Zinc in PDB 9nlg: Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions)

The structure of Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions), PDB code: 9nlg 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)	45.87 / 1.64
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	70.564, 77.833, 80.989, 63.4, 80.84, 79.17
R / Rfree (%)	15.6 / 18.1

The binding sites of Zinc atom in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions) (pdb code 9nlg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions), PDB code: 9nlg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions)


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 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:14.1 occ:1.00 SG A:CYS90 2.3 14.8 1.0 SG A:CYS35 2.3 202.5 1.0 SG A:CYS32 2.3 13.2 1.0 SG A:CYS87 2.3 14.7 1.0 HB2 A:CYS90 3.0 16.7 1.0 HB3 A:CYS35 3.0 25.4 1.0 H A:CYS87 3.1 17.4 1.0 CB A:CYS35 3.2 21.2 1.0 HB3 A:CYS32 3.3 15.9 1.0 HB3 A:CYS87 3.3 15.6 1.0 CB A:CYS90 3.3 13.9 1.0 CB A:CYS32 3.3 13.3 1.0 H A:CYS35 3.3 17.7 1.0 HB2 A:CYS32 3.4 15.9 1.0 CB A:CYS87 3.4 13.0 1.0 H A:CYS90 3.7 17.9 1.0 N A:CYS35 3.8 14.7 1.0 HB3 A:CYS90 3.9 16.7 1.0 N A:CYS87 3.9 14.5 1.0 HB2 A:LEU34 4.0 17.5 1.0 HB2 A:CYS35 4.0 25.4 1.0 CA A:CYS35 4.1 12.9 1.0 HG22 A:THR37 4.1 26.4 1.0 HB2 A:CYS87 4.2 15.6 1.0 CA A:CYS87 4.2 15.5 1.0 HG21 A:THR37 4.3 26.4 1.0 N A:CYS90 4.4 14.9 1.0 H A:LEU34 4.4 14.5 1.0 CA A:CYS90 4.4 15.7 1.0 O A:HOH782 4.5 23.4 1.0 O A:HOH887 4.5 22.5 1.0 H A:THR37 4.6 15.8 1.0 C A:LEU34 4.6 17.1 1.0 CG2 A:THR37 4.7 22.0 1.0 HA A:LEU86 4.7 16.8 1.0 CA A:CYS32 4.7 13.9 1.0 H A:GLY36 4.8 14.6 1.0 HB3 A:LEU86 4.8 14.5 1.0 CB A:LEU34 4.8 14.6 1.0 HA A:CYS90 4.8 18.8 1.0 C A:CYS35 4.9 15.6 1.0 HA A:CYS35 4.9 15.5 1.0 O A:CYS87 4.9 13.8 1.0 C A:CYS87 4.9 13.7 1.0 HD22 A:LEU86 4.9 15.5 1.0 HB A:THR37 4.9 23.5 1.0

Zinc binding site 2 out of 4 in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions)


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 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:22.2 occ:1.00 SG B:CYS35 2.3 22.2 1.0 SG B:CYS87 2.3 23.4 1.0 SG B:CYS90 2.4 21.8 1.0 SG B:CYS32 2.4 17.4 1.0 HB2 B:CYS90 2.8 26.6 1.0 HB3 B:CYS35 3.0 25.7 1.0 HB3 B:CYS32 3.1 23.7 1.0 CB B:CYS90 3.2 22.2 1.0 CB B:CYS32 3.2 19.7 1.0 H B:CYS87 3.2 21.4 1.0 CB B:CYS35 3.3 21.4 1.0 H B:CYS35 3.3 23.3 1.0 HB2 B:CYS32 3.3 23.7 1.0 HB3 B:CYS87 3.3 24.2 1.0 CB B:CYS87 3.5 20.1 1.0 H B:CYS90 3.6 30.3 1.0 HG22 B:THR37 3.8 31.8 1.0 HB3 B:CYS90 3.8 26.6 1.0 N B:CYS35 3.8 19.4 1.0 HG23 B:THR37 3.8 31.8 1.0 N B:CYS87 4.0 17.8 1.0 HB2 B:CYS35 4.0 25.7 1.0 HB2 B:LEU34 4.1 23.3 1.0 CA B:CYS35 4.1 21.9 1.0 HB2 B:CYS87 4.2 24.2 1.0 N B:CYS90 4.2 25.3 1.0 CG2 B:THR37 4.3 26.5 1.0 CA B:CYS87 4.3 20.6 1.0 CA B:CYS90 4.3 23.7 1.0 H B:LEU34 4.4 25.2 1.0 H B:THR37 4.4 22.4 1.0 O B:HOH636 4.4 39.0 1.0 CA B:CYS32 4.7 14.3 1.0 H B:GLY36 4.7 25.6 1.0 HD22 B:LEU86 4.7 28.7 1.0 HA B:CYS90 4.7 28.5 1.0 C B:LEU34 4.8 24.2 1.0 HA B:LEU86 4.8 21.2 1.0 C B:CYS35 4.8 21.2 1.0 O B:CYS87 4.9 24.0 1.0 HB3 B:LEU86 4.9 27.1 1.0 C B:CYS87 4.9 22.8 1.0 HA B:CYS35 4.9 26.4 1.0 HB B:THR37 4.9 25.3 1.0 HG21 B:THR37 4.9 31.8 1.0 CB B:LEU34 5.0 19.4 1.0

