Calcium in PDB 6x7j: Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain

The structure of Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7j 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)	39.69 / 0.97
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.12, 50.67, 79.37, 90, 90, 90
R / Rfree (%)	12.2 / 13.7

The binding sites of Calcium atom in the Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain (pdb code 6x7j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7j:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Fucose-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 Fucose-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 HO4 A:FUL201 2.0 6.5 0.5 OD1 A:ASP155 2.3 5.6 1.0 O A:ASP159 2.4 6.2 1.0 OD1 A:ASP110 2.4 5.9 1.0 O A:GLY157 2.4 6.6 1.0 OD2 A:ASP111 2.4 5.7 1.0 O3 A:FUC209 2.5 6.6 0.5 O4 A:FUC209 2.5 6.4 0.5 O3 A:FUL201 2.5 6.7 0.5 O4 A:FUL201 2.5 6.5 0.5 HO3 A:FUL201 3.0 6.7 0.5 CG A:ASP110 3.3 5.9 1.0 H A:GLY157 3.3 6.1 1.0 CG A:ASP111 3.3 5.5 1.0 C4 A:FUC209 3.4 7.4 0.5 C4 A:FUL201 3.4 7.4 0.5 C3 A:FUC209 3.4 7.5 0.5 C3 A:FUL201 3.4 7.4 0.5 C A:GLY157 3.5 6.5 1.0 C A:ASP159 3.5 6.1 1.0 CG A:ASP155 3.5 5.3 1.0 H4 A:FUL201 3.6 7.4 0.5 HG3 A:GLN156 3.6 6.9 1.0 H4 A:FUC209 3.6 7.4 0.5 OD2 A:ASP110 3.6 6.8 1.0 H2 A:FUC209 3.6 8.8 0.5 H2 A:FUL201 3.7 8.7 0.5 HE21 A:GLN156 3.7 9.7 1.0 OD1 A:ASP111 3.7 6.0 1.0 H A:GLN156 3.7 5.7 1.0 H A:ASP159 3.8 6.8 0.5 H A:ASP159 3.8 6.8 0.5 HA A:ASP155 3.8 5.2 1.0 N A:ASP159 3.9 6.8 1.0 N A:GLY157 3.9 6.1 1.0 C2 A:FUL201 4.1 8.7 0.5 C2 A:FUC209 4.1 8.8 0.5 C A:GLY158 4.2 6.6 1.0 HA A:TYR160 4.2 6.5 1.0 HA3 A:GLY158 4.2 7.1 1.0 H3 A:FUL201 4.2 7.4 0.5 N A:GLN156 4.3 5.7 1.0 CA A:ASP159 4.3 6.9 0.5 CA A:ASP159 4.3 6.8 0.5 N A:GLY158 4.3 6.8 1.0 H3 A:FUC209 4.3 7.5 0.5 CA A:GLY157 4.3 6.4 1.0 OD2 A:ASP155 4.4 5.9 1.0 HB3 A:TYR160 4.4 6.4 1.0 CA A:GLY158 4.4 7.1 1.0 CB A:ASP155 4.5 5.2 1.0 N A:ASP111 4.5 5.5 1.0 CA A:ASP155 4.5 5.2 1.0 C A:ASP110 4.5 5.3 1.0 NE2 A:GLN156 4.5 9.7 1.0 CG A:GLN156 4.5 6.9 1.0 N A:TYR160 4.6 6.3 1.0 HB2 A:ASP155 4.6 5.2 1.0 CB A:ASP111 4.6 5.5 1.0 H A:ASP111 4.6 5.6 1.0 CB A:ASP110 4.6 6.1 1.0 HB2 A:ASP159 4.6 8.0 0.5 O A:ASP110 4.7 5.7 1.0 HB2 A:ASP111 4.7 5.5 1.0 HA A:ASP111 4.7 5.7 1.0 CA A:TYR160 4.8 6.5 1.0 HB2 A:ASP159 4.8 8.0 0.5 C5 A:FUC209 4.8 8.4 0.5 C A:ASP155 4.8 5.3 1.0 C5 A:FUL201 4.8 8.3 0.5 O A:GLY158 4.8 7.1 1.0 O2 A:FUC209 4.8 10.5 0.5 O2 A:FUL201 4.8 10.5 0.5 HB3 A:ASP110 4.9 6.1 1.0 HA2 A:GLY157 4.9 6.4 1.0 C A:GLN156 4.9 5.9 1.0 HD1 A:TYR160 4.9 6.2 1.0 HG2 A:GLN156 4.9 6.9 1.0 CA A:ASP111 4.9 5.7 1.0 O A:GLN129 4.9 7.2 1.0

