Calcium in PDB 6x9m: 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x9m 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)	42.47 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.2, 50.33, 79.14, 90, 90, 90
R / Rfree (%)	14.2 / 15.9

The binding sites of Calcium atom in the 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x9m). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x9m:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the 3-O-Methyl-Glucose-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 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:6.1 occ:1.00 HO2 A:3MG1007 2.0 9.0 0.5 HO2 A:3MG1007 2.0 7.6 0.5 HO1 A:3MG1007 2.1 8.7 0.5 HO1 A:3MG1007 2.1 9.5 0.5 OD1 A:ASP155 2.3 6.2 1.0 OD1 A:ASP110 2.3 6.4 1.0 O A:ASP159 2.4 6.4 0.5 O A:GLY157 2.4 7.2 1.0 O A:ASP159 2.4 7.0 0.5 OD2 A:ASP111 2.4 6.3 1.0 O1 A:3MG1007 2.5 7.9 0.5 O1 A:3MG1007 2.5 7.2 0.5 O2 A:3MG1007 2.6 7.5 0.5 O2 A:3MG1007 2.6 6.3 0.5 C1 A:3MG1007 3.3 7.3 0.5 CG A:ASP110 3.3 7.2 1.0 CG A:ASP111 3.3 6.1 1.0 H1 A:3MG1007 3.3 8.8 0.5 H A:GLY157 3.3 8.5 0.5 C1 A:3MG1007 3.3 8.2 0.5 C2 A:3MG1007 3.4 8.7 0.5 H A:GLY157 3.4 8.5 0.5 C2 A:3MG1007 3.4 8.1 0.5 C A:GLY157 3.5 6.8 1.0 H2 A:3MG1007 3.5 10.5 0.5 HG3 A:GLN156 3.5 10.0 0.5 CG A:ASP155 3.5 5.5 1.0 H1 A:3MG1007 3.5 9.8 0.5 C A:ASP159 3.6 6.5 0.5 C A:ASP159 3.6 6.1 0.5 OD2 A:ASP110 3.6 7.8 1.0 H2 A:3MG1007 3.6 9.7 0.5 OD1 A:ASP111 3.7 7.1 1.0 H A:ASP159 3.7 8.8 0.5 H A:GLN156 3.7 6.9 0.5 H A:GLN156 3.7 6.9 0.5 HE21 A:GLN156 3.8 11.1 0.5 HA A:ASP155 3.8 6.7 1.0 HG3 A:GLN156 3.8 10.7 0.5 N A:ASP159 3.8 7.4 0.5 H A:ASP159 3.8 9.4 0.5 N A:ASP159 3.9 7.9 0.5 HG2 A:GLN156 3.9 10.7 0.5 N A:GLY157 4.0 7.1 1.0 HA3 A:GLY158 4.1 9.1 1.0 C A:GLY158 4.2 7.0 1.0 HA A:TYR160 4.2 8.0 1.0 N A:GLN156 4.2 5.8 0.5 N A:GLN156 4.2 5.8 0.5 CA A:ASP159 4.3 7.0 0.5 N A:GLY158 4.3 7.1 1.0 CG A:GLN156 4.3 8.9 0.5 CA A:GLY157 4.3 7.0 1.0 CA A:ASP159 4.3 7.5 0.5 OD2 A:ASP155 4.4 6.2 1.0 CA A:GLY158 4.4 7.6 1.0 CB A:ASP155 4.4 5.8 1.0 CA A:ASP155 4.4 5.6 1.0 N A:ASP111 4.5 5.9 1.0 C A:ASP110 4.5 6.2 1.0 HB3 A:TYR160 4.5 8.0 1.0 CG A:GLN156 4.5 8.3 0.5 H A:ASP111 4.5 7.1 1.0 HB2 A:ASP155 4.6 6.9 1.0 CB A:ASP111 4.6 6.1 1.0 NE2 A:GLN156 4.6 9.2 0.5 HE21 A:GLN156 4.6 11.6 0.5 CB A:ASP110 4.6 6.8 1.0 N A:TYR160 4.6 6.7 1.0 O5 A:3MG1007 4.6 12.7 0.5 O A:ASP110 4.7 5.9 1.0 O5 A:3MG1007 4.7 12.1 0.5 HB2 A:ASP111 4.7 7.3 1.0 HB2 A:ASP159 4.7 12.5 0.5 C3 A:3MG1007 4.7 13.5 0.5 C A:ASP155 4.8 5.8 1.0 H3 A:3MG1007 4.8 16.2 0.5 H71 A:3MG1007 4.8 23.7 0.5 HB2 A:ASP159 4.8 10.2 0.5 HG2 A:GLN156 4.8 10.0 0.5 C3 A:3MG1007 4.8 12.8 0.5 CA A:TYR160 4.8 6.7 1.0 O A:GLY158 4.8 7.6 1.0 HB3 A:ASP110 4.8 8.2 1.0 HA A:ASP111 4.8 7.3 1.0 HA2 A:GLY157 4.9 8.4 1.0 C A:GLN156 4.9 6.5 0.5 C A:GLN156 4.9 6.2 0.5 CA A:ASP111 4.9 6.1 1.0 O A:GLN129 4.9 8.6 1.0 HD1 A:TYR160 5.0 7.6 1.0

