Magnesium 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:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 7 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 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 Magnesium with other atoms in the Mg 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:Mg408 b:38.9 occ:1.00 NE2 A:HIS91 1.9 27.7 1.0 O A:HOH579 2.1 26.5 1.0 O A:HOH552 2.1 29.9 1.0 O A:HOH544 2.1 28.7 1.0 O A:HOH606 2.1 30.6 1.0 OD2 A:ASP95 2.1 31.3 1.0 CD2 A:HIS91 2.8 28.9 1.0 CE1 A:HIS91 2.9 30.2 1.0 HD2 A:HIS91 3.0 34.9 1.0 CG A:ASP95 3.0 33.5 1.0 HE1 A:HIS91 3.2 36.4 1.0 OD1 A:ASP95 3.3 28.2 1.0 H A:HIS56 3.4 42.3 1.0 HB1 A:ALA55 3.5 37.9 1.0 HA A:ALA55 3.9 27.5 1.0 CG A:HIS91 4.0 27.5 1.0 O A:HOH636 4.0 33.4 1.0 ND1 A:HIS91 4.0 29.6 1.0 O A:HOH577 4.2 37.8 1.0 O A:HOH568 4.2 38.3 1.0 CB A:ALA55 4.2 31.4 1.0 N A:HIS56 4.2 35.1 1.0 HB2 A:ALA55 4.2 37.9 1.0 O A:HIS56 4.4 33.6 1.0 CB A:ASP95 4.4 32.7 1.0 CA A:ALA55 4.5 23.6 1.0 O A:HOH565 4.5 30.4 1.0 HB2 A:HIS56 4.5 33.2 1.0 HD11 A:ILE94 4.6 39.9 1.0 HB2 A:ASP95 4.6 39.5 1.0 HB3 A:ASP95 4.7 39.5 1.0 HD1 A:HIS91 4.8 35.7 1.0 C A:ALA55 4.9 32.2 1.0 O A:HOH641 4.9 50.2 1.0 HG2 A:PRO65 4.9 47.5 1.0 O A:HIS91 4.9 29.1 1.0 HD1 A:HIS56 4.9 48.8 1.0 HG13 A:ILE94 5.0 39.7 1.0

Magnesium binding site 2 out of 7 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 Magnesium with other atoms in the Mg 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 A:Mg409 b:37.0 occ:1.00 O A:HOH517 2.1 30.8 1.0 O A:HOH598 2.1 38.7 1.0 O A:HOH592 2.1 42.7 1.0 O A:HOH528 2.1 38.0 1.0 O A:HOH531 2.1 33.9 1.0 OD1 A:ASP92 2.1 37.1 1.0 CG A:ASP92 2.9 33.3 1.0 OD2 A:ASP92 3.1 36.2 1.0 HH21 A:ARG96 3.7 56.4 1.0 OE1 A:GLU53 4.0 36.1 1.0 O A:HOH640 4.1 44.7 1.0 O A:HOH568 4.2 38.3 1.0 O A:PRO88 4.2 28.1 1.0 NH2 A:ARG96 4.3 46.9 1.0 HH22 A:ARG96 4.3 56.4 1.0 CB A:ASP92 4.3 30.9 1.0 HA A:ASP92 4.4 38.1 1.0 HB3 A:HIS91 4.4 38.9 1.0 HB3 C:PRO88 4.5 23.8 1.0 O A:HOH586 4.5 38.8 1.0 OE2 C:GLU53 4.6 38.6 1.0 H A:ASP92 4.6 39.8 1.0 OE2 A:GLU53 4.6 47.7 1.0 HB3 A:PRO88 4.7 35.9 1.0 O C:HOH599 4.7 28.6 1.0 CA A:ASP92 4.7 31.6 1.0 CD A:GLU53 4.7 37.1 1.0 N A:ASP92 4.8 33.0 1.0 HB3 A:ASP92 4.8 37.2 1.0 O C:HOH541 4.8 44.2 1.0 O A:HOH641 4.8 50.2 1.0 HB2 A:ASP92 4.9 37.2 1.0 HD1 A:HIS91 4.9 35.7 1.0 HA A:PRO88 4.9 31.9 1.0

