Calcium in PDB 6x7y: N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x7y 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)	39.71 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.24, 50.65, 79.42, 90, 90, 90
R / Rfree (%)	12.7 / 14.1

The binding sites of Calcium atom in the N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x7y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x7y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the N-Acetyl-Glucosamine-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 N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:4.7 occ:0.99 HO4 A:NAG202 2.0 7.3 0.5 HO4 A:NDG201 2.0 7.0 0.5 HO3 A:NAG202 2.1 7.0 0.5 HO3 A:NDG201 2.1 7.5 0.5 OD1 A:ASP155 2.3 5.3 1.0 OD1 A:ASP110 2.3 5.5 1.0 O A:ASP159 2.4 5.7 1.0 O A:GLY157 2.4 5.8 1.0 OD2 A:ASP111 2.4 5.3 1.0 O4 A:NDG201 2.5 5.9 0.5 O4 A:NAG202 2.5 6.0 0.5 O3 A:NAG202 2.5 5.9 0.5 O3 A:NDG201 2.5 6.2 0.5 CG A:ASP110 3.3 5.5 1.0 H A:GLY157 3.3 6.8 1.0 CG A:ASP111 3.3 5.1 1.0 C3 A:NAG202 3.3 6.4 0.5 C3 A:NDG201 3.4 6.6 0.5 C4 A:NAG202 3.4 6.5 0.5 C4 A:NDG201 3.4 6.5 0.5 C A:GLY157 3.4 5.5 1.0 H3 A:NAG202 3.5 7.7 0.5 CG A:ASP155 3.5 4.8 1.0 H3 A:NDG201 3.5 7.9 0.5 C A:ASP159 3.6 5.4 1.0 HG3 A:GLN156 3.6 8.0 1.0 H4 A:NAG202 3.6 7.8 0.5 H4 A:NDG201 3.6 7.8 0.5 OD2 A:ASP110 3.6 6.3 1.0 H A:GLN156 3.7 6.1 1.0 OD1 A:ASP111 3.7 5.8 1.0 HE21 A:GLN156 3.7 9.7 1.0 H A:ASP159 3.8 7.2 1.0 HA A:ASP155 3.8 5.9 1.0 N A:ASP159 3.8 6.0 1.0 N A:GLY157 3.9 5.6 1.0 HA3 A:GLY158 4.1 7.4 1.0 C A:GLY158 4.2 5.7 1.0 N A:GLN156 4.2 5.0 1.0 HA A:TYR160 4.2 6.8 1.0 N A:GLY158 4.3 6.0 1.0 CA A:GLY157 4.3 5.9 1.0 CA A:ASP159 4.3 6.1 1.0 H12 A:EDO208 4.3 40.5 1.0 OD2 A:ASP155 4.3 5.7 1.0 CA A:GLY158 4.4 6.2 1.0 CB A:ASP155 4.4 5.0 1.0 CA A:ASP155 4.4 5.0 1.0 C A:ASP110 4.4 5.2 1.0 N A:ASP111 4.5 4.9 1.0 HB3 A:TYR160 4.5 7.2 1.0 CG A:GLN156 4.5 6.7 1.0 HB2 A:ASP155 4.5 6.0 1.0 NE2 A:GLN156 4.6 8.0 1.0 CB A:ASP111 4.6 5.3 1.0 CB A:ASP110 4.6 5.9 1.0 H A:ASP111 4.6 5.9 1.0 N A:TYR160 4.6 5.7 1.0 O A:ASP110 4.6 5.1 1.0 HB2 