Calcium binding site 2 out of 5 in the 3-O-Methyl-Glucose-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 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:6.2 occ:1.00 O A:PRO82 2.3 7.3 1.0 O A:HOH1145 2.4 9.5 1.0 O A:HOH1212 2.4 7.6 1.0 O A:HOH1228 2.4 7.5 1.0 O A:GLY64 2.4 7.0 1.0 O A:HOH1195 2.4 6.4 1.0 OD1 A:ASP81 2.5 6.5 1.0 CG A:ASP81 3.5 6.5 1.0 C A:GLY64 3.5 6.4 1.0 C A:PRO82 3.5 6.9 1.0 HE22 A:GLN68 3.8 7.7 1.0 HD2 A:PRO82 3.9 9.0 1.0 OD2 A:ASP81 3.9 7.3 1.0 HA A:THR65 4.0 7.6 1.0 HA2 A:GLY83 4.1 9.6 1.0 O A:HOH1141 4.1 6.6 1.0 HA2 A:GLY64 4.1 8.8 1.0 N A:PRO82 4.2 6.9 1.0 CA A:GLY64 4.2 7.3 1.0 HB2 A:PRO82 4.3 11.7 1.0 OE1 A:GLN68 4.4 6.7 1.0 C A:ASP81 4.4 6.7 1.0 CA A:PRO82 4.4 7.4 1.0 N A:GLY64 4.4 6.7 1.0 H A:GLY64 4.4 8.0 0.5 O A:GLY83 4.5 6.6 1.0 H A:GLY64 4.5 8.0 0.5 N A:GLY83 4.5 7.3 1.0 N A:THR65 4.5 6.7 1.0 C A:GLY83 4.5 6.5 1.0 CD A:PRO82 4.5 7.5 1.0 CA A:GLY83 4.5 8.0 1.0 O A:HOH1353 4.6 34.0 1.0 NE2 A:GLN68 4.6 6.4 1.0 O A:ASP81 4.7 8.0 1.0 CA A:THR65 4.7 6.4 1.0 HG22 A:THR65 4.8 10.2 1.0 CB A:ASP81 4.8 7.2 1.0 O A:HOH1364 4.8 14.2 1.0 CB A:PRO82 4.8 9.7 1.0 OD1 A:ASP84 4.8 8.1 1.0 O A:HOH1181 4.8 25.1 1.0 HA A:ASP81 4.8 8.3 1.0 CD A:GLN68 4.9 5.8 1.0 CA A:ASP81 5.0 6.9 1.0 C A:LYS63 5.0 6.1 1.0 HA A:ASP84 5.0 7.5 1.0

Calcium binding site 3 out of 5 in the 3-O-Methyl-Glucose-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 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:6.5 occ:1.00 OE1 A:GLN27 2.3 8.0 1.0 O A:GLN156 2.3 7.1 0.5 O A:GLN156 2.3 7.1 0.5 O A:HOH1290 2.4 8.3 1.0 O A:HOH1318 2.4 8.0 1.0 OD1 A:ASP87 2.4 6.5 1.0 O A:HOH1106 2.4 12.7 1.0 OD2 A:ASP87 2.5 6.5 1.0 CG A:ASP87 2.8 6.0 1.0 HA A:GLN27 3.3 7.8 1.0 HB2 A:GLN156 3.4 9.3 0.5 HB2 A:GLN156 3.4 8.7 0.5 C A:GLN156 3.4 6.5 0.5 C A:GLN156 3.5 6.2 0.5 CD A:GLN27 3.5 7.5 1.0 HA A:GLN156 3.7 7.8 0.5 HA A:GLN156 3.7 7.5 0.5 HG1 A:THR86 3.9 7.9 1.0 CA A:GLN156 4.0 6.5 0.5 CA A:GLN156 4.0 6.2 0.5 H A:LEU28 4.0 7.9 1.0 OE1 A:GLN156 4.1 9.7 0.5 HB2 A:GLN27 4.1 8.9 1.0 CB A:GLN156 4.1 7.8 0.5 CB A:GLN156 4.1 7.3 0.5 HE22 A:GLN27 4.2 10.1 1.0 CA A:GLN27 4.2 6.5 1.0 CB A:ASP87 4.3 6.1 1.0 NE2 A:GLN27 4.3 8.4 1.0 HB A:THR86 4.4 7.5 1.0 HA3 A:GLY157 4.4 8.4 1.0 O A:HOH1391 4.4 23.8 1.0 O A:HOH1177 4.4 9.0 1.0 CD A:GLN156 4.5 7.4 0.5 O A:HOH1174 4.5 8.0 1.0 OE1 A:GLN156 4.5 9.8 0.5 CB A:GLN27 4.5 7.4 1.0 OG1 A:THR86 4.5 6.6 1.0 N A:GLY157 4.6 7.1 1.0 CG A:GLN27 4.6 7.7 1.0 O A:SER26 4.7 7.6 1.0 HB3 A:ASP87 4.7 7.3 1.0 N A:LEU28 4.8 6.6 1.0 HB2 A:ASP87 4.8 7.3 1.0 O A:THR86 4.8 6.7 1.0 HG3 A:GLN156 4.8 10.7 0.5 HB3 A:GLN156 4.8 9.3 0.5 HB3 A:GLN156 4.8 8.7 0.5 HA A:ASP87 4.9 7.2 1.0 CG A:GLN156 4.9 8.3 0.5 CG A:GLN156 4.9 8.9 0.5 CB A:THR86 5.0 6.2 1.0 CA A:GLY157 5.0 7.0 1.0

