Calcium in PDB 6xa5: Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6xa5 was solved by S.Guo, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.70 / 1.03
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.27, 50.64, 79.43, 90, 90, 90
R / Rfree (%)	11.8 / 13.1

The binding sites of Calcium atom in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6xa5). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6xa5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:4.7 occ:1.00 HO4 B:GLC2 2.0 6.8 1.0 HO3 B:GLC2 2.1 7.0 1.0 OD1 A:ASP155 2.3 4.4 1.0 OD1 A:ASP110 2.3 4.8 1.0 O A:ASP159 2.4 5.3 1.0 O A:GLY157 2.4 5.3 1.0 OD2 A:ASP111 2.4 4.7 1.0 O3 B:GLC2 2.5 5.8 1.0 O4 B:GLC2 2.5 5.7 1.0 CG A:ASP110 3.3 4.8 1.0 C4 B:GLC2 3.3 6.9 1.0 CG A:ASP111 3.3 4.3 1.0 C3 B:GLC2 3.3 7.0 1.0 H A:GLY157 3.4 6.0 1.0 C A:GLY157 3.4 4.9 1.0 HG3 A:GLN156 3.5 7.4 1.0 H4 B:GLC2 3.5 8.3 1.0 CG A:ASP155 3.5 4.0 1.0 H3 B:GLC2 3.5 8.4 1.0 C A:ASP159 3.5 5.5 1.0 OD2 A:ASP110 3.6 5.9 1.0 OD1 A:ASP111 3.7 5.1 1.0 H A:GLN156 3.7 5.1 1.0 HE21 A:GLN156 3.7 10.5 1.0 H A:ASP159 3.8 7.0 0.5 H A:ASP159 3.8 7.0 0.5 HA A:ASP155 3.8 4.8 1.0 N A:ASP159 3.9 5.8 1.0 N A:GLY157 4.0 5.0 1.0 HA3 A:GLY158 4.1 7.2 1.0 HA A:TYR160 4.2 6.8 1.0 C A:GLY158 4.2 5.5 1.0 N A:GLN156 4.2 4.2 1.0 N A:GLY158 4.3 5.7 1.0 CA A:ASP159 4.3 6.2 0.5 CA A:ASP159 4.3 6.3 0.5 CA A:GLY157 4.3 5.3 1.0 OD2 A:ASP155 4.3 4.8 1.0 HB3 A:TYR160 4.4 6.5 1.0 CA A:GLY158 4.4 6.0 1.0 CB A:ASP155 4.4 4.2 1.0 CG A:GLN156 4.5 6.1 1.0 CA A:ASP155 4.5 4.0 1.0 N A:ASP111 4.5 4.5 1.0 C A:ASP110 4.5 4.3 1.0 H A:ASP111 4.5 5.4 1.0 CB A:ASP111 4.6 4.4 1.0 HB2 A:ASP155 4.6 5.0 1.0 NE2 A:GLN156 4.6 8.8 1.0 N A:TYR160 4.6 5.6 1.0 CB A:ASP110 4.6 4.8 1.0 O A:ASP110 4.7 4.3 1.0 HB2 A:ASP159 4.7 9.1 0.5 HB2 A:ASP111 4.7 5.3 1.0 C2 B:GLC2 4.7 10.3 1.0 C5 B:GLC2 4.7 9.3 1.0 C A:ASP155 4.8 4.1 1.0 HG2 A:GLN156 4.8 7.4 1.0 CA A:TYR160 4.8 5.6 1.0 HB2 A:ASP159 4.8 8.5 0.5 HA A:ASP111 4.8 5.2 1.0 H2 B:GLC2 4.8 12.4 1.0 HB3 A:ASP110 4.8 5.8 1.0 O A:GLY158 4.8 6.0 1.0 C A:GLN156 4.9 4.9 1.0 H5 B:GLC2 4.9 11.2 1.0 HA2 A:GLY157 4.9 6.3 1.0 CA A:ASP111 4.9 4.4 1.0 HD1 A:TYR160 4.9 6.3 1.0 O A:GLN129 5.0 6.5 1.0