Calcium binding site 2 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:6.0 occ:1.00 O A:PRO82 2.3 6.7 1.0 O A:HOH358 2.4 8.8 1.0 O A:HOH429 2.4 7.4 1.0 O A:GLY64 2.4 6.7 1.0 O A:HOH434 2.4 7.2 1.0 O A:HOH405 2.4 6.5 1.0 OD1 A:ASP81 2.5 6.4 1.0 C A:GLY64 3.5 6.2 1.0 CG A:ASP81 3.5 6.6 1.0 C A:PRO82 3.5 6.5 1.0 HE22 A:GLN68 3.8 6.8 1.0 HD2 A:PRO82 3.9 6.8 1.0 OD2 A:ASP81 3.9 7.0 1.0 HA A:THR65 4.0 6.3 1.0 HA2 A:GLY64 4.1 7.0 1.0 HB2 A:PRO82 4.1 9.3 1.0 O A:HOH345 4.1 6.3 1.0 HA2 A:GLY83 4.1 7.6 1.0 CA A:GLY64 4.2 7.0 1.0 N A:PRO82 4.2 6.9 1.0 OE1 A:GLN68 4.4 6.4 1.0 CA A:PRO82 4.4 7.3 1.0 O A:HOH608 4.4 23.8 1.0 C A:ASP81 4.4 7.0 1.0 N A:GLY64 4.4 6.7 1.0 O A:GLY83 4.4 6.4 1.0 H A:GLY64 4.5 6.7 0.2 H A:GLY64 4.5 6.7 0.2 H A:GLY64 4.5 6.7 0.5 N A:THR65 4.5 6.2 1.0 C A:GLY83 4.5 6.3 1.0 N A:GLY83 4.5 7.5 1.0 CD A:PRO82 4.5 6.8 1.0 CA A:GLY83 4.6 7.6 1.0 NE2 A:GLN68 4.6 6.8 1.0 CB A:PRO82 4.7 9.3 1.0 O A:ASP81 4.7 7.8 1.0 CA A:THR65 4.7 6.3 1.0 CB A:ASP81 4.7 6.7 1.0 HG22 A:THR65 4.8 9.2 1.0 O A:HOH588 4.8 14.1 1.0 HA A:ASP81 4.8 6.8 1.0 OD1 A:ASP84 4.8 7.7 1.0 CA A:ASP81 4.9 6.8 1.0 CD A:GLN68 4.9 5.8 1.0 C A:LYS63 5.0 6.3 0.5 C A:LYS63 5.0 5.8 0.2 O A:HOH333 5.0 20.7 1.0 C A:LYS63 5.0 5.8 0.2

