Zinc in PDB 8fmf: Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au)

The structure of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au), PDB code: 8fmf was solved by O.Rechkoblit, D.F.Kreitler, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.99 / 2.10
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	83.536, 83.536, 401.96, 90, 90, 120
R / Rfree (%)	19 / 23.7

The structure of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) also contains other interesting chemical elements:

Magnesium

(Mg)

7 atoms

The binding sites of Zinc atom in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) (pdb code 8fmf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au), PDB code: 8fmf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn407 b:25.4 occ:1.00 SG A:CYS35 2.3 26.9 1.0 SG A:CYS32 2.3 21.5 1.0 SG A:CYS90 2.3 24.1 1.0 SG A:CYS87 2.3 22.5 1.0 HB3 A:CYS35 2.7 20.3 1.0 HB2 A:CYS90 2.9 31.6 1.0 CB A:CYS35 3.0 16.8 1.0 H A:CYS87 3.1 35.3 1.0 H A:CYS35 3.1 24.7 1.0 CB A:CYS90 3.2 26.2 1.0 HB3 A:CYS32 3.2 31.9 1.0 HB3 A:CYS87 3.2 29.8 1.0 CB A:CYS32 3.2 26.5 1.0 HB2 A:CYS32 3.3 31.9 1.0 CB A:CYS87 3.4 24.6 1.0 H A:CYS90 3.7 29.8 1.0 N A:CYS35 3.7 20.5 1.0 HB3 A:CYS90 3.8 31.6 1.0 HG22 A:THR37 3.8 33.7 1.0 HB2 A:CYS35 3.8 20.3 1.0 N A:CYS87 3.9 29.3 1.0 CA A:CYS35 3.9 22.2 1.0 HB2 A:LEU34 4.0 33.3 1.0 HB2 A:CYS87 4.1 29.8 1.0 CA A:CYS87 4.2 19.9 1.0 N A:CYS90 4.3 24.7 1.0 H A:LEU34 4.3 33.2 1.0 CA A:CYS90 4.4 25.0 1.0 H A:GLY36 4.5 28.9 1.0 O A:HOH615 4.5 26.3 1.0 HG21 A:THR37 4.5 33.7 1.0 H A:THR37 4.5 29.9 1.0 CG2 A:THR37 4.6 27.9 1.0 HB3 A:LEU86 4.6 27.0 1.0 C A:LEU34 4.6 20.6 1.0 HA A:LEU86 4.7 33.4 1.0 CA A:CYS32 4.7 23.4 1.0 HA A:CYS35 4.7 26.8 1.0 C A:CYS35 4.7 23.9 1.0 O C:HOH542 4.8 25.7 1.0 HA A:CYS90 4.8 30.1 1.0 O A:CYS87 4.8 29.8 1.0 O A:HOH643 4.8 34.7 1.0 CB A:LEU34 4.8 27.6 1.0 N A:GLY36 4.8 23.9 1.0 C A:CYS87 4.9 27.7 1.0 HD22 A:LEU86 4.9 28.6 1.0

Zinc binding site 2 out of 4 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn403 b:31.8 occ:1.00 SG B:CYS32 2.3 32.8 1.0 SG B:CYS35 2.3 33.0 1.0 SG B:CYS87 2.3 28.9 1.0 SG B:CYS90 2.3 35.3 1.0 HB2 B:CYS90 2.5 43.0 1.0 CB B:CYS90 2.9 35.7 1.0 HB3 B:CYS32 3.0 36.7 1.0 H B:CYS35 3.1 43.0 1.0 CB B:CYS32 3.1 30.4 1.0 HB3 B:CYS35 3.1 39.1 1.0 HB2 B:CYS32 3.2 36.7 1.0 H B:CYS87 3.2 39.5 1.0 CB B:CYS35 3.3 32.4 1.0 HB3 B:CYS87 3.4 41.9 1.0 HB3 B:CYS90 3.5 43.0 1.0 CB B:CYS87 3.5 34.8 1.0 H B:CYS90 3.7 39.8 1.0 HB2 B:LEU34 3.7 41.9 1.0 N B:CYS35 3.7 35.7 1.0 HG22 B:THR37 3.8 36.2 1.0 N B:CYS87 4.0 32.8 1.0 HB2 B:CYS35 4.1 39.1 1.0 CA B:CYS35 4.1 26.8 1.0 CA B:CYS90 4.2 36.3 1.0 H B:LEU34 4.2 40.6 1.0 N B:CYS90 4.2 33.0 1.0 H B:GLY36 4.3 39.6 1.0 HB2 B:CYS87 4.3 41.9 1.0 CA B:CYS87 4.3 33.4 1.0 HG21 B:THR37 4.4 36.2 1.0 CG2 B:THR37 4.5 30.0 1.0 H B:THR37 4.5 37.5 1.0 CA B:CYS32 4.6 28.1 1.0 CB B:LEU34 4.6 34.8 1.0 HA B:CYS90 4.6 43.7 1.0 C B:LEU34 4.7 25.8 1.0 HD22 B:LEU86 4.8 45.9 1.0 HA B:LEU86 4.8 38.0 1.0 N B:GLY36 4.8 32.8 1.0 O B:CYS87 4.9 38.5 1.0 HB3 B:LEU34 4.9 41.9 1.0 N B:LEU34 4.9 33.7 1.0 HA B:CYS35 4.9 32.4 1.0 C B:CYS35 4.9 34.1 1.0 C B:CYS87 4.9 38.5 1.0 HA B:CYS32 5.0 34.0 1.0 HD12 B:LEU34 5.0 58.2 1.0 HB3 B:LEU86 5.0 41.0 1.0 C B:CYS32 5.0 28.4 1.0 CA B:LEU34 5.0 31.3 1.0