A:ASP111 4.7 6.4 1.0 HA A:ASP111 4.7 6.2 1.0 C5 A:NAG202 4.7 7.5 0.5 C A:ASP155 4.8 5.1 1.0 C2 A:NDG201 4.8 9.0 0.5 C2 A:NAG202 4.8 7.2 0.5 C5 A:NDG201 4.8 8.1 0.5 HB2 A:ASP159 4.8 8.5 1.0 HB3 A:ASP110 4.8 7.1 1.0 O A:GLY158 4.8 6.4 1.0 CA A:TYR160 4.8 5.7 1.0 HA2 A:GLY157 4.9 7.1 1.0 C A:GLN156 4.9 5.7 1.0 HG2 A:GLN156 4.9 8.0 1.0 H5 A:NAG202 4.9 9.0 0.5 CA A:ASP111 4.9 5.1 1.0 H5 A:NDG201 4.9 9.7 0.5 O A:GLN129 4.9 7.2 1.0 H2 A:NAG202 4.9 8.6 0.5 HD1 A:TYR160 5.0 6.6 1.0 H2 A:NDG201 5.0 10.8 0.5 HA3 A:GLY157 5.0 7.1 1.0

Calcium binding site 2 out of 4 in the N-Acetyl-Glucosamine-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 N-Acetyl-Glucosamine-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:0.97 O A:PRO82 2.3 6.7 1.0 O A:HOH337 2.4 9.7 1.0 O A:GLY64 2.4 6.7 1.0 O A:HOH389 2.4 7.4 1.0 O A:HOH407 2.4 7.0 1.0 O A:HOH381 2.4 6.1 1.0 OD1 A:ASP81 2.5 6.2 1.0 CG A:ASP81 3.5 6.2 1.0 C A:GLY64 3.5 6.1 1.0 C A:PRO82 3.6 6.4 1.0 HE22 A:GLN68 3.8 7.8 1.0 HD2 A:PRO82 3.9 7.9 1.0 OD2 A:ASP81 3.9 6.8 1.0 HA A:THR65 4.0 7.1 1.0 HA2 A:GLY83 4.1 8.5 1.0 O A:HOH335 4.1 6.0 1.0 HA2 A:GLY64 4.1 8.3 1.0 CA A:GLY64 4.2 7.0 1.0 N A:PRO82 4.2 6.3 1.0 HB2 A:PRO82 4.3 11.8 1.0 OE1 A:GLN68 4.4 6.3 1.0 C A:ASP81 4.4 6.5 1.0 N A:GLY64 4.4 5.9 1.0 CA A:PRO82 4.4 6.7 1.0 H A:GLY64 4.4 7.1 1.0 O A:GLY83 4.5 6.4 1.0 N A:THR65 4.5 5.9 1.0 C A:GLY83 4.5 6.3 1.0 N A:GLY83 4.5 7.1 1.0 CD A:PRO82 4.5 6.6 1.0 CA A:GLY83 4.6 7.1 1.0 NE2 A:GLN68 4.6 6.5 1.0 O A:ASP81 4.7 7.7 1.0 CA A:THR65 4.7 5.9 1.0 CB A:ASP81 4.8 6.6 1.0 O A:HOH526 4.8 13.8 1.0 HG22 A:THR65 4.8 10.4 1.0 OD1 A:ASP84 4.8 7.4 1.0 CB A:PRO82 4.8 9.8 1.0 HA A:ASP81 4.9 7.7 1.0 O A:HOH354 4.9 25.1 1.0 CA A:ASP81 5.0 6.4 1.0 CD A:GLN68 5.0 5.5 1.0 C A:LYS63 5.0 6.0 1.0