Calcium binding site 4 out of 5 in the 3-O-Methyl-Glucose-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 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:11.3 occ:0.50 O A:VAL38 2.3 9.8 1.0 O A:LYS41 2.4 9.7 1.0 O A:HOH1322 2.4 18.4 1.0 O A:HOH1313 2.5 19.5 1.0 OH A:TYR22 2.6 10.4 1.0 HE2 A:TYR22 3.1 10.2 1.0 CZ A:TYR22 3.5 8.3 1.0 HA A:GLU42 3.5 13.2 1.0 C A:LYS41 3.5 9.2 1.0 C A:VAL38 3.5 9.2 1.0 HG13 A:VAL38 3.6 11.6 1.0 H A:LYS41 3.6 11.1 1.0 CE2 A:TYR22 3.6 8.5 1.0 HG12 A:VAL38 3.9 11.6 1.0 O A:HOH1227 4.0 24.2 1.0 HA A:ASP39 4.0 12.5 1.0 HA A:VAL38 4.1 9.7 1.0 CG1 A:VAL38 4.2 9.7 1.0 CA A:GLU42 4.2 11.0 1.0 N A:GLU42 4.3 10.3 1.0 N A:LYS41 4.3 9.2 1.0 H A:ALA43 4.4 10.3 1.0 O A:HOH1258 4.4 17.7 1.0 CA A:VAL38 4.4 8.1 1.0 N A:ASP39 4.5 9.4 1.0 O A:HOH1306 4.5 29.3 1.0 CA A:ASP39 4.5 10.4 1.0 C A:GLU42 4.6 9.2 1.0 N A:ALA43 4.6 8.6 1.0 O A:HOH1129 4.6 32.5 1.0 CA A:LYS41 4.6 10.1 1.0 C A:ASP39 4.6 9.8 1.0 OE1 A:GLU20 4.7 161.2 1.0 CE1 A:TYR22 4.7 7.9 1.0 O A:ASP39 4.8 13.7 1.0 OE2 A:GLU42 4.9 37.7 1.0 CD2 A:TYR22 4.9 7.3 1.0 HG11 A:VAL38 4.9 11.6 1.0 CB A:VAL38 5.0 8.1 1.0 N A:SER40 5.0 10.3 1.0

Calcium binding site 5 out of 5 in the 3-O-Methyl-Glucose-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 3-O-Methyl-Glucose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:10.1 occ:1.00 O A:HOH1332 2.4 14.9 1.0 O A:HOH1176 2.5 9.4 1.0 O A:HOH1247 2.5 9.4 1.0 O A:HOH1359 2.5 16.6 1.0 O A:HOH1271 2.5 9.3 1.0 O A:HOH1205 2.5 9.9 1.0 O A:HOH1283 2.7 14.4 1.0 HA3 A:GLY72 3.5 9.6 1.0 O A:SER53 4.1 6.9 1.0 O A:HOH1394 4.4 40.1 1.0 H A:SER73 4.4 11.8 1.0 CA A:GLY72 4.4 8.0 1.0 O A:HOH1335 4.4 18.6 1.0 O A:GLY55 4.4 9.2 1.0 HA A:TYR54 4.5 6.9 1.0 O A:HOH1120 4.5 10.8 1.0 O A:HOH1248 4.5 10.9 1.0 H A:GLY55 4.5 8.3 1.0 O A:HOH1149 4.5 19.5 1.0 O A:HOH1190 4.6 31.8 1.0 HA2 A:GLY72 4.6 9.6 1.0 O A:PHE70 4.7 6.2 1.0 O A:HOH1323 4.7 19.7 1.0 O A:GLU69 4.8 6.5 1.0 N A:GLY72 5.0 7.6 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