Calcium binding site 3 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:6.3 occ:1.00 OE1 A:GLN27 2.3 8.0 1.0 O A:GLN156 2.3 6.6 1.0 O A:HOH517 2.4 7.9 1.0 O A:HOH534 2.4 8.0 1.0 OD1 A:ASP87 2.4 6.6 1.0 O A:HOH371 2.4 10.4 1.0 OD2 A:ASP87 2.5 6.2 1.0 CG A:ASP87 2.8 6.1 1.0 HA A:GLN27 3.3 7.0 1.0 C A:GLN156 3.4 5.9 1.0 HB2 A:GLN156 3.5 6.4 1.0 CD A:GLN27 3.5 7.6 1.0 HA A:GLN156 3.7 5.9 1.0 HG1 A:THR86 3.9 6.5 1.0 OE1 A:GLN156 4.0 8.1 1.0 CA A:GLN156 4.0 5.9 1.0 H A:LEU28 4.0 6.5 1.0 HE22 A:GLN27 4.1 8.1 1.0 HB2 A:GLN27 4.1 7.2 1.0 CA A:GLN27 4.2 7.0 1.0 CB A:GLN156 4.2 6.4 1.0 NE2 A:GLN27 4.3 8.1 1.0 CB A:ASP87 4.3 6.0 1.0 HA3 A:GLY157 4.3 6.4 1.0 HB A:THR86 4.3 6.5 1.0 O A:HOH582 4.4 26.0 1.0 O A:HOH369 4.4 7.7 1.0 O A:HOH364 4.5 9.8 1.0 OG1 A:THR86 4.5 6.5 1.0 CB A:GLN27 4.5 7.2 1.0 CD A:GLN156 4.5 7.3 1.0 N A:GLY157 4.6 6.1 1.0 CG A:GLN27 4.6 7.4 1.0 O A:HOH616 4.6 30.8 1.0 O A:SER26 4.7 7.8 1.0 HB3 A:ASP87 4.7 6.0 1.0 N A:LEU28 4.8 6.5 1.0 O A:THR86 4.8 6.4 1.0 HB2 A:ASP87 4.8 6.0 1.0 HA A:ASP87 4.9 5.7 1.0 CA A:GLY157 4.9 6.4 1.0 CB A:THR86 4.9 6.5 1.0 HB3 A:GLN156 5.0 6.4 1.0 CG A:GLN156 5.0 6.9 1.0

Calcium binding site 4 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:12.8 occ:0.60 O A:VAL38 2.3 9.3 1.0 O A:HOH540 2.3 17.6 1.0 O A:LYS41 2.4 9.1 1.0 O A:HOH525 2.4 21.0 1.0 O A:HOH530 2.5 17.7 1.0 OH A:TYR22 2.6 10.1 1.0 HE2 A:TYR22 3.1 8.0 1.0 C A:VAL38 3.5 8.4 1.0 HA A:GLU42 3.5 10.4 1.0 C A:LYS41 3.5 8.8 1.0 CZ A:TYR22 3.5 8.0 1.0 HG13 A:VAL38 3.6 8.8 1.0 H A:LYS41 3.6 8.9 1.0 CE2 A:TYR22 3.6 8.0 1.0 HG12 A:VAL38 4.0 8.8 1.0 HA A:VAL38 4.1 7.7 1.0 HA A:ASP39 4.1 9.7 1.0 O A:HOH426 4.2 18.4 1.0 CA A:GLU42 4.2 10.4 1.0 CG1 A:VAL38 4.2 8.8 1.0 N A:GLU42 4.3 10.1 1.0 N A:LYS41 4.3 8.9 1.0 H A:ALA43 4.4 9.0 1.0 CA A:VAL38 4.4 7.7 1.0 O A:HOH309 4.4 35.0 1.0 O A:HOH340 4.4 26.3 1.0 O A:HOH489 4.4 19.6 1.0 N A:ASP39 4.5 8.5 1.0 CA A:ASP39 4.5 9.7 1.0 O A:HOH437 4.5 24.0 1.0 C A:GLU42 4.6 9.2 1.0 CA A:LYS41 4.6 9.2 1.0 C A:ASP39 4.6 9.4 1.0 N A:ALA43 4.6 9.0 1.0 OE2 A:GLU42 4.6 33.5 1.0 O A:HOH552 4.6 30.3 1.0 OE1 A:GLU20 4.8 11.3 1.0 CE1 A:TYR22 4.8 7.5 1.0 O A:ASP39 4.8 13.3 1.0 CD2 A:TYR22 4.9 7.1 1.0 N A:SER40 4.9 9.0 1.0 H A:SER40 4.9 9.0 1.0 CB A:VAL38 5.0 7.9 1.0 HG11 A:VAL38 5.0 8.8 1.0