Magnesium binding site 3 out of 7 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 Magnesium with other atoms in the Mg 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 B:Mg404 b:63.2 occ:1.00 O B:TYR101 2.0 61.2 1.0 OD1 B:ASP97 2.0 77.2 1.0 O B:HOH505 2.1 68.2 1.0 OD1 B:ASP95 2.1 66.7 1.0 OD1 B:ASP99 2.1 69.8 1.0 OE2 B:GLU103 2.1 59.1 1.0 HA B:ASP95 2.9 82.9 1.0 CD B:GLU103 3.0 75.2 1.0 CG B:ASP97 3.1 73.9 1.0 CG B:ASP99 3.2 63.1 1.0 H B:TYR101 3.2 62.6 1.0 C B:TYR101 3.2 55.0 1.0 CG B:ASP95 3.3 63.3 1.0 OE1 B:GLU103 3.4 88.9 1.0 OD2 B:ASP97 3.5 71.4 1.0 H B:ASP99 3.5 82.6 1.0 H B:ASP97 3.5 84.4 1.0 OD2 B:ASP99 3.6 71.0 1.0 CA B:ASP95 3.7 68.9 1.0 HA B:PRO102 3.8 63.1 1.0 N B:TYR101 3.9 52.0 1.0 H B:ALA98 4.0 81.1 1.0 CB B:ASP95 4.0 64.1 1.0 CA B:TYR101 4.1 55.8 1.0 H B:ARG96 4.1 76.5 1.0 N B:PRO102 4.1 48.9 1.0 N B:ASP99 4.2 68.7 1.0 C B:PRO102 4.2 57.1 1.0 CA B:PRO102 4.2 52.5 1.0 H B:GLU103 4.2 69.3 1.0 C B:ASP95 4.2 65.1 1.0 HB2 B:ASP95 4.2 77.1 1.0 OD2 B:ASP95 4.2 69.9 1.0 N B:ASP97 4.2 70.2 1.0 HB2 B:TYR101 4.2 61.4 1.0 N B:GLU103 4.2 57.6 1.0 H B:GLY100 4.2 87.3 1.0 HG2 B:GLU103 4.3 90.3 1.0 CG B:GLU103 4.3 75.1 1.0 N B:ARG96 4.3 63.6 1.0 N B:ALA98 4.4 67.4 1.0 CB B:ASP97 4.4 63.8 1.0 O B:ILE94 4.4 70.6 1.0 CB B:ASP99 4.5 61.0 1.0 N B:GLY100 4.6 72.6 1.0 HA B:GLU103 4.6 66.4 1.0 CA B:ASP97 4.6 76.1 1.0 O B:PRO102 4.7 59.3 1.0 HB3 B:ASP97 4.7 76.8 1.0 C B:ASP97 4.7 73.5 1.0 CB B:TYR101 4.7 51.0 1.0 CA B:ASP99 4.7 70.0 1.0 HB3 B:ASP99 4.8 73.4 1.0 HB3 B:ASP95 4.8 77.1 1.0 N B:ASP95 4.8 60.7 1.0 HA B:TYR101 4.9 67.1 1.0 HG3 B:GLU103 4.9 90.3 1.0 CA B:GLU103 4.9 55.2 1.0 C B:ASP99 4.9 63.9 1.0 HD11 B:LEU58 5.0 84.0 1.0 C B:GLY100 5.0 48.7 1.0 HD12 B:ILE94 5.0 75.0 1.0 O B:ASP95 5.0 65.0 1.0

