Calcium in PDB 6x8d: Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x8d 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)	42.77 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.12, 50.71, 79.62, 90, 90, 90
R / Rfree (%)	14.6 / 16.6

The binding sites of Calcium atom in the Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x8d). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x8d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:5.2 occ:1.00 OD1 A:ASP155 2.3 5.3 1.0 OD1 A:ASP110 2.3 5.6 1.0 O A:ASP159 2.4 6.0 1.0 O A:GLY157 2.4 6.2 1.0 OD2 A:ASP111 2.4 5.5 1.0 O2 A:ARA207 2.5 6.4 1.0 O1 A:ARA207 2.5 6.4 1.0 HO2 A:ARA207 3.1 7.7 1.0 HO1 A:ARA207 3.2 7.6 1.0 CG A:ASP110 3.3 5.5 1.0 C1 A:ARA207 3.3 7.4 1.0 C2 A:ARA207 3.3 7.1 1.0 CG A:ASP111 3.3 5.5 1.0 H A:GLY157 3.4 7.1 0.5 H A:GLY157 3.4 7.1 0.6 C A:GLY157 3.5 6.3 1.0 H2 A:ARA207 3.5 8.5 1.0 HG3 A:GLN156 3.5 8.9 0.5 CG A:ASP155 3.5 4.7 1.0 H1 A:ARA207 3.5 8.9 1.0 C A:ASP159 3.6 5.8 1.0 OD2 A:ASP110 3.6 6.7 1.0 H A:GLN156 3.7 6.0 0.6 OD1 A:ASP111 3.7 6.1 1.0 H A:GLN156 3.7 5.8 0.5 HG3 A:GLN156 3.7 9.0 0.6 HE21 A:GLN156 3.8 10.2 0.5 HA A:ASP155 3.8 6.0 1.0 H A:ASP159 3.8 7.9 1.0 N A:ASP159 3.8 6.6 1.0 N A:GLY157 4.0 5.9 1.0 HG2 A:GLN156 4.1 9.0 0.6 HA A:TYR160 4.1 7.4 1.0 HA3 A:GLY158 4.2 7.8 1.0 C A:GLY158 4.2 6.3 1.0 N A:GLN156 4.2 5.0 0.6 N A:GLN156 4.2 4.9 0.5 CA A:ASP159 4.3 6.1 1.0 CA A:GLY157 4.3 6.2 1.0 N A:GLY158 4.3 6.5 1.0 OD2 A:ASP155 4.3 5.8 1.0 CG A:GLN156 4.4 7.5 0.6 CG A:GLN156 4.4 7.4 0.5 CA A:GLY158 4.4 6.5 1.0 HB3 A:TYR160 4.5 7.9 1.0 CB A:ASP155 4.5 5.3 1.0 CA A:ASP155 4.5 5.0 1.0 N A:ASP111 4.5 4.9 1.0 C A:ASP110 4.5 5.1 1.0 HE21 A:GLN156 4.5 10.3 0.6 H A:ASP111 4.6 5.9 1.0 CB A:ASP111 4.6 5.1 1.0 CB A:ASP110 4.6 5.7 1.0 NE2 A:GLN156 4.6 8.5 0.5 HB2 A:ASP155 4.6 6.4 1.0 O5 A:ARA207 4.6 10.9 1.0 N A:TYR160 4.6 6.2 1.0 HG2 A:GLN156 4.6 8.9 0.5 O A:ASP110 4.7 5.3 1.0 C3 A:ARA207 4.7 10.6 1.0 HB2 A:ASP111 4.7 6.1 1.0 HB2 A:ASP159 4.8 10.4 1.0 C A:ASP155 4.8 4.9 1.0 HA A:ASP111 4.8 6.2 1.0 CA A:TYR160 4.8 6.2 1.0 HB3 A:ASP110 4.8 6.8 1.0 O A:GLY158 4.9 6.8 1.0 C A:GLN156 4.9 6.1 0.6 C A:GLN156 4.9 6.1 0.5 H3 A:ARA207 4.9 12.8 1.0 HA2 A:GLY157 4.9 7.4 1.0 HD1 A:TYR160 4.9 7.8 1.0 CA A:ASP111 4.9 5.2 1.0 O A:GLN129 4.9 7.2 1.0