Calcium binding site 5 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:6.3 occ:0.70 O A:HOH580 2.4 14.7 1.0 O A:HOH645 2.4 14.2 1.0 O A:HOH548 2.4 13.7 1.0 O A:HOH458 2.4 8.0 1.0 O A:HOH373 2.4 8.5 1.0 O A:HOH501 2.5 8.2 1.0 O A:HOH441 2.5 9.1 1.0 O A:HOH524 2.7 12.9 1.0 HA3 A:GLY72 3.6 6.8 1.0 O A:SER53 4.1 6.5 1.0 O A:HOH647 4.4 24.9 1.0 O A:GLY55 4.4 8.6 1.0 H A:GLY55 4.4 6.7 1.0 H A:SER73 4.5 9.4 1.0 O A:HOH479 4.5 9.5 1.0 CA A:GLY72 4.5 6.8 1.0 HA A:TYR54 4.5 5.2 1.0 O A:HOH331 4.5 10.7 1.0 O A:HOH343 4.6 19.9 1.0 O A:HOH536 4.6 19.7 1.0 O A:PHE70 4.7 5.7 1.0 HA2 A:GLY72 4.7 6.8 1.0 O A:GLU69 4.7 6.2 1.0 N A:GLY55 4.9 6.7 1.0 O A:HOH554 4.9 48.6 1.0

Calcium binding site 6 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca207 b:9.6 occ:0.60 O A:HOH301 2.0 22.9 1.0 O A:HOH519 2.2 16.4 1.0 O A:HOH446 2.4 24.7 1.0 O A:GLY119 2.4 13.8 1.0 C A:GLY119 3.6 12.1 1.0 HD3 A:PRO121 3.9 11.3 1.0 HA2 A:GLY119 4.0 13.7 1.0 HA3 A:GLY119 4.2 13.7 1.0 CA A:GLY119 4.2 13.7 1.0 HA A:ASN120 4.3 10.3 1.0 O A:HOH507 4.4 16.8 1.0 HG21 A:THR116 4.6 7.7 1.0 O A:HOH445 4.6 18.9 1.0 N A:ASN120 4.7 9.6 1.0 HD22 A:ASN120 4.8 24.6 1.0 CD A:PRO121 4.9 11.3 1.0 CA A:ASN120 4.9 10.3 1.0

Calcium binding site 7 out of 7 in the Fucose-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 Fucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca210 b:11.5 occ:1.00 O A:SER73 2.3 10.0 1.0 O A:HOH546 2.4 14.3 1.0 O A:HOH535 2.4 17.9 1.0 O A:HOH537 2.5 12.4 1.0 O A:HOH491 2.5 11.5 1.0 O A:HOH449 2.6 10.8 1.0 OG A:SER76 2.6 9.3 1.0 O A:HOH443 2.6 17.1 1.0 C A:SER73 3.4 9.2 1.0 HA A:SER73 3.5 9.7 1.0 HB3 A:SER76 3.6 7.8 1.0 CB A:SER76 3.7 7.8 1.0 H A:SER76 3.7 6.5 1.0 CA A:SER73 4.0 9.7 1.0 HB2 A:SER73 4.1 10.5 1.0 HA A:ASP74 4.2 6.5 1.0 HB2 A:SER76 4.3 7.8 1.0 N A:ASP74 4.4 7.5 1.0 N A:SER76 4.5 6.5 1.0 CB A:SER73 4.6 10.5 1.0 O A:HOH600 4.6 15.5 1.0 O A:HOH648 4.6 22.0 1.0 CA A:SER76 4.7 6.7 1.0 CA A:ASP74 4.7 6.5 1.0 HG23 A:THR77 4.7 8.3 1.0 O A:HOH359 4.8 9.9 1.0 C A:ASP74 5.0 6.7 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