Zinc binding site 3 out of 4 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn403 b:28.7 occ:1.00 SG C:CYS35 2.3 24.3 1.0 SG C:CYS32 2.3 27.9 1.0 SG C:CYS90 2.3 24.5 1.0 SG C:CYS87 2.3 22.9 1.0 HB2 C:CYS90 2.9 21.7 1.0 HB3 C:CYS35 2.9 19.6 1.0 HB3 C:CYS87 3.1 27.5 1.0 H C:CYS87 3.1 28.0 1.0 CB C:CYS35 3.2 16.5 1.0 CB C:CYS90 3.2 18.0 1.0 HB3 C:CYS32 3.2 32.2 1.0 CB C:CYS32 3.2 26.7 1.0 HB2 C:CYS32 3.3 32.2 1.0 CB C:CYS87 3.3 22.8 1.0 H C:CYS35 3.4 26.5 1.0 H C:CYS90 3.7 31.3 1.0 HB3 C:CYS90 3.8 21.7 1.0 HG22 C:THR37 3.8 34.3 1.0 N C:CYS35 3.8 21.9 1.0 N C:CYS87 3.9 23.1 1.0 HB2 C:CYS35 3.9 19.6 1.0 CA C:CYS35 4.1 19.6 1.0 HB2 C:LEU34 4.1 32.8 1.0 HB2 C:CYS87 4.1 27.5 1.0 CA C:CYS87 4.2 26.2 1.0 HG21 C:THR37 4.3 34.3 1.0 N C:CYS90 4.3 25.9 1.0 CA C:CYS90 4.4 23.7 1.0 H C:LEU34 4.4 26.0 1.0 H C:THR37 4.5 33.5 1.0 CG2 C:THR37 4.5 28.5 1.0 O C:HOH530 4.5 25.6 1.0 H C:GLY36 4.6 31.1 1.0 CA C:CYS32 4.7 25.5 1.0 C C:LEU34 4.7 20.9 1.0 HA C:LEU86 4.7 31.5 1.0 HA C:CYS90 4.7 28.6 1.0 C C:CYS35 4.8 22.6 1.0 HB3 C:LEU86 4.8 30.2 1.0 O C:CYS87 4.8 23.5 1.0 HD22 C:LEU86 4.8 34.7 1.0 HB C:THR37 4.8 24.9 1.0 C C:CYS87 4.8 21.6 1.0 O C:HOH620 4.8 24.2 1.0 HA C:CYS35 4.9 23.7 1.0 CB C:LEU34 4.9 27.2 1.0 N C:GLY36 4.9 25.8 1.0 HA C:CYS87 5.0 31.6 1.0 HA C:CYS32 5.0 30.8 1.0

Zinc binding site 4 out of 4 in the Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Cbass CAP5 From Pseudomonas Syringae As An Activated Tetramer with the Cyclic Dinucleotide 3'2'-C-Diamp Ligand (1 Tetramer in the Au) within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn403 b:39.7 occ:1.00 SG D:CYS32 2.3 37.9 1.0 SG D:CYS35 2.3 41.8 1.0 SG D:CYS90 2.3 44.0 1.0 SG D:CYS87 2.3 41.6 1.0 HB2 D:CYS90 2.6 53.6 1.0 HB3 D:CYS35 2.9 45.3 1.0 CB D:CYS90 3.0 44.5 1.0 H D:CYS35 3.1 43.4 1.0 HB3 D:CYS32 3.1 44.8 1.0 CB D:CYS35 3.2 38.5 1.0 CB D:CYS32 3.2 37.1 1.0 H D:CYS87 3.3 47.0 1.0 HB3 D:CYS87 3.3 50.6 1.0 HB2 D:CYS32 3.4 44.8 1.0 CB D:CYS87 3.5 42.0 1.0 H D:CYS90 3.5 60.8 1.0 HB3 D:CYS90 3.6 53.6 1.0 N D:CYS35 3.7 36.9 1.0 HB2 D:LEU34 3.8 45.3 1.0 HB2 D:CYS35 4.0 45.3 1.0 N D:CYS87 4.0 39.9 1.0 CA D:CYS35 4.0 37.0 1.0 N D:CYS90 4.1 50.5 1.0 CA D:CYS90 4.2 55.0 1.0 HB2 D:CYS87 4.2 50.6 1.0 H D:LEU34 4.3 43.4 1.0 CA D:CYS87 4.3 41.0 1.0 HB D:THR37 4.3 43.5 1.0 O D:HOH597 4.3 44.6 1.0 H D:THR37 4.4 41.6 1.0 H D:GLY36 4.5 40.7 1.0 HA D:CYS90 4.6 66.2 1.0 O D:CYS87 4.6 43.3 1.0 CA D:CYS32 4.7 35.1 1.0 C D:LEU34 4.7 36.8 1.0 CB D:LEU34 4.7 38.5 1.0 HA D:LEU86 4.8 45.9 1.0 C D:CYS35 4.8 35.6 1.0 HG1 D:THR37 4.8 53.0 1.0 HA D:CYS35 4.8 43.5 1.0 C D:CYS87 4.8 42.8 1.0 N D:GLY36 4.9 34.6 1.0 N D:LEU34 4.9 36.0 1.0 HD22 D:LEU86 5.0 46.4 1.0 OG1 D:THR37 5.0 44.0 1.0 HD21 D:LEU39 5.0 51.4 1.0

O.Rechkoblit, D.Sciaky, D.F.Kreitler, A.Buku, J.Kottur, A.K.Aggarwal. Activation of Cbass-CAP5 Endonuclease Immune Effector By Cyclic Nucleotides: A View at High Resolution Nat.Struct.Mol.Biol. 2024.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-024-01220-X