Calcium binding site 2 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:5.5 occ:1.00 OE1 A:GLN27 2.3 6.7 1.0 O A:GLN156 2.3 5.5 1.0 O A:HOH489 2.4 7.2 1.0 O A:HOH505 2.4 7.3 1.0 OD1 A:ASP87 2.4 5.2 1.0 O A:HOH349 2.4 11.1 1.0 OD2 A:ASP87 2.5 5.0 1.0 CG A:ASP87 2.8 4.7 1.0 HA A:GLN27 3.3 7.1 1.0 C A:GLN156 3.4 4.9 1.0 HB2 A:GLN156 3.5 6.6 1.0 CD A:GLN27 3.5 6.2 1.0 HA A:GLN156 3.7 6.0 1.0 HG1 A:THR86 3.9 6.3 1.0 CA A:GLN156 4.0 5.0 1.0 H A:LEU28 4.0 6.5 1.0 OE1 A:GLN156 4.0 8.9 1.0 HB2 A:GLN27 4.1 7.5 1.0 HE22 A:GLN27 4.2 8.8 1.0 CA A:GLN27 4.2 5.9 1.0 CB A:GLN156 4.2 5.5 1.0 O A:HOH521 4.2 11.0 1.0 NE2 A:GLN27 4.3 7.3 1.0 CB A:ASP87 4.3 4.8 1.0 HA3 A:GLY157 4.3 6.3 1.0 HB A:THR86 4.3 6.4 1.0 O A:HOH365 4.4 6.8 1.0 CB A:GLN27 4.5 6.2 1.0 CD A:GLN156 4.5 7.8 1.0 O A:HOH552 4.5 28.3 1.0 O A:HOH361 4.5 8.2 1.0 OG1 A:THR86 4.5 5.3 1.0 N A:GLY157 4.6 5.0 1.0 CG A:GLN27 4.6 6.8 1.0 O A:SER26 4.7 6.7 1.0 HB3 A:ASP87 4.7 5.8 1.0 N A:LEU28 4.7 5.5 1.0 HB2 A:ASP87 4.8 5.8 1.0 O A:THR86 4.8 5.3 1.0 HA A:ASP87 4.8 5.2 1.0 CA A:GLY157 4.9 5.3 1.0 HB3 A:GLN156 4.9 6.6 1.0 CB A:THR86 4.9 5.3 1.0 CG A:GLN156 4.9 6.1 1.0 N A:GLN27 5.0 5.5 1.0

Calcium binding site 3 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:8.0 occ:0.49 O A:SER73 2.4 10.6 1.0 O A:HOH507 2.4 20.4 1.0 O A:HOH449 2.5 13.3 1.0 O A:HOH456 2.6 12.1 1.0 OG A:SER76 2.6 8.4 1.0 O A:HOH415 2.7 21.2 1.0 C A:SER73 3.4 9.2 1.0 HB3 A:SER76 3.5 8.1 1.0 HA A:SER73 3.6 12.0 1.0 CB A:SER76 3.6 6.7 1.0 H A:SER76 3.7 6.3 1.0 HB2 A:SER73 4.0 12.4 1.0 CA A:SER73 4.0 10.0 1.0 HB2 A:SER76 4.2 8.1 1.0 HA A:ASP74 4.3 6.5 1.0 N A:SER76 4.4 5.3 1.0 O A:HOH377 4.4 12.0 1.0 N A:ASP74 4.4 6.5 1.0 CB A:SER73 4.5 10.3 1.0 CA A:SER76 4.6 5.7 1.0 HG23 A:THR77 4.7 8.4 1.0 O A:HOH570 4.7 16.2 1.0 CA A:ASP74 4.7 5.5 1.0 O A:HOH329 4.9 12.2 1.0 C A:ASP74 5.0 5.3 1.0