Calcium binding site 2 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:5.6 occ:1.00 O A:PRO82 2.3 6.5 1.0 O A:HOH347 2.4 9.8 1.0 O A:HOH398 2.4 7.3 1.0 O A:HOH393 2.4 6.0 1.0 O A:HOH419 2.4 7.1 1.0 O A:GLY64 2.4 6.4 1.0 OD1 A:ASP81 2.5 6.5 1.0 CG A:ASP81 3.5 6.4 1.0 C A:GLY64 3.5 6.0 1.0 C A:PRO82 3.5 6.5 1.0 HE22 A:GLN68 3.8 7.4 1.0 HD2 A:PRO82 3.8 8.4 1.0 OD2 A:ASP81 3.9 7.4 1.0 HA2 A:GLY64 4.0 7.7 1.0 HA A:THR65 4.0 7.6 1.0 O A:HOH335 4.1 6.3 1.0 HA2 A:GLY83 4.2 8.6 1.0 CA A:GLY64 4.2 6.4 1.0 HB2 A:PRO82 4.2 10.8 1.0 N A:PRO82 4.2 6.5 1.0 O A:HOH557 4.3 31.8 1.0 CA A:PRO82 4.4 7.0 1.0 OE1 A:GLN68 4.4 6.3 1.0 C A:ASP81 4.4 6.9 1.0 O A:GLY83 4.5 6.4 1.0 N A:GLY83 4.5 7.0 1.0 CD A:PRO82 4.5 7.0 1.0 C A:GLY83 4.5 6.2 1.0 N A:GLY64 4.5 84.1 1.0 N A:THR65 4.5 6.1 1.0 CA A:GLY83 4.6 7.2 1.0 NE2 A:GLN68 4.6 6.2 1.0 O A:ASP81 4.7 7.8 1.0 CA A:THR65 4.8 6.4 1.0 CB A:PRO82 4.8 9.0 1.0 CB A:ASP81 4.8 6.5 1.0 O A:HOH546 4.8 14.1 1.0 HG22 A:THR65 4.8 10.5 1.0 O A:HOH390 4.8 26.0 1.0 OD1 A:ASP84 4.8 7.8 1.0 HA A:ASP81 4.8 7.6 1.0 C A:LYS63 4.9 84.0 0.4 C A:LYS63 4.9 53.4 0.6 CA A:ASP81 4.9 6.3 1.0 CD A:GLN68 5.0 5.7 1.0

Calcium binding site 3 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:6.1 occ:1.00 OE1 A:GLN27 2.3 7.4 1.0 O A:GLN156 2.3 6.8 0.5 O A:GLN156 2.3 7.0 0.6 O A:HOH486 2.3 7.6 1.0 O A:HOH498 2.4 7.5 1.0 O A:HOH389 2.4 12.2 1.0 OD1 A:ASP87 2.4 6.5 1.0 OD2 A:ASP87 2.5 6.1 1.0 CG A:ASP87 2.8 5.8 1.0 HA A:GLN27 3.3 7.8 1.0 HB2 A:GLN156 3.4 8.0 0.5 HB2 A:GLN156 3.4 7.7 0.6 C A:GLN156 3.5 6.1 0.6 C A:GLN156 3.5 6.1 0.5 CD A:GLN27 3.5 7.2 1.0 HA A:GLN156 3.7 6.1 0.6 HA A:GLN156 3.7 6.1 0.5 HG1 A:THR86 4.0 7.9 1.0 CA A:GLN156 4.0 5.1 0.6 CA A:GLN156 4.0 5.1 0.5 H A:LEU28 4.0 7.3 1.0 CB A:GLN156 4.1 6.7 0.5 HB2 A:GLN27 4.1 8.6 1.0 CB A:GLN156 4.1 6.4 0.6 HE22 A:GLN27 4.2 9.5 1.0 OE1 A:GLN156 4.2 11.6 0.5 CA A:GLN27 4.2 6.5 1.0 CB A:ASP87 4.3 6.0 1.0 NE2 A:GLN27 4.3 7.9 1.0 OE1 A:GLN156 4.3 10.7 0.6 HA3 A:GLY157 4.4 7.4 1.0 HB A:THR86 4.4 7.2 1.0 O A:HOH575 4.4 22.7 1.0 O A:HOH363 4.4 8.8 1.0 O A:HOH365 4.5 7.8 1.0 O A:HOH409 4.5 29.1 1.0 CB A:GLN27 4.5 7.2 1.0 CD A:GLN156 4.5 8.2 0.5 OG1 A:THR86 4.5 6.6 1.0 CG A:GLN27 4.6 7.5 1.0 N A:GLY157 4.6 5.9 1.0 HB3 A:ASP87 4.7 7.2 1.0 O A:SER26 4.7 7.4 1.0 N A:LEU28 4.7 6.1 1.0 HB2 A:ASP87 4.8 7.2 1.0 O A:THR86 4.8 6.1 1.0 HB3 A:GLN156 4.8 8.0 0.5 HB3 A:GLN156 4.8 7.7 0.6 HA A:ASP87 4.9 6.1 1.0 CG A:GLN156 4.9 7.4 0.5 HG3 A:GLN156 4.9 9.0 0.6 CG A:GLN156 4.9 7.5 0.6 CA A:GLY157 5.0 6.2 1.0 CB A:THR86 5.0 6.0 1.0