Magnesium binding site 4 out of 7 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 Magnesium with other atoms in the Mg 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 C:Mg404 b:28.4 occ:1.00 NE2 C:HIS91 1.9 26.4 1.0 O C:HOH522 2.1 25.0 1.0 O C:HOH581 2.1 25.6 1.0 O C:HOH586 2.1 27.5 1.0 O C:HOH565 2.1 36.2 1.0 OD2 C:ASP95 2.1 27.0 1.0 CE1 C:HIS91 2.9 25.4 1.0 CD2 C:HIS91 2.9 25.9 1.0 HE1 C:HIS91 3.1 30.6 1.0 CG C:ASP95 3.1 27.2 1.0 HD2 C:HIS91 3.1 31.2 1.0 OD1 C:ASP95 3.4 23.4 1.0 H C:HIS56 3.5 42.4 1.0 O C:HOH572 3.5 27.8 1.0 HB1 C:ALA55 3.6 36.2 1.0 HA C:ALA55 3.9 36.1 1.0 O C:HOH564 4.0 35.5 1.0 ND1 C:HIS91 4.0 22.4 1.0 CG C:HIS91 4.0 21.5 1.0 N C:HIS56 4.2 35.2 1.0 O C:HIS56 4.3 27.0 1.0 CB C:ALA55 4.3 30.1 1.0 O C:HOH536 4.4 26.6 1.0 HB2 C:HIS56 4.4 37.6 1.0 O C:HOH606 4.4 26.8 1.0 HB2 C:ALA55 4.4 36.2 1.0 CB C:ASP95 4.5 25.4 1.0 CA C:ALA55 4.5 29.9 1.0 O C:HOH621 4.6 37.1 1.0 HB3 C:ASP95 4.7 30.7 1.0 HB2 C:ASP95 4.7 30.7 1.0 HD11 C:ILE94 4.7 28.4 1.0 HG2 C:PRO65 4.8 44.2 1.0 HD1 C:HIS91 4.8 25.9 1.0 C C:ALA55 4.8 31.0 1.0 HH21 C:ARG66 4.9 38.6 1.0

Magnesium binding site 5 out of 7 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg405 b:42.1 occ:1.00 O C:HOH529 2.1 34.2 1.0 O C:HOH583 2.1 36.5 1.0 O C:HOH599 2.1 28.6 1.0 O C:HOH541 2.1 44.2 1.0 O C:HOH596 2.1 42.2 1.0 OD1 C:ASP92 2.1 27.9 1.0 CG C:ASP92 3.0 31.5 1.0 OD2 C:ASP92 3.3 38.0 1.0 HH21 C:ARG96 3.8 50.6 1.0 O C:HOH564 4.0 35.5 1.0 OE1 C:GLU53 4.2 30.1 1.0 O C:HOH617 4.2 36.2 1.0 HA C:ASP92 4.2 33.3 1.0 O C:PRO88 4.3 20.4 1.0 CB C:ASP92 4.3 28.4 1.0 NH2 C:ARG96 4.4 42.1 1.0 HH22 C:ARG96 4.4 50.6 1.0 O A:HOH640 4.4 44.7 1.0 HB3 A:PRO88 4.5 35.9 1.0 H C:ASP92 4.6 26.1 1.0 HB3 C:HIS91 4.6 24.4 1.0 CA C:ASP92 4.6 27.6 1.0 HB2 C:ASP92 4.7 34.2 1.0 N C:ASP92 4.7 21.6 1.0 O A:HOH598 4.8 38.7 1.0 HD1 C:HIS91 4.8 25.9 1.0 O A:HOH528 4.8 38.0 1.0 OE2 A:GLU53 4.9 47.7 1.0 HB3 C:PRO88 4.9 23.8 1.0 O C:HOH592 4.9 39.1 1.0 OE2 C:GLU53 4.9 38.6 1.0 HB3 C:ASP92 5.0 34.2 1.0 CD C:GLU53 5.0 36.0 1.0 HA C:PRO88 5.0 26.5 1.0

