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

The structure of Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Gamp Cyclic Dinucleotide Ligand, PDB code: 9dif 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)	39.32 / 1.67
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	105.021, 194.171, 118.626, 90, 90, 90
R / Rfree (%)	17 / 21.1

The binding sites of Zinc atom in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Gamp Cyclic Dinucleotide Ligand (pdb code 9dif). 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- Gamp Cyclic Dinucleotide Ligand, PDB code: 9dif:
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- Gamp 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- Gamp Cyclic Dinucleotide Ligand within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:9.7 occ:1.00 SG A:CYS35 2.3 18.7 1.0 SG A:CYS90 2.3 10.2 1.0 SG A:CYS32 2.4 10.0 1.0 SG A:CYS87 2.4 20.7 1.0 HB2 A:CYS90 2.9 19.5 1.0 HB3 A:CYS35 3.1 13.3 1.0 HB3 A:CYS32 3.2 23.4 1.0 H A:CYS87 3.2 20.5 1.0 HB3 A:CYS87 3.2 14.7 1.0 CB A:CYS32 3.2 19.4 1.0 CB A:CYS90 3.2 16.1 1.0 HB2 A:CYS32 3.3 23.4 1.0 CB A:CYS35 3.4 11.0 1.0 CB A:CYS87 3.4 12.1 1.0 H A:CYS35 3.5 15.5 1.0 H A:CYS90 3.6 22.7 1.0 HB3 A:CYS90 3.8 19.5 1.0 N A:CYS35 3.9 12.8 1.0 HG22 A:THR37 3.9 21.2 1.0 N A:CYS87 3.9 16.9 1.0 HB2 A:LEU34 4.1 13.8 1.0 HB2 A:CYS35 4.1 13.3 1.0 HB2 A:CYS87 4.2 14.7 1.0 HG21 A:THR37 4.2 21.2 1.0 CA A:CYS35 4.2 12.7 1.0 CA A:CYS87 4.2 16.0 1.0 N A:CYS90 4.3 18.8 1.0 CA A:CYS90 4.4 18.9 1.0 H A:LEU34 4.5 17.8 1.0 CG2 A:THR37 4.5 17.5 1.0 O A:HOH630 4.5 16.4 1.0 H A:THR37 4.5 20.0 1.0 O A:HOH810 4.5 37.4 1.0 C A:LEU34 4.7 19.7 1.0 CA A:CYS32 4.7 9.5 1.0 HA A:CYS90 4.7 22.9 1.0 HA A:LEU86 4.7 20.0 1.0 H A:GLY36 4.8 18.5 1.0 CB A:LEU34 4.9 11.4 1.0 HB3 A:LEU86 4.9 23.1 1.0 O A:CYS87 4.9 17.4 1.0 C A:CYS35 4.9 17.8 1.0 C A:CYS87 4.9 19.4 1.0 O A:HOH786 5.0 36.2 1.0 HD22 A:LEU86 5.0 19.1 1.0 HA A:CYS35 5.0 15.4 1.0

Zinc binding site 2 out of 2 in the Cbass Pseudomonas Syringae CAP5 Tetramer with Dna Duplex and 3'2'-C- Gamp 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- Gamp Cyclic Dinucleotide Ligand within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:21.7 occ:1.00 SG B:CYS32 2.2 25.7 1.0 SG B:CYS87 2.3 32.1 1.0 SG B:CYS90 2.3 31.9 1.0 SG B:CYS35 2.3 31.9 1.0 HB2 B:CYS90 2.9 27.4 1.0 HB3 B:CYS35 3.1 37.8 1.0 HB3 B:CYS32 3.1 28.8 1.0 CB B:CYS32 3.2 23.8 1.0 CB B:CYS90 3.2 22.6 1.0 HB2 B:CYS32 3.3 28.8 1.0 H B:CYS35 3.3 34.6 1.0 H B:CYS87 3.3 28.6 1.0 CB B:CYS35 3.3 31.3 1.0 HB3 B:CYS87 3.4 33.5 1.0 CB B:CYS87 3.5 27.8 1.0 H B:CYS90 3.6 48.6 1.0 HG22 B:THR37 3.6 49.2 1.0 N B:CYS35 3.8 28.7 1.0 HB3 B:CYS90 3.8 27.4 1.0 HG21 B:THR37 3.9 49.2 1.0 N B:CYS87 4.0 23.6 1.0 HB2 B:LEU34 4.1 30.7 1.0 HB2 B:CYS35 4.1 37.8 1.0 CA B:CYS35 4.2 30.9 1.0 N B:CYS90 4.2 40.4 1.0 HB2 B:CYS87 4.2 33.5 1.0 CG2 B:THR37 4.2 40.9 1.0 CA B:CYS87 4.3 27.4 1.0 CA B:CYS90 4.3 27.1 1.0 H B:LEU34 4.3 29.4 1.0 O B:HOH606 4.4 40.1 1.0 H B:THR37 4.5 28.5 1.0 CA B:CYS32 4.6 16.8 1.0 O B:CYS87 4.7 27.7 1.0 H B:GLY36 4.7 28.0 1.0 C B:LEU34 4.7 29.2 1.0 HA B:CYS90 4.7 32.7 1.0 C B:CYS87 4.8 32.7 1.0 HA B:LEU86 4.8 29.1 1.0 HD22 B:LEU86 4.8 32.9 1.0 HB3 B:LEU86 4.9 32.6 1.0 HG23 B:THR37 4.9 49.2 1.0 CB B:LEU34 4.9 25.5 1.0 C B:CYS35 4.9 32.1 1.0 HA B:CYS32 4.9 20.4 1.0 HB B:THR37 5.0 28.2 1.0 HA B:CYS35 5.0 37.2 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