Calcium binding site 4 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:4.9 occ:1.00 O A:PRO82 2.3 5.6 1.0 O A:HOH341 2.4 8.6 1.0 O A:HOH408 2.4 6.5 1.0 O A:GLY64 2.4 5.7 1.0 O A:HOH398 2.4 5.1 1.0 O A:HOH422 2.4 6.2 1.0 OD1 A:ASP81 2.5 5.2 1.0 CG A:ASP81 3.5 5.1 1.0 C A:GLY64 3.5 5.2 1.0 C A:PRO82 3.5 5.4 1.0 HD2 A:PRO82 3.8 7.4 1.0 HE22 A:GLN68 3.8 6.9 1.0 OD2 A:ASP81 3.9 6.1 1.0 HA A:THR65 4.0 6.4 1.0 HA2 A:GLY83 4.1 7.6 1.0 O A:HOH334 4.1 4.9 1.0 HA2 A:GLY64 4.1 7.2 1.0 N A:PRO82 4.2 5.5 1.0 CA A:GLY64 4.2 6.0 1.0 HB2 A:PRO82 4.3 10.9 1.0 O A:HOH568 4.4 27.5 1.0 C A:ASP81 4.4 5.5 1.0 N A:GLY64 4.4 5.6 1.0 OE1 A:GLN68 4.4 5.3 1.0 CA A:PRO82 4.4 6.3 1.0 O A:GLY83 4.4 5.5 1.0 H A:GLY64 4.5 6.7 1.0 CD A:PRO82 4.5 6.2 1.0 C A:GLY83 4.5 5.2 1.0 N A:GLY83 4.5 6.2 1.0 N A:THR65 4.5 5.2 1.0 CA A:GLY83 4.5 6.3 1.0 NE2 A:GLN68 4.6 5.8 1.0 O A:ASP81 4.7 6.5 1.0 HG22 A:THR65 4.7 9.1 1.0 CA A:THR65 4.7 5.3 1.0 O A:HOH549 4.7 13.4 1.0 CB A:ASP81 4.8 5.8 1.0 CB A:PRO82 4.8 9.0 1.0 OD1 A:ASP84 4.8 6.5 1.0 HA A:ASP81 4.8 6.5 1.0 O A:HOH340 4.9 23.3 1.0 O A:HOH506 4.9 24.1 1.0 CA A:ASP81 4.9 5.4 1.0 C A:LYS63 4.9 5.1 1.0 CD A:GLN68 5.0 4.6 1.0

Calcium binding site 5 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:13.8 occ:0.58 OD1 A:ASP7 2.3 25.1 1.0 O A:HOH306 2.3 28.7 1.0 O A:HOH303 2.4 31.7 1.0 OE1 A:GLN5 2.4 18.1 1.0 O A:THR9 2.4 18.2 1.0 OD1 A:ASP11 2.5 19.6 1.0 OD2 A:ASP11 2.5 20.7 1.0 CG A:ASP11 2.8 19.1 1.0 HB A:THR9 3.1 30.7 1.0 HE22 A:GLN5 3.2 22.1 1.0 CG A:ASP7 3.3 26.6 1.0 CD A:GLN5 3.4 19.2 1.0 H A:THR9 3.5 24.5 1.0 C A:THR9 3.5 16.7 1.0 OD2 A:ASP7 3.6 33.0 1.0 NE2 A:GLN5 3.7 18.4 1.0 H A:ASP7 3.9 32.6 1.0 H A:ASP6 3.9 31.9 1.0 CB A:THR9 4.0 25.6 1.0 CA A:THR9 4.1 20.8 1.0 N A:THR9 4.1 20.4 1.0 CB A:ASP11 4.3 14.7 1.0 HG22 A:THR9 4.3 36.9 1.0 HA A:GLN5 4.4 33.3 1.0 OD1 A:ASP6 4.4 43.0 1.0 N A:ASP7 4.4 27.2 1.0 O A:HOH314 4.5 27.2 1.0 HE21 A:GLN5 4.5 22.1 1.0 N A:ASP11 4.6 13.8 1.0 C A:PRO10 4.6 13.9 1.0 CB A:ASP7 4.6 24.8 1.0 N A:PRO10 4.6 15.7 1.0 HA A:PRO10 4.7 16.6 1.0 N A:ASP6 4.7 26.5 1.0 HA A:ASP11 4.7 14.2 1.0 CG2 A:THR9 4.7 30.8 1.0 HB2 A:ASP11 4.8 17.7 1.0 CG A:GLN5 4.8 21.2 1.0 C A:ASP7 4.8 22.8 1.0 HB3 A:ASP11 4.8 17.7 1.0 H A:ASP11 4.8 16.6 1.0 CA A:ASP7 4.8 24.8 1.0 CA A:ASP11 4.8 11.8 1.0 O A:ASP7 4.9 23.1 1.0 HG3 A:GLN5 4.9 25.4 1.0 CA A:PRO10 4.9 13.8 1.0 O A:PRO10 4.9 16.6 1.0 HG1 A:THR9 5.0 36.7 1.0 OG1 A:THR9 5.0 30.6 1.0

