Calcium in PDB 6eq8: Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58

The structure of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58, PDB code: 6eq8 was solved by A.Vigouroux, S.Morera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.06 / 2.19
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	355.260, 73.660, 108.080, 90.00, 105.49, 90.00
R / Rfree (%)	18.4 / 21.7

The structure of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 also contains other interesting chemical elements:

Chlorine

(Cl)

35 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 (pdb code 6eq8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58, PDB code: 6eq8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca709 b:46.0 occ:1.00 OD1 D:ASP462 2.2 44.5 1.0 O D:PHE464 2.3 46.7 1.0 OD1 D:ASN476 2.4 39.0 1.0 OD1 D:ASP458 2.5 55.8 1.0 ND2 D:ASN466 2.5 43.7 1.0 CG D:ASP460 2.9 47.6 1.0 OD2 D:ASP460 3.3 48.3 1.0 CG D:ASP462 3.4 44.0 1.0 C D:PHE464 3.4 46.6 1.0 CG D:ASN476 3.4 42.4 1.0 CG D:ASN466 3.5 57.3 1.0 CG D:ASP458 3.6 58.7 1.0 OD1 D:ASN466 3.7 52.5 1.0 ND2 D:ASN476 3.8 37.2 1.0 OD2 D:ASP462 3.9 40.9 1.0 CA D:ASP458 4.0 52.3 1.0 N D:ASP460 4.0 52.3 1.0 N D:PHE464 4.1 43.9 1.0 CA D:PHE464 4.1 41.6 1.0 CB D:ASP458 4.2 54.0 1.0 CB D:ASP460 4.2 51.9 1.0 N D:ASP462 4.2 45.8 1.0 CB D:PHE464 4.2 41.8 1.0 N D:THR459 4.2 53.9 1.0 N D:LEU465 4.4 44.6 1.0 CA D:ASP460 4.5 51.7 1.0 C D:ASP458 4.5 57.5 1.0 C D:LEU465 4.5 48.7 1.0 CB D:ASP462 4.5 44.8 1.0 N D:GLY461 4.5 51.6 1.0 OD2 D:ASP458 4.5 68.8 1.0 N D:ASN466 4.7 48.5 1.0 CA D:LEU465 4.7 45.1 1.0 N D:GLY463 4.7 45.5 1.0 CA D:ASP462 4.7 44.5 1.0 CB D:ASN466 4.7 45.9 1.0 C D:ASP460 4.8 56.1 1.0 CB D:ASN476 4.8 36.2 1.0 O D:LEU465 4.8 46.1 1.0 C D:GLY463 4.9 50.3 1.0 C D:ASP462 4.9 48.2 1.0

Calcium binding site 2 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca707 b:75.8 occ:1.00 O B:ARG96 3.8 40.8 1.0 CB B:ARG96 3.9 38.0 1.0 O B:PRO97 4.0 43.7 1.0 O1 B:EDO701 4.1 53.8 1.0 CG B:GLU98 4.2 46.0 1.0 C B:ARG96 4.2 41.2 1.0 OD1 B:ASN516 4.3 77.1 1.0 C1 B:EDO701 4.4 54.3 1.0 ND2 B:ASN516 4.4 72.7 1.0 C B:PRO97 4.4 44.0 1.0 CG B:ASN516 4.5 79.0 1.0 CA B:ARG96 4.6 37.2 1.0 N B:GLU98 4.7 41.3 1.0 CA B:GLU98 4.7 41.4 1.0 N B:PRO97 5.0 37.9 1.0