Zinc binding site 3 out of 4 in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:15.4 occ:1.00 SG C:CYS32 2.3 13.6 1.0 SG C:CYS35 2.3 15.9 1.0 SG C:CYS90 2.3 16.4 1.0 SG C:CYS87 2.4 14.3 1.0 HB2 C:CYS90 2.9 22.2 1.0 HB3 C:CYS35 3.0 19.4 1.0 H C:CYS87 3.1 19.6 1.0 HB3 C:CYS32 3.2 21.9 1.0 HB3 C:CYS87 3.2 17.5 1.0 CB C:CYS32 3.2 18.2 1.0 CB C:CYS90 3.2 18.5 1.0 CB C:CYS35 3.3 16.2 1.0 H C:CYS35 3.3 16.1 1.0 HB2 C:CYS32 3.3 21.9 1.0 CB C:CYS87 3.4 14.6 1.0 H C:CYS90 3.7 17.8 1.0 N C:CYS35 3.8 13.4 1.0 HB3 C:CYS90 3.8 22.2 1.0 N C:CYS87 3.9 16.3 1.0 HB2 C:LEU34 4.0 18.2 1.0 HB2 C:CYS35 4.0 19.4 1.0 CA C:CYS35 4.1 14.9 1.0 HG22 C:THR37 4.1 20.4 1.0 HB2 C:CYS87 4.2 17.5 1.0 CA C:CYS87 4.2 14.7 1.0 HG21 C:THR37 4.3 20.4 1.0 N C:CYS90 4.3 14.8 1.0 H C:LEU34 4.4 15.6 1.0 CA C:CYS90 4.4 16.6 1.0 O C:HOH869 4.4 36.9 1.0 H C:THR37 4.5 17.4 1.0 O C:HOH713 4.6 21.7 1.0 C C:LEU34 4.6 14.0 1.0 CG2 C:THR37 4.6 16.9 1.0 O C:HOH862 4.6 40.3 1.0 CA C:CYS32 4.7 13.5 1.0 H C:GLY36 4.7 16.1 1.0 HA C:LEU86 4.7 18.9 1.0 HA C:CYS90 4.8 19.9 1.0 HB3 C:LEU86 4.8 17.6 1.0 C C:CYS35 4.8 18.2 1.0 CB C:LEU34 4.8 15.1 1.0 HA C:CYS35 4.9 17.9 1.0 HB C:THR37 4.9 24.5 1.0 C C:CYS87 4.9 13.1 1.0 O C:CYS87 4.9 13.8 1.0 HD22 C:LEU86 4.9 19.6 1.0 HA C:CYS32 5.0 16.2 1.0

Zinc binding site 4 out of 4 in the Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cbass Pseudomonas Syringae CAP5 Tetramer with 3'2'-C-Gamp Cyclic Dinucleotide Ligand (HIS56ALA Mutant Without MG2+ Ions) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn401 b:26.9 occ:1.00 SG D:CYS35 2.3 27.9 1.0 SG D:CYS87 2.3 23.8 1.0 SG D:CYS32 2.3 22.5 1.0 SG D:CYS90 2.3 26.1 1.0 HB2 D:CYS90 2.9 34.1 1.0 HB3 D:CYS35 3.0 30.3 1.0 HB3 D:CYS32 3.1 26.3 1.0 CB D:CYS90 3.2 28.4 1.0 H D:CYS35 3.2 28.6 1.0 CB D:CYS32 3.2 21.9 1.0 H D:CYS87 3.2 28.6 1.0 CB D:CYS35 3.2 25.2 1.0 HB2 D:CYS32 3.3 26.3 1.0 HB3 D:CYS87 3.3 30.2 1.0 CB D:CYS87 3.5 25.2 1.0 H D:CYS90 3.6 35.4 1.0 N D:CYS35 3.7 23.8 1.0 HB3 D:CYS90 3.8 34.1 1.0 HB2 D:LEU34 3.9 30.7 1.0 N D:CYS87 4.0 23.9 1.0 HB2 D:CYS35 4.0 30.3 1.0 CA D:CYS35 4.0 25.4 1.0 HB2 D:CYS87 4.2 30.2 1.0 N D:CYS90 4.3 29.5 1.0 CA D:CYS87 4.3 23.2 1.0 CA D:CYS90 4.3 26.3 1.0 H D:LEU34 4.4 30.3 1.0 HB D:THR37 4.4 37.0 1.0 H D:THR37 4.5 32.1 1.0 CA D:CYS32 4.7 21.2 1.0 H D:GLY36 4.7 34.7 1.0 C D:LEU34 4.7 24.4 1.0 HA D:CYS90 4.7 31.6 1.0 O D:CYS87 4.8 23.6 1.0 HA D:LEU86 4.8 22.2 1.0 CB D:LEU34 4.8 25.6 1.0 C D:CYS35 4.8 25.1 1.0 HA D:CYS35 4.8 30.5 1.0 C D:CYS87 4.9 29.8 1.0 HG1 D:THR37 4.9 53.0 1.0 HB3 D:LEU86 4.9 25.8 1.0 N D:GLY36 5.0 28.9 1.0 OG1 D:THR37 5.0 44.2 1.0 HA D:CYS32 5.0 25.5 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