Calcium in PDB 9gco: Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix

The structure of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix, PDB code: 9gco was solved by D.Jurenas, L.Terradot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.92 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.955, 82.353, 121.607, 90, 90, 90
R / Rfree (%)	18.8 / 22.3

The binding sites of Calcium atom in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix (pdb code 9gco). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix, PDB code: 9gco:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:48.5 occ:1.00 O A:ASP112 2.2 42.6 1.0 OD1 F:ASP110 2.5 40.3 1.0 OD2 F:ASP110 2.5 40.8 1.0 O F:HOH334 2.7 46.0 1.0 CG F:ASP110 2.8 37.2 1.0 C A:ILE115 3.1 62.8 1.0 O A:ILE115 3.2 70.8 1.0 C A:ASP112 3.3 42.1 1.0 HA A:ASP112 3.6 55.4 1.0 HB3 A:ASP112 3.6 55.6 1.0 CA A:ASP112 3.9 46.1 1.0 H F:PHE111 4.0 43.6 1.0 CB A:ASP112 4.2 46.3 1.0 HA A:SER113 4.2 55.1 1.0 HB3 F:PHE111 4.2 43.9 1.0 CB F:ASP110 4.3 36.1 1.0 H A:ILE115 4.3 74.9 1.0 O F:PHE111 4.4 33.7 1.0 N A:SER113 4.4 41.7 1.0 CA A:ILE115 4.5 59.8 1.0 N F:PHE111 4.5 36.3 1.0 N A:ILE115 4.6 62.3 1.0 HG22 A:ILE115 4.6 87.3 1.0 HE2 F:LYS70 4.6 50.5 1.0 CA A:SER113 4.7 45.9 1.0 HB2 F:ASP110 4.7 43.4 1.0 HB3 F:ASP110 4.7 43.4 1.0 C A:SER113 4.8 47.6 1.0 HE3 F:LYS70 4.8 50.5 1.0 CG A:ASP112 4.8 55.4 1.0 HB A:ILE115 4.9 77.2 1.0 OD2 A:ASP112 5.0 59.8 1.0

Calcium binding site 2 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:39.7 occ:0.50 O B:TYR11 2.4 35.0 1.0 OD1 B:ASP10 2.6 45.0 1.0 H B:TYR11 3.4 44.3 1.0 CG B:ASP10 3.5 48.1 1.0 C B:TYR11 3.6 38.4 1.0 OD2 B:ASP10 3.8 49.3 1.0 N B:TYR11 3.9 36.9 1.0 HB2 B:TYR11 4.0 45.1 1.0 CA B:TYR11 4.2 36.2 1.0 HA B:ILE12 4.3 40.8 1.0 HG22 B:ILE12 4.4 49.2 1.0 HA B:ASP10 4.5 52.9 1.0 CB B:TYR11 4.6 37.5 1.0 C B:ASP10 4.7 39.3 1.0 N B:ILE12 4.7 33.6 1.0 CB B:ASP10 4.8 42.5 1.0 HG23 B:ILE12 4.9 49.2 1.0 CA B:ASP10 4.9 44.0 1.0

Calcium binding site 3 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:57.0 occ:1.00 OD2 C:ASP48 2.5 55.7 1.0 O C:ASN47 2.7 52.5 1.0 HB2 C:ASP48 3.1 61.1 1.0 CG C:ASP48 3.4 56.7 1.0 CB C:ASP48 3.7 50.8 1.0 HA C:ASP48 3.7 61.1 1.0 HH21 B:ARG47 3.7 88.2 1.0 OD2 C:ASP57 3.8 71.8 1.0 C C:ASN47 3.9 56.4 1.0 CA C:ASP48 4.1 50.8 1.0 NH2 B:ARG47 4.2 73.5 1.0 HH22 B:ARG47 4.2 88.2 1.0 HG C:SER46 4.2 75.2 1.0 HB2 C:ASP57 4.4 64.1 1.0 N C:ASP48 4.5 53.5 1.0 HB3 C:ASP48 4.5 61.1 1.0 OG C:SER46 4.5 62.6 1.0 OD1 C:ASP48 4.6 54.8 1.0 H C:ASN47 4.6 68.1 1.0 HB3 C:SER53 4.7 59.9 1.0 CG C:ASP57 4.7 59.4 1.0 CB C:ASP57 4.9 53.3 1.0 HB3 C:ASP57 4.9 64.1 1.0

