0 HD22 B:LEU86 4.9 51.8 1.0 C B:CYS35 4.9 46.2 1.0 HA B:CYS32 4.9 42.4 1.0 HA B:CYS35 5.0 49.9 1.0 N B:GLY36 5.0 41.5 1.0 N B:LEU34 5.0 41.2 1.0

O.Rechkoblit, D.Sciaky, M.Ni, Y.Li, J.Kottur, G.Fang, A.K.Aggarwal. Mechanism of Dna Degradation By Cbass CAP5 Endonuclease Immune Effector. Nat Commun V. 16 5243 2025.
ISSN: ESSN 2041-1723
PubMed: 40473611
DOI: 10.1038/S41467-025-60484-Z