Calcium binding site 3 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca708 b:41.0 occ:1.00 OD1 B:ASP460 2.2 62.1 1.0 O B:PHE464 2.3 45.6 1.0 OD1 B:ASN476 2.3 39.6 1.0 OD1 B:ASN466 2.3 36.8 1.0 OD1 B:ASP462 2.3 37.0 1.0 OD1 B:ASP458 2.5 53.4 1.0 CG B:ASP460 3.2 60.7 1.0 CG B:ASN466 3.2 45.9 1.0 CG B:ASN476 3.3 44.0 1.0 C B:PHE464 3.3 44.1 1.0 CG B:ASP462 3.4 41.4 1.0 CG B:ASP458 3.6 55.0 1.0 OD2 B:ASP460 3.6 63.7 1.0 ND2 B:ASN466 3.6 38.0 1.0 ND2 B:ASN476 3.7 36.8 1.0 OD2 B:ASP462 3.8 42.6 1.0 CA B:PHE464 4.0 41.4 1.0 N B:PHE464 4.0 44.4 1.0 CA B:ASP458 4.1 48.6 1.0 CB B:ASP458 4.2 49.7 1.0 CB B:PHE464 4.2 42.6 1.0 N B:ASP460 4.2 51.1 1.0 N B:THR459 4.3 49.7 1.0 N B:ASP462 4.4 49.1 1.0 N B:LEU465 4.4 38.2 1.0 C B:LEU465 4.4 38.8 1.0 N B:ASN466 4.5 37.2 1.0 CB B:ASP460 4.5 54.8 1.0 OD2 B:ASP458 4.5 63.3 1.0 CB B:ASN466 4.5 35.2 1.0 C B:ASP458 4.6 53.9 1.0 CB B:ASP462 4.6 47.0 1.0 CB B:ASN476 4.6 37.0 1.0 CA B:LEU465 4.7 36.9 1.0 O B:LEU465 4.7 36.5 1.0 CA B:ASP460 4.8 52.8 1.0 N B:GLY461 4.8 55.3 1.0 N B:GLY463 4.9 46.5 1.0 CA B:ASP462 4.9 47.4 1.0 CA B:ASN466 4.9 38.0 1.0 C B:ASP460 5.0 58.9 1.0

Calcium binding site 4 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca709 b:68.8 occ:1.00 OD1 B:ASP114 2.3 51.0 1.0 N B:GLN108 2.9 33.0 1.0 CG B:ASP114 3.0 49.2 1.0 N B:TRP110 3.1 36.2 1.0 OG B:SER107 3.3 45.7 1.0 CB B:ASP114 3.4 40.0 1.0 N B:GLY109 3.4 33.3 1.0 CA B:TRP110 3.6 35.4 1.0 CA B:GLN108 3.7 32.9 1.0 CA B:SER107 3.8 37.3 1.0 C B:SER107 3.8 38.7 1.0 CD2 B:LEU191 3.8 43.6 1.0 CD2 B:TRP110 3.8 34.8 1.0 OD2 B:ASP114 3.8 54.6 1.0 C B:GLN108 3.9 36.2 1.0 CE3 B:TRP110 3.9 35.7 1.0 OE1 B:GLN108 3.9 53.0 1.0 CB B:GLN108 4.0 33.5 1.0 CB B:SER107 4.0 38.9 1.0 CG2 B:ILE113 4.1 37.8 1.0 CG B:TRP110 4.1 34.9 1.0 C B:GLY109 4.2 38.4 1.0 N B:ASP114 4.2 36.6 1.0 CE2 B:TRP110 4.3 39.0 1.0 CA B:GLY109 4.3 33.8 1.0 CZ3 B:TRP110 4.4 36.9 1.0 CA B:ASP114 4.4 37.7 1.0 CB B:TRP110 4.5 33.5 1.0 CD B:GLN108 4.5 55.2 1.0 O B:HOH810 4.6 24.3 1.0 CD1 B:TRP110 4.6 38.0 1.0 NE1 B:TRP110 4.7 36.8 1.0 CZ2 B:TRP110 4.8 38.3 1.0 CH2 B:TRP110 4.8 37.8 1.0 C B:TRP110 4.8 39.1 1.0 CG B:GLN108 4.8 38.9 1.0 O B:GLN108 4.9 34.7 1.0 O B:SER107 5.0 37.9 1.0