Calcium binding site 4 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:51.4 occ:1.00 O C:GLY97 2.4 41.6 1.0 O C:HOH321 2.8 38.9 1.0 C C:GLY97 3.5 40.2 1.0 HA2 C:GLY97 3.8 50.6 1.0 CA C:GLY97 4.1 42.1 1.0 HA3 C:GLY97 4.1 50.6 1.0 HD3 C:PRO99 4.1 46.7 1.0 OD1 C:ASP136 4.2 79.9 1.0 HA C:LEU134 4.2 54.3 1.0 OD2 C:ASP136 4.3 69.9 1.0 HA C:GLN98 4.4 51.2 1.0 N C:GLN98 4.7 38.2 1.0 O C:LEU134 4.7 49.9 1.0 CG C:ASP136 4.7 74.1 1.0 O C:SER133 4.9 41.2 1.0

Calcium binding site 5 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:43.5 occ:1.00 O D:ASP112 2.2 44.9 1.0 O C:HOH302 2.2 41.0 1.0 O D:ILE115 2.5 55.0 1.0 OD2 C:ASP110 2.5 43.7 1.0 OD1 C:ASP110 2.5 41.2 1.0 O D:HOH321 2.5 42.9 1.0 CG C:ASP110 2.8 42.1 1.0 C D:ILE115 3.3 58.3 1.0 C D:ASP112 3.4 41.2 1.0 HA D:ASP112 3.6 51.2 1.0 HB3 D:ASP112 3.8 56.4 1.0 CA D:ASP112 4.0 42.6 1.0 H C:PHE111 4.0 44.8 1.0 HA D:SER113 4.2 54.8 1.0 HB3 C:PHE111 4.2 51.6 1.0 H D:ILE115 4.2 62.5 1.0 CB C:ASP110 4.4 39.9 1.0 CB D:ASP112 4.4 46.9 1.0 N D:SER113 4.4 41.7 1.0 CA D:ILE115 4.4 57.0 1.0 N D:ILE115 4.5 52.0 1.0 OD1 D:ASP112 4.5 61.5 1.0 O C:PHE111 4.6 44.3 1.0 N C:PHE111 4.6 37.3 1.0 CA D:SER113 4.6 45.6 1.0 C D:SER113 4.7 49.1 1.0 HB3 C:ASP110 4.8 48.0 1.0 HB2 C:ASP110 4.8 48.0 1.0 O C:HOH318 4.8 39.6 1.0 HG22 D:ILE115 4.8 78.7 1.0 HE2 C:LYS70 4.8 55.0 1.0 O D:SER113 4.9 46.1 1.0 HE3 C:LYS70 4.9 55.0 1.0 N D:HIS114 5.0 45.8 1.0 CG D:ASP112 5.0 51.0 1.0

Calcium binding site 6 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca201 b:45.3 occ:1.00 OD1 F:ASP117 2.4 49.2 1.0 O F:HOH344 2.5 51.0 1.0 O F:HOH347 2.7 52.9 1.0 OD2 F:ASP117 3.0 47.8 1.0 CG F:ASP117 3.0 44.8 1.0 HG12 F:ILE66 4.2 44.9 1.0 HD11 F:ILE66 4.4 49.5 1.0 O F:ASP117 4.5 40.7 1.0 CB F:ASP117 4.5 42.5 1.0 C F:ASP117 4.7 39.1 1.0 HA F:ASP117 4.7 44.8 1.0 HB3 F:ASP117 4.9 51.0 1.0 CA F:ASP117 4.9 37.3 1.0 CG1 F:ILE66 4.9 37.4 1.0 CD1 F:ILE66 5.0 41.2 1.0

Calcium binding site 7 out of 7 in the Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Xenorhabdus Bovienii Thioredoxin Complex with Rhs Toxin Trex and Immunity Protein Trix within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca202 b:41.6 occ:1.00 O F:HOH303 2.2 37.3 1.0 O F:GLY97 2.4 35.1 1.0 O F:HOH309 2.4 39.7 1.0 O F:HOH310 3.1 45.6 1.0 C F:GLY97 3.5 33.2 1.0 HA2 F:GLY97 3.6 39.9 1.0 CA F:GLY97 3.9 33.5 1.0 HA3 F:GLY97 3.9 39.9 1.0 HD3 F:PRO99 4.1 47.0 1.0 HA F:LEU134 4.1 43.1 1.0 OD1 F:ASP136 4.3 43.6 1.0 HA F:GLN98 4.3 43.6 1.0 OD2 F:ASP136 4.4 42.8 1.0 N F:GLN98 4.6 33.9 1.0 O F:SER133 4.8 36.2 1.0 CG F:ASP136 4.8 44.5 1.0 O F:LEU134 4.8 39.6 1.0 HD23 F:LEU134 4.8 39.5 1.0 HD22 F:LEU134 4.8 39.5 1.0 CA F:GLN98 5.0 36.2 1.0 CD F:PRO99 5.0 39.1 1.0

B.Dumont, L.Terradot, E.Cascales, L.Van Melderen, D.Jurenas. Thioredoxin 1 Moonlights As A Chaperone For An Interbacterial Adp-Ribosyltransferase Toxin Nat Commun 2024.
ISSN: ESSN 2041-1723