Calcium in PDB 6x8y: Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain

The structure of Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x8y 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)	42.78 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.14, 50.72, 79.61, 90, 90, 90
R / Rfree (%)	15.5 / 16.7

The binding sites of Calcium atom in the Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain (pdb code 6x8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x8y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Ribose-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 Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:4.2 occ:0.88 OD1 A:ASP155 2.3 5.2 1.0 O A:ASP159 2.4 5.8 1.0 OD1 A:ASP110 2.4 5.2 1.0 O A:GLY157 2.4 5.9 1.0 OD2 A:ASP111 2.4 5.1 1.0 O3 A:RIP201 2.5 6.1 1.0 O2 A:RIP201 2.5 6.2 1.0 CG A:ASP110 3.3 5.4 1.0 CG A:ASP111 3.4 5.2 1.0 C3 A:RIP201 3.4 7.0 1.0 C2 A:RIP201 3.4 7.3 1.0 C A:GLY157 3.5 5.8 1.0 CG A:ASP155 3.5 4.7 1.0 C A:ASP159 3.5 6.1 1.0 OD2 A:ASP110 3.6 5.9 1.0 OD1 A:ASP111 3.7 5.6 1.0 N A:ASP159 3.9 6.3 1.0 N A:GLY157 4.0 5.6 1.0 C1 A:RIP201 4.1 9.3 1.0 C A:GLY158 4.2 6.1 1.0 N A:GLN156 4.2 5.2 1.0 CA A:ASP159 4.3 6.4 0.5 CA A:ASP159 4.3 6.5 0.5 OD2 A:ASP155 4.3 5.2 1.0 CA A:GLY157 4.3 5.7 1.0 N A:GLY158 4.3 6.3 1.0 CG A:GLN156 4.4 7.7 1.0 CA A:GLY158 4.4 6.3 1.0 CB A:ASP155 4.5 5.0 1.0 CA A:ASP155 4.5 4.8 1.0 C A:ASP110 4.5 5.3 1.0 N A:ASP111 4.5 5.1 1.0 N A:TYR160 4.6 6.1 1.0 CB A:ASP111 4.6 5.3 1.0 CB A:ASP110 4.7 5.7 1.0 O A:ASP110 4.7 5.0 1.0 C4 A:RIP201 4.8 8.8 1.0 C A:ASP155 4.8 4.9 1.0 CA A:TYR160 4.8 6.1 1.0 O1 A:RIP201 4.8 10.8 1.0 O A:GLY158 4.9 6.2 1.0 C A:GLN156 4.9 5.5 1.0 CA A:ASP111 4.9 5.2 1.0 O A:GLN129 5.0 6.7 1.0

Calcium binding site 2 out of 4 in the Ribose-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 Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:5.6 occ:1.00 O A:PRO82 2.3 6.3 1.0 O A:HOH322 2.4 8.9 1.0 O A:HOH425 2.4 6.9 1.0 O A:GLY64 2.4 6.2 1.0 O A:HOH427 2.4 6.6 1.0 O A:HOH381 2.4 5.8 1.0 OD1 A:ASP81 2.5 6.0 1.0 C A:GLY64 3.5 5.9 1.0 CG A:ASP81 3.5 6.2 1.0 C A:PRO82 3.6 6.3 1.0 OD2 A:ASP81 3.9 6.6 1.0 O A:HOH334 4.1 6.0 1.0 CA A:GLY64 4.2 6.3 1.0 N A:PRO82 4.2 6.3 1.0 OE1 A:GLN68 4.4 5.8 1.0 CA A:PRO82 4.4 7.0 1.0 C A:ASP81 4.4 6.3 1.0 N A:GLY64 4.4 5.8 1.0 O A:GLY83 4.5 6.1 1.0 N A:THR65 4.5 5.8 1.0 C A:GLY83 4.5 6.2 1.0 CD A:PRO82 4.5 7.3 1.0 N A:GLY83 4.5 6.7 1.0 NE2 A:GLN68 4.6 6.1 1.0 CA A:GLY83 4.6 6.9 1.0 O A:ASP81 4.7 7.0 1.0 CA A:THR65 4.7 5.9 1.0 O A:HOH544 4.7 13.4 1.0 CB A:PRO82 4.8 9.3 1.0 CB A:ASP81 4.8 6.4 1.0 OD1 A:ASP84 4.8 7.3 1.0 O A:HOH354 4.9 25.6 1.0 CD A:GLN68 4.9 5.4 1.0 CA A:ASP81 5.0 6.3 1.0 C A:LYS63 5.0 5.9 1.0