Calcium binding site 5 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


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 Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca714 b:57.1 occ:1.00 O C:PHE464 2.3 52.0 1.0 OD1 C:ASN466 2.3 46.6 1.0 OD1 C:ASP462 2.4 60.9 1.0 OD1 C:ASP458 2.4 56.9 1.0 OD1 C:ASN476 2.5 64.2 1.0 CG C:ASN466 3.2 56.0 1.0 C C:PHE464 3.4 51.7 1.0 CG C:ASP462 3.4 62.3 1.0 CG C:ASP458 3.5 60.3 1.0 OD2 C:ASP460 3.5 90.3 1.0 CG C:ASN476 3.5 66.9 1.0 ND2 C:ASN466 3.6 43.4 1.0 CG C:ASP460 3.9 88.0 1.0 ND2 C:ASN476 3.9 61.1 1.0 OD2 C:ASP462 3.9 68.0 1.0 CA C:ASP458 4.0 55.8 1.0 N C:ASP460 4.1 67.1 1.0 CA C:PHE464 4.1 49.5 1.0 N C:PHE464 4.1 51.2 1.0 CB C:ASP458 4.1 56.4 1.0 N C:THR459 4.2 61.7 1.0 CB C:PHE464 4.3 51.0 1.0 N C:ASP462 4.3 57.8 1.0 CB C:ASP460 4.4 70.3 1.0 N C:LEU465 4.4 46.4 1.0 OD2 C:ASP458 4.4 67.3 1.0 C C:LEU465 4.4 46.9 1.0 C C:ASP458 4.5 63.1 1.0 OD1 C:ASP460 4.5 93.1 1.0 N C:ASN466 4.5 44.6 1.0 CB C:ASN466 4.6 45.4 1.0 CA C:ASP460 4.6 67.7 1.0 N C:GLY461 4.6 65.5 1.0 CB C:ASP462 4.6 56.9 1.0 O C:LEU465 4.7 45.0 1.0 CA C:LEU465 4.7 45.8 1.0 CB C:ASN476 4.8 47.8 1.0 C C:ASP460 4.8 70.3 1.0 N C:GLY463 4.9 53.6 1.0 CA C:ASP462 4.9 55.7 1.0 CA C:ASN466 5.0 45.5 1.0

Calcium binding site 6 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca715 b:96.0 occ:1.00 CE1 C:HIS511 3.8 51.2 1.0 ND1 C:HIS511 3.8 51.4 1.0 O2 D:EDO704 3.9 54.9 1.0 O C:GLN526 4.4 37.2 1.0 CB C:GLN526 4.9 35.1 1.0 CB C:ALA521 4.9 37.8 1.0 NE2 C:HIS511 4.9 51.8 1.0 CG C:HIS511 5.0 48.8 1.0 O D:HOH967 5.0 50.8 1.0

Calcium binding site 7 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca716 b:77.8 occ:1.00 CG C:MET267 3.0 47.9 1.0 O C:PRO264 3.5 34.5 1.0 CA C:MET267 3.7 37.2 1.0 CB C:TYR280 3.7 31.5 1.0 C C:SER279 3.8 35.5 1.0 O C:TYR266 3.8 35.7 1.0 N C:TYR280 3.8 31.5 1.0 CB C:MET267 3.9 41.5 1.0 N C:SER279 3.9 31.4 1.0 CA C:SER279 4.0 31.5 1.0 C C:VAL278 4.1 33.2 1.0 N C:MET267 4.2 36.1 1.0 C C:TYR266 4.2 37.4 1.0 O C:GLU265 4.3 32.4 1.0 O C:SER279 4.3 32.6 1.0 O C:VAL278 4.3 32.4 1.0 O C:HOH967 4.3 49.8 1.0 CA C:TYR280 4.4 30.7 1.0 C C:GLU265 4.4 33.5 1.0 O C:HOH987 4.4 45.1 1.0 CE C:MET267 4.5 53.3 1.0 O C:HOH859 4.5 33.6 1.0 SD C:MET267 4.6 56.2 1.0 C C:PRO264 4.6 34.5 1.0 CZ2 C:TRP100 4.7 33.6 1.0 CA C:GLU265 4.8 31.7 1.0 O C:PRO277 4.8 31.1 1.0 CA C:VAL278 4.9 28.1 1.0 C C:PRO277 4.9 31.4 1.0 N C:TYR266 4.9 31.2 1.0 N C:VAL278 4.9 28.9 1.0 CG C:TYR280 4.9 32.1 1.0 C C:MET267 5.0 36.3 1.0