Magnesium binding site 6 out of 7 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg404 b:62.6 occ:1.00 O D:TYR101 2.0 56.4 1.0 OD1 D:ASP99 2.1 67.0 1.0 O D:HOH513 2.1 69.4 1.0 OD1 D:ASP97 2.1 62.6 1.0 OE2 D:GLU103 2.1 63.6 1.0 OD1 D:ASP95 2.1 61.0 1.0 CG D:ASP97 2.9 66.1 1.0 CD D:GLU103 3.0 67.2 1.0 HA D:ASP95 3.1 71.0 1.0 CG D:ASP99 3.1 63.9 1.0 H D:TYR101 3.1 70.9 1.0 CG D:ASP95 3.2 56.8 1.0 C D:TYR101 3.2 60.2 1.0 OD2 D:ASP97 3.3 76.2 1.0 H D:ASP99 3.3 77.4 1.0 OE1 D:GLU103 3.3 68.7 1.0 H D:ASP97 3.4 70.3 1.0 OD2 D:ASP99 3.6 63.0 1.0 CA D:ASP95 3.8 59.0 1.0 N D:TYR101 3.8 58.9 1.0 HB2 D:TYR101 3.9 75.2 1.0 CB D:ASP95 3.9 60.5 1.0 HA D:PRO102 4.0 66.2 1.0 CA D:TYR101 4.0 57.0 1.0 OD2 D:ASP95 4.1 60.3 1.0 HB2 D:ASP95 4.1 72.8 1.0 N D:ASP99 4.1 64.3 1.0 C D:ASP95 4.1 60.7 1.0 N D:ASP97 4.2 58.4 1.0 N D:PRO102 4.2 62.2 1.0 H D:ALA98 4.2 76.0 1.0 CB D:ASP97 4.2 63.8 1.0 C D:PRO102 4.2 59.1 1.0 H D:ARG96 4.2 83.4 1.0 CB D:ASP99 4.2 59.9 1.0 CA D:PRO102 4.3 55.0 1.0 CG D:GLU103 4.3 72.0 1.0 HG2 D:GLU103 4.3 86.5 1.0 N D:GLU103 4.4 56.6 1.0 N D:ARG96 4.4 69.3 1.0 CB D:TYR101 4.4 62.5 1.0 HB3 D:ASP99 4.4 72.0 1.0 H D:GLU103 4.4 68.1 1.0 HB3 D:ASP97 4.5 76.7 1.0 N D:ALA98 4.5 63.2 1.0 H D:GLY100 4.5 68.6 1.0 CA D:ASP97 4.6 60.2 1.0 CA D:ASP99 4.6 60.5 1.0 O D:PRO102 4.6 59.0 1.0 HB3 D:TYR101 4.6 75.2 1.0 N D:GLY100 4.7 57.0 1.0 HA D:GLU103 4.7 72.0 1.0 C D:ASP97 4.7 65.0 1.0 C D:ASP99 4.7 64.5 1.0 O D:ASP95 4.7 60.1 1.0 HB3 D:ASP95 4.8 72.8 1.0 O D:ILE94 4.8 53.5 1.0 HA D:TYR101 4.9 68.5 1.0 HG3 D:GLU103 4.9 86.5 1.0 HB2 D:ASP97 4.9 76.7 1.0 C D:GLY100 5.0 58.5 1.0 CA D:GLU103 5.0 59.8 1.0

Magnesium binding site 7 out of 7 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg405 b:43.0 occ:1.00 O D:HOH528 2.1 41.6 1.0 O D:HOH582 2.1 42.0 1.0 O D:HOH547 2.1 36.7 1.0 O D:HOH602 2.1 43.5 1.0 O D:HOH532 2.1 38.7 1.0 O D:ARG44 2.2 44.0 1.0 C D:ARG44 3.2 39.6 1.0 HA D:ARG44 3.4 47.5 1.0 CA D:ARG44 3.8 39.5 1.0 HB3 D:ARG44 4.2 47.7 1.0 H D:GLY46 4.2 59.9 1.0 HA D:ALA45 4.3 48.2 1.0 N D:ALA45 4.3 45.0 1.0 O D:TYR43 4.5 39.0 1.0 N D:GLY46 4.6 49.8 1.0 CB D:ARG44 4.6 39.6 1.0 O D:HOH576 4.6 37.4 1.0 CA D:ALA45 4.7 40.0 1.0 C D:ALA45 4.9 45.9 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