Calcium binding site 4 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:12.3 occ:0.47 O A:HOH508 2.3 28.1 1.0 O A:VAL38 2.4 10.1 1.0 O A:LYS41 2.4 9.8 1.0 O A:HOH476 2.4 27.6 1.0 O A:HOH497 2.5 22.9 1.0 OH A:TYR22 2.6 10.5 1.0 HE2 A:TYR22 3.1 9.9 1.0 CZ A:TYR22 3.5 8.4 1.0 HG13 A:VAL38 3.5 11.1 1.0 HA A:GLU42 3.5 13.1 1.0 C A:LYS41 3.5 9.9 1.0 C A:VAL38 3.6 9.0 1.0 CE2 A:TYR22 3.6 8.3 1.0 H A:LYS41 3.7 11.6 1.0 HG12 A:VAL38 3.9 11.1 1.0 O A:HOH444 4.0 24.6 1.0 HA A:VAL38 4.2 9.6 1.0 CG1 A:VAL38 4.2 9.2 1.0 HA A:ASP39 4.2 12.9 1.0 CA A:GLU42 4.2 10.9 1.0 N A:GLU42 4.3 11.3 1.0 N A:LYS41 4.4 9.7 1.0 H A:ALA43 4.4 10.9 1.0 O A:HOH445 4.4 21.4 1.0 CA A:VAL38 4.4 8.0 1.0 N A:ASP39 4.5 9.1 1.0 C A:GLU42 4.6 9.6 1.0 N A:ALA43 4.6 9.1 1.0 CA A:LYS41 4.6 10.0 1.0 OE2 A:GLU42 4.6 41.5 1.0 CA A:ASP39 4.6 10.7 1.0 C A:ASP39 4.7 10.8 1.0 OE1 A:GLU20 4.7 11.8 1.0 CE1 A:TYR22 4.7 7.8 1.0 O A:ASP39 4.8 14.5 1.0 HG11 A:VAL38 4.9 11.1 1.0 CD2 A:TYR22 4.9 7.4 1.0 HE1 A:TYR22 5.0 9.3 1.0 CB A:VAL38 5.0 8.1 1.0

Calcium binding site 5 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:13.6 occ:0.76 O A:HOH413 2.4 21.1 1.0 O A:GLY119 2.4 14.4 1.0 C A:GLY119 3.6 12.5 1.0 HD3 A:PRO121 3.8 14.5 1.0 HA2 A:GLY119 4.1 15.6 1.0 HA3 A:GLY119 4.1 15.6 1.0 HA A:ASN120 4.1 13.1 1.0 CA A:GLY119 4.2 13.0 1.0 O A:HOH507 4.4 22.0 1.0 O A:HOH474 4.5 23.9 1.0 HD22 A:ASN120 4.5 194.9 1.0 N A:ASN120 4.6 10.2 1.0 HG21 A:THR116 4.7 10.7 1.0 O A:HOH349 4.7 20.6 1.0 CD A:PRO121 4.8 12.1 1.0 CA A:ASN120 4.8 10.9 1.0

Calcium binding site 6 out of 6 in the Arabinose-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 Arabinose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:8.7 occ:0.69 O A:HOH522 2.4 20.4 1.0 O A:HOH450 2.4 10.3 1.0 O A:HOH378 2.4 10.8 1.0 O A:HOH548 2.5 17.1 1.0 O A:HOH577 2.5 20.4 1.0 O A:HOH439 2.6 10.0 1.0 O A:HOH410 2.6 10.4 1.0 O A:HOH482 2.7 15.3 1.0 HA3 A:GLY72 3.5 8.9 1.0 O A:SER53 4.0 6.9 1.0 CA A:GLY72 4.4 7.4 1.0 HA A:TYR54 4.5 6.3 1.0 O A:HOH580 4.5 36.9 1.0 H A:GLY55 4.5 7.9 1.0 O A:GLY55 4.5 9.0 1.0 O A:HOH316 4.5 12.9 1.0 H A:SER73 4.5 11.9 1.0 O A:HOH456 4.5 12.6 1.0 O A:HOH320 4.6 38.6 1.0 O A:HOH501 4.6 22.1 1.0 O A:PHE70 4.6 5.9 1.0 HA2 A:GLY72 4.7 8.9 1.0 O A:GLU69 4.8 6.7 1.0 N A:GLY72 5.0 7.8 1.0 N A:GLY55 5.0 6.6 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