Calcium binding site 6 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:15.7 occ:0.66 O A:HOH503 2.3 21.9 1.0 O A:VAL38 2.4 10.1 1.0 O A:HOH516 2.4 27.8 1.0 O A:HOH500 2.5 19.0 1.0 O A:LYS41 2.5 9.4 1.0 OH A:TYR22 2.7 11.2 1.0 HH A:TYR22 3.2 13.4 1.0 HE2 A:TYR22 3.2 9.8 1.0 HG13 A:VAL38 3.4 10.2 1.0 CZ A:TYR22 3.5 8.4 1.0 HA A:GLU42 3.6 13.0 1.0 C A:VAL38 3.6 8.9 1.0 O A:HOH441 3.7 25.7 1.0 C A:LYS41 3.7 9.8 1.0 CE2 A:TYR22 3.7 8.2 1.0 H A:LYS41 3.8 11.2 1.0 HG12 A:VAL38 3.9 10.2 1.0 CG1 A:VAL38 4.1 8.5 1.0 HA A:ASP39 4.1 13.2 1.0 HA A:VAL38 4.2 9.1 1.0 CA A:GLU42 4.3 10.8 1.0 N A:GLU42 4.4 10.7 1.0 CA A:VAL38 4.4 7.6 1.0 H A:ALA43 4.4 10.7 1.0 O A:HOH454 4.4 22.1 1.0 N A:LYS41 4.5 9.3 1.0 N A:ASP39 4.5 8.5 1.0 CA A:ASP39 4.6 11.0 1.0 N A:ALA43 4.7 8.9 1.0 OE1 A:GLU20 4.7 11.4 1.0 C A:ASP39 4.7 10.1 1.0 C A:GLU42 4.7 9.3 1.0 CA A:LYS41 4.7 10.1 1.0 CE1 A:TYR22 4.8 7.0 1.0 OE2 A:GLU42 4.8 31.6 1.0 O A:HOH487 4.8 27.0 1.0 HG11 A:VAL38 4.8 10.2 1.0 O A:ASP39 4.9 12.2 1.0 CB A:VAL38 4.9 7.4 1.0 CD2 A:TYR22 5.0 6.9 1.0

Calcium binding site 7 out of 7 in the Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Trehalose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:8.5 occ:0.68 O A:HOH557 2.4 17.3 1.0 O A:HOH385 2.4 11.1 1.0 O A:HOH467 2.4 10.4 1.0 O A:HOH518 2.5 16.4 1.0 O A:HOH430 2.5 10.5 1.0 O A:HOH484 2.7 15.2 1.0 HA3 A:GLY72 3.4 9.2 1.0 O A:SER53 4.1 5.4 1.0 CA A:GLY72 4.3 7.7 1.0 H A:SER73 4.4 11.1 1.0 O A:GLY55 4.5 8.1 1.0 HA A:TYR54 4.5 4.9 1.0 HA2 A:GLY72 4.5 9.2 1.0 O A:HOH448 4.5 12.5 1.0 H A:GLY55 4.5 7.3 1.0 O A:HOH326 4.6 11.8 1.0 O A:HOH338 4.6 20.2 1.0 O A:HOH509 4.6 22.1 1.0 O A:PHE70 4.7 4.8 1.0 O A:GLU69 4.8 5.5 1.0 N A:GLY72 4.9 6.9 1.0

S.Guo, T.D.R.Vance, H.Zahiri, R.Eves, C.Stevens, J.H.Hehemann, S.Vidal-Melgosa, P.L.Davies. Structural Basis of Ligand Selectivity By A Bacterial Adhesin Lectin Involved in Multispecies Biofilm Formation. Mbio V. 12 2021.
ISSN: ESSN 2150-7511
PubMed: 33824212
DOI: 10.1128/MBIO.00130-21