Calcium in PDB 6tg2: Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10

The structure of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10, PDB code: 6tg2 was solved by S.Morera, L.Marty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.19 / 2.21
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	67.920, 132.130, 69.460, 90.00, 91.23, 90.00
R / Rfree (%)	18.5 / 21.8

The binding sites of Calcium atom in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 (pdb code 6tg2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10, PDB code: 6tg2:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:48.8 occ:1.00 NH1 A:ARG238 3.1 25.0 1.0 O A:HOH544 3.2 21.8 1.0 N A:GLY40 3.3 27.4 1.0 CD A:ARG238 3.6 27.9 1.0 CA A:ALA218 3.9 27.8 1.0 CA A:GLY40 4.0 26.7 1.0 CB A:ALA221 4.1 25.6 1.0 CZ A:ARG238 4.1 35.7 1.0 CB A:ALA218 4.2 28.6 1.0 CA A:GLY39 4.2 27.0 1.0 N A:ALA218 4.3 28.0 1.0 NE A:ARG238 4.3 29.8 1.0 C A:GLY39 4.3 31.1 1.0 O A:GLY217 4.3 29.8 1.0 C A:GLY217 4.5 31.1 1.0 CE1 A:PHE295 4.7 34.2 1.0 CA A:ARG238 4.8 27.1 1.0 O A:HOH534 4.8 39.7 1.0 CG A:ARG238 4.8 28.8 1.0 CB A:ARG238 4.9 24.6 1.0 N A:TRP41 5.0 23.5 1.0

Calcium binding site 2 out of 5 in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:87.8 occ:1.00 O A:VAL331 3.4 33.1 1.0 O A:HOH546 3.9 47.8 1.0 CA A:ASP332 3.9 31.1 1.0 CB A:ASP332 4.0 33.5 1.0 C A:VAL331 4.1 33.1 1.0 O A:SER330 4.1 31.4 1.0 CB A:SER330 4.1 31.8 1.0 OD1 A:ASP332 4.2 39.1 1.0 N A:ASP332 4.3 31.5 1.0 CG A:ASP332 4.3 36.3 1.0 C A:SER330 4.5 32.2 1.0 CD A:PRO333 4.7 30.0 1.0 CA A:SER330 4.9 28.8 1.0

Calcium binding site 3 out of 5 in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca407 b:62.6 occ:1.00 OE1 A:GLN67 2.6 29.0 1.0 N A:GLY217 2.9 31.4 1.0 CB A:SER37 3.2 27.7 1.0 OG A:SER37 3.2 41.5 1.0 CZ3 A:TRP235 3.3 27.6 1.0 NH2 A:ARG238 3.4 25.9 1.0 O A:SER37 3.5 32.0 1.0 CD A:GLN67 3.5 27.7 1.0 CA A:SER216 3.6 33.2 1.0 O A:HOH532 3.7 34.4 1.0 C A:SER216 3.7 37.0 1.0 NE2 A:GLN67 3.7 24.4 1.0 CA A:GLY217 3.8 29.0 1.0 OXT A:N72401 3.8 29.9 1.0 CB A:SER216 3.9 31.3 1.0 CH2 A:TRP235 4.0 28.2 1.0 C A:SER37 4.2 32.4 1.0 CZ A:ARG238 4.2 35.7 1.0 CA A:SER37 4.3 28.4 1.0 CE3 A:TRP235 4.3 25.8 1.0 OAD A:N72401 4.5 37.0 1.0 NE A:ARG238 4.7 29.8 1.0 O A:GLU215 4.8 40.7 1.0 C A:N72401 4.8 26.5 1.0 NH1 A:ARG238 4.9 25.0 1.0 N A:SER216 4.9 34.6 1.0 O A:SER216 4.9 36.4 1.0 N A:ALA218 4.9 28.0 1.0 C A:GLY217 4.9 31.1 1.0 CG A:GLN67 4.9 25.9 1.0 O A:HOH509 5.0 36.6 1.0

Calcium binding site 4 out of 5 in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca403 b:55.6 occ:1.00 O B:GLY237 2.6 32.9 1.0 N B:ALA296 2.9 32.8 1.0 N B:GLY241 3.3 28.5 1.0 C B:GLY237 3.4 30.3 1.0 CA B:GLY237 3.5 24.7 1.0 CB B:ALA296 3.6 33.3 1.0 CD1 B:PHE295 3.6 31.9 1.0 CA B:GLY241 3.7 28.0 1.0 CA B:PHE295 3.7 31.0 1.0 C B:PHE295 3.8 34.4 1.0 CA B:ALA296 3.8 33.3 1.0 CB B:GLN240 3.8 28.0 1.0 CG B:PHE295 3.9 29.9 1.0 C B:GLN240 4.0 32.2 1.0 CE1 B:PHE295 4.0 30.9 1.0 CG B:GLN240 4.3 50.3 1.0 CA B:GLN240 4.4 26.4 1.0 CB B:PHE295 4.4 30.9 1.0 O B:HOH557 4.5 45.1 1.0 O B:ALA296 4.5 38.5 1.0 CD2 B:PHE295 4.5 29.0 1.0 C B:ALA296 4.6 39.2 1.0 CZ B:PHE295 4.6 27.9 1.0 N B:ARG238 4.7 24.0 1.0 O B:GLN240 4.7 33.9 1.0 N B:GLN240 4.8 25.2 1.0 CE2 B:PHE295 4.8 30.0 1.0 N B:PHE295 4.9 35.5 1.0 N B:GLY237 4.9 25.4 1.0 O B:SER294 4.9 46.5 1.0 ND2 B:ASN244 4.9 48.9 1.0 O B:GLY236 4.9 30.8 1.0 O B:PHE295 5.0 33.1 1.0

Calcium binding site 5 out of 5 in the Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Pbp/Sbp Mota in Complex with Mannopinic Acid From A.Tumefacien R10 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca402 b:83.2 occ:1.00 NZ D:LYS314 3.6 82.0 1.0 CD D:GLU313 3.8 66.3 1.0 OE2 D:GLU313 3.9 51.5 1.0 OE1 D:GLU313 4.0 48.8 1.0 CG D:GLU313 4.2 53.7 1.0 CD D:LYS314 4.2 69.5 1.0 CE D:LYS314 4.5 79.6 1.0 CA D:LYS314 4.7 43.9 1.0 N D:LYS314 4.7 44.4 1.0 CB D:LYS314 4.8 46.8 1.0 CB D:GLU313 4.8 45.7 1.0

A.Vigouroux, J.Dore, L.Marty, M.Aumont-Nicaise, P.Legrand, Y.Dessaux, L.Vial, S.Morera. Import Pathways of the Mannityl-Opines Into the Bacterial Pathogen Agrobacterium Tumefaciens: Structural, Affinity and in Vivo Approaches. Biochem.J. 2020.
ISSN: ESSN 1470-8728
PubMed: 31922182
DOI: 10.1042/BCJ20190886