Calcium binding site 3 out of 4 in the N-Acetyl-Glucosamine-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 N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:5.6 occ:0.93 OE1 A:GLN27 2.3 7.5 1.0 O A:GLN156 2.3 6.3 1.0 O A:HOH469 2.4 7.6 1.0 O A:HOH482 2.4 7.6 1.0 OD1 A:ASP87 2.4 6.1 1.0 O A:HOH359 2.4 10.7 1.0 OD2 A:ASP87 2.5 5.8 1.0 CG A:ASP87 2.8 5.7 1.0 HA A:GLN27 3.3 7.7 1.0 C A:GLN156 3.5 5.7 1.0 HB2 A:GLN156 3.5 7.4 1.0 CD A:GLN27 3.5 6.9 1.0 HA A:GLN156 3.7 6.7 1.0 HG1 A:THR86 3.9 7.6 1.0 CA A:GLN156 4.0 5.5 1.0 OE1 A:GLN156 4.0 8.1 1.0 H A:LEU28 4.1 7.6 1.0 HB2 A:GLN27 4.1 8.7 1.0 HE22 A:GLN27 4.1 9.3 1.0 CB A:GLN156 4.2 6.2 1.0 CA A:GLN27 4.2 6.4 1.0 NE2 A:GLN27 4.3 7.7 1.0 CB A:ASP87 4.3 5.8 1.0 HB A:THR86 4.4 7.4 1.0 HA3 A:GLY157 4.4 7.1 1.0 O A:HOH513 4.4 31.8 1.0 O A:HOH363 4.4 7.6 1.0 CB A:GLN27 4.5 7.2 1.0 O A:HOH357 4.5 9.2 1.0 CD A:GLN156 4.5 6.9 1.0 OG1 A:THR86 4.5 6.3 1.0 N A:GLY157 4.6 5.6 1.0 CG A:GLN27 4.6 7.1 1.0 O A:SER26 4.7 7.6 1.0 HB3 A:ASP87 4.7 7.0 1.0 N A:LEU28 4.8 6.3 1.0 HB2 A:ASP87 4.8 7.0 1.0 O A:THR86 4.8 6.2 1.0 HA A:ASP87 4.9 6.4 1.0 HB3 A:GLN156 4.9 7.4 1.0 CA A:GLY157 4.9 5.9 1.0 CB A:THR86 5.0 6.2 1.0 CG A:GLN156 5.0 6.7 1.0

Calcium binding site 4 out of 4 in the N-Acetyl-Glucosamine-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 N-Acetyl-Glucosamine-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:20.6 occ:0.60 O A:VAL38 2.4 10.6 1.0 O A:LYS41 2.5 9.8 1.0 O A:HOH481 2.5 21.1 1.0 OH A:TYR22 2.7 12.8 1.0 HE2 A:TYR22 3.1 11.0 1.0 HH A:TYR22 3.2 15.4 1.0 HG13 A:VAL38 3.5 11.8 1.0 CZ A:TYR22 3.5 9.1 1.0 HA A:GLU42 3.6 13.7 1.0 C A:VAL38 3.6 9.4 1.0 C A:LYS41 3.6 9.5 1.0 CE2 A:TYR22 3.6 9.2 1.0 H A:LYS41 3.7 11.2 1.0 HG12 A:VAL38 3.9 11.8 1.0 HA A:ASP39 4.1 13.5 1.0 HA A:VAL38 4.2 9.6 1.0 CG1 A:VAL38 4.2 9.8 1.0 CA A:GLU42 4.3 11.4 1.0 N A:GLU42 4.4 10.8 1.0 O A:HOH431 4.4 24.4 1.0 H A:ALA43 4.4 11.1 1.0 N A:LYS41 4.4 9.3 1.0 CA A:VAL38 4.4 8.0 1.0 N A:ASP39 4.5 9.1 1.0 O A:HOH477 4.6 37.4 1.0 C A:GLU42 4.6 10.1 1.0 CA A:ASP39 4.6 11.3 1.0 N A:ALA43 4.6 9.3 1.0 CA A:LYS41 4.7 10.3 1.0 C A:ASP39 4.7 10.3 1.0 OE2 A:GLU42 4.8 36.0 1.0 OE1 A:GLU20 4.8 16.7 1.0 CE1 A:TYR22 4.8 8.3 1.0 CD2 A:TYR22 4.9 8.1 1.0 HG11 A:VAL38 4.9 11.8 1.0 O A:ASP39 4.9 14.5 1.0 CB A:VAL38 5.0 8.4 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