Calcium binding site 3 out of 4 in the Ribose-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 Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:5.5 occ:0.98 OE1 A:GLN27 2.3 6.7 1.0 O A:HOH464 2.3 29.3 1.0 O A:GLN156 2.3 6.1 1.0 O A:HOH495 2.4 7.4 1.0 OD1 A:ASP87 2.4 5.6 1.0 O A:HOH428 2.4 9.6 1.0 OD2 A:ASP87 2.5 5.5 1.0 CG A:ASP87 2.8 5.5 1.0 C A:GLN156 3.5 5.5 1.0 CD A:GLN27 3.5 6.8 1.0 CA A:GLN156 4.0 5.3 1.0 CB A:GLN156 4.1 6.6 1.0 CA A:GLN27 4.2 6.4 1.0 CB A:ASP87 4.3 5.5 1.0 NE2 A:GLN27 4.4 7.5 1.0 O A:HOH573 4.4 16.1 1.0 OE1 A:GLN156 4.4 9.4 1.0 O A:HOH370 4.4 8.7 1.0 O A:HOH360 4.5 29.3 1.0 CB A:GLN27 4.5 6.8 1.0 O A:HOH514 4.5 27.3 1.0 OG1 A:THR86 4.5 5.8 1.0 CG A:GLN27 4.6 7.4 1.0 N A:GLY157 4.6 5.6 1.0 N A:LEU28 4.7 5.9 1.0 O A:SER26 4.7 6.8 1.0 O A:THR86 4.8 5.6 1.0 CG A:GLN156 4.9 7.7 1.0 CB A:THR86 5.0 5.9 1.0

Calcium binding site 4 out of 4 in the Ribose-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 Ribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:21.2 occ:0.62 O A:HOH499 2.3 30.0 1.0 O A:HOH501 2.3 30.0 1.0 O A:LYS41 2.3 9.8 1.0 O A:VAL38 2.4 9.6 1.0 O A:HOH491 2.5 23.5 1.0 OH A:TYR22 2.7 11.2 1.0 C A:LYS41 3.5 10.1 1.0 CZ A:TYR22 3.6 9.0 1.0 CE2 A:TYR22 3.6 8.6 1.0 C A:VAL38 3.6 8.9 1.0 O A:HOH449 4.0 26.3 1.0 CA A:GLU42 4.2 11.8 1.0 CG1 A:VAL38 4.2 9.0 1.0 N A:GLU42 4.2 11.1 1.0 O A:HOH450 4.4 29.9 1.0 N A:LYS41 4.4 9.8 1.0 CA A:VAL38 4.4 7.9 1.0 O A:HOH497 4.5 37.2 1.0 C A:GLU42 4.5 9.9 1.0 N A:ALA43 4.5 9.1 1.0 N A:ASP39 4.6 8.9 1.0 CA A:LYS41 4.6 10.7 1.0 C A:ASP39 4.7 10.1 1.0 CA A:ASP39 4.7 10.5 1.0 OE2 A:GLU42 4.7 31.5 1.0 OE1 A:GLU20 4.8 12.4 1.0 CE1 A:TYR22 4.8 8.1 1.0 CD2 A:TYR22 4.9 7.5 1.0 O A:ASP39 4.9 11.9 1.0 CB A:VAL38 5.0 8.2 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