Calcium binding site 8 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca717 b:66.5 occ:1.00 O C:ASP185 2.4 40.9 1.0 O C:VAL188 2.5 40.0 1.0 O C:ALA182 2.5 37.8 1.0 O C:VAL183 2.6 41.7 1.0 C C:VAL183 3.2 41.4 1.0 C C:ASP185 3.5 41.7 1.0 C C:ALA182 3.5 38.4 1.0 CA C:VAL183 3.6 36.7 1.0 C C:VAL188 3.6 39.8 1.0 N C:VAL183 3.9 36.7 1.0 N C:ASP185 4.2 38.0 1.0 N C:VAL184 4.3 38.1 1.0 CA C:PRO186 4.3 38.7 1.0 O C:ALA195 4.3 44.8 1.0 CA C:VAL188 4.3 35.7 1.0 N C:VAL188 4.3 36.4 1.0 N C:PRO186 4.3 39.3 1.0 CA C:ASP185 4.4 37.7 1.0 C C:VAL184 4.4 43.0 1.0 CB C:VAL188 4.4 39.3 1.0 CD C:PRO190 4.5 39.9 1.0 C C:PRO186 4.5 41.5 1.0 N C:SER189 4.6 38.7 1.0 O C:VAL184 4.7 44.0 1.0 O C:PRO186 4.8 41.1 1.0 CA C:ALA182 4.8 34.9 1.0 CA C:SER189 4.8 39.0 1.0 CA C:VAL184 4.9 38.7 1.0 CB C:ASP185 4.9 38.2 1.0

Calcium binding site 9 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca717 b:79.2 occ:1.00 O A:GLY415 2.9 38.6 1.0 OD1 A:ASP410 3.7 56.9 1.0 N A:GLY415 3.7 35.7 1.0 C A:GLY415 3.8 40.0 1.0 O A:HOH1015 4.0 36.4 1.0 O A:HOH869 4.1 48.4 1.0 CA A:GLY415 4.1 35.9 1.0 O A:HOH905 4.2 31.4 1.0 C A:LYS414 4.7 37.8 1.0 CG A:ASP410 4.7 57.6 1.0 N A:PRO416 4.9 36.6 1.0 CA A:LYS414 5.0 34.7 1.0

Calcium binding site 10 out of 13 in the Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of the Periplasmic Binding Protein (Pbp) Melb (ATU4661) in Complex with Galactinol From Agrobacterium Fabrum C58 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca718 b:44.2 occ:1.00 OH A:TYR280 2.9 38.0 1.0 N A:ASP283 3.2 33.3 1.0 CD A:ARG96 3.6 27.8 1.0 CD A:PRO97 3.7 31.0 1.0 CE1 A:TYR280 3.8 33.9 1.0 CZ A:TYR280 3.8 38.8 1.0 CD1 A:LEU314 3.8 29.7 1.0 CA A:PRO282 3.8 29.4 1.0 O A:HOH1017 4.0 50.2 1.0 C A:PRO282 4.0 34.9 1.0 CA A:ASP283 4.1 33.2 1.0 CB A:ARG96 4.2 24.6 1.0 OD1 A:ASP283 4.2 49.2 1.0 CG A:ARG96 4.2 30.7 1.0 CG A:PRO97 4.3 35.8 1.0 CG A:ASP283 4.3 49.8 1.0 CB A:PRO282 4.3 31.3 1.0 NE A:ARG96 4.5 29.0 1.0 OD2 A:ASP283 4.6 57.3 1.0 N A:PRO97 4.6 30.0 1.0 CA A:ARG96 4.8 26.4 1.0 CB A:ASP283 4.8 36.6 1.0 O A:PRO97 4.9 37.0 1.0

T.Meyer, A.Vigouroux, M.Aumont-Nicaise, G.Comte, L.Vial, C.Lavire, S.Morera. The Plant Defense Signal Galactinol Is Specifically Used As A Nutrient By the Bacterial Pathogenagrobacterium Fabrum. J. Biol. Chem. V. 293 7930 2018.
ISSN: ESSN 1083-351X
PubMed: 29602905
DOI: 10.1074/JBC.RA118.001856