Calcium in PDB 6x7z: Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x7z 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)	42.69 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.153, 50.567, 79.617, 90, 90, 90
R / Rfree (%)	12.5 / 13.1

The binding sites of Calcium atom in the Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x7z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x7z:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:4.4 occ:1.00 HO6 A:INS1006 2.0 7.9 0.4 HO6 A:INS1006 2.0 7.1 0.3 HO1 A:INS1006 2.1 9.0 0.4 OD1 A:ASP155 2.3 4.6 1.0 OD1 A:ASP110 2.3 4.8 1.0 O A:ASP159 2.4 5.2 0.5 O A:ASP159 2.4 5.1 0.5 O A:GLY157 2.4 5.4 1.0 OD2 A:ASP111 2.4 4.7 1.0 O4 A:INS1006 2.5 7.5 0.3 O1 A:INS1006 2.5 5.8 0.3 O1 A:INS1006 2.5 7.5 0.4 O6 A:INS1006 2.5 6.6 0.4 HO1 A:INS1006 2.5 7.0 0.3 O6 A:INS1006 2.5 5.9 0.3 O3 A:INS1006 2.5 7.5 0.3 HO4 A:INS1006 3.1 9.0 0.3 HO3 A:INS1006 3.1 9.0 0.3 CG A:ASP110 3.3 4.8 1.0 C1 A:INS1006 3.3 9.1 0.4 CG A:ASP111 3.3 4.4 1.0 C4 A:INS1006 3.3 9.1 0.3 H A:GLY157 3.3 5.9 0.5 H A:GLY157 3.3 5.9 0.5 C6 A:INS1006 3.4 7.6 0.4 C6 A:INS1006 3.4 6.3 0.3 H1 A:INS1006 3.4 10.9 0.4 H4 A:INS1006 3.4 10.8 0.3 C1 A:INS1006 3.4 5.1 0.3 C A:GLY157 3.5 5.1 1.0 C3 A:INS1006 3.5 9.8 0.3 HG3 A:GLN156 3.5 7.2 0.5 H6 A:INS1006 3.5 9.1 0.4 CG A:ASP155 3.5 4.0 1.0 C A:ASP159 3.6 5.2 0.5 C A:ASP159 3.6 5.2 0.5 OD2 A:ASP110 3.6 5.9 1.0 H6 A:INS1006 3.6 7.6 0.3 H2 A:INS1006 3.7 7.8 0.3 HE21 A:GLN156 3.7 7.6 0.5 OD1 A:ASP111 3.7 5.2 1.0 H A:GLN156 3.7 5.3 0.5 H A:GLN156 3.7 5.3 0.5 H A:ASP159 3.7 7.1 0.5 HA A:ASP155 3.8 5.0 1.0 H3 A:INS1006 3.8 11.8 0.3 H A:ASP159 3.8 7.0 0.5 N A:ASP159 3.9 5.9 0.5 N A:ASP159 3.9 5.8 0.5 HG2 A:GLN156 3.9 7.9 0.5 N A:GLY157 4.0 4.9 1.0 HG3 A:GLN156 4.0 7.9 0.5 C2 A:INS1006 4.1 6.5 0.3 HA3 A:GLY158 4.1 7.1 1.0 H1 A:INS1006 4.2 6.2 0.3 HA A:TYR160 4.2 6.5 1.0 C A:GLY158 4.2 5.7 1.0 N A:GLN156 4.2 4.4 0.5 N A:GLN156 4.2 4.4 0.5 CA A:ASP159 4.3 5.8 0.5 N A:GLY158 4.3 5.6 1.0 CA A:ASP159 4.3 6.0 0.5 CA A:GLY157 4.3 5.0 1.0 OD2 A:ASP155 4.3 4.7 1.0 HB3 A:TYR160 4.4 6.3 1.0 CA A:GLY158 4.4 5.9 1.0 CG A:GLN156 4.4 6.6 0.5 CB A:ASP155 4.4 4.1 1.0 CA A:ASP155 4.5 4.2 1.0 CG A:GLN156 4.5 6.0 0.5 N A:ASP111 4.5 4.1 1.0 C A:ASP110 4.5 4.3 1.0 NE2 A:GLN156 4.5 6.4 0.5 H5 A:INS1006 4.6 11.9 0.3 CB A:ASP111 4.6 4.6 1.0 HB2 A:ASP155 4.6 4.9 1.0 H A:ASP111 4.6 4.9 1.0 N A:TYR160 4.6 5.4 1.0 CB A:ASP110 4.6 5.0 1.0 HB2 A:ASP159 4.6 8.6 0.5 C5 A:INS1006 4.7 9.9 0.3 O A:ASP110 4.7 4.1 1.0 HB2 A:ASP111 4.7 5.5 1.0 C5 A:INS1006 4.7 11.1 0.4 C2 A:INS1006 4.7 14.7 0.4 HA A:ASP111 4.7 5.2 1.0 C A:ASP155 4.8 4.0 1.0 CA A:TYR160 4.8 5.4 1.0 O2 A:INS1006 4.8 6.9 0.3 HB2 A:ASP159 4.8 8.4 0.5 C5 A:INS1006 4.8 9.2 0.3 H5 A:INS1006 4.8 13.3 0.4 HG2 A:GLN156 4.8 7.2 0.5 O A:GLY158 4.9 5.8 1.0 HB3 A:ASP110 4.9 6.0 1.0 HA2 A:GLY157 4.9 6.0 1.0 C A:GLN156 4.9 5.0 0.5 C A:GLN156 4.9 5.0 0.5 HE21 A:GLN156 4.9 9.5 0.5 HD1 A:TYR160 4.9 6.0 1.0 CA A:ASP111 4.9 4.4 1.0 C2 A:INS1006 4.9 13.2 0.3 O A:GLN129 4.9 6.4 1.0 H6 A:INS1006 5.0 11.1 0.3

Calcium binding site 2 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:4.3 occ:0.97 O A:PRO82 2.3 5.5 1.0 O A:HOH1154 2.4 8.2 1.0 O A:HOH1208 2.4 6.2 1.0 O A:GLY64 2.4 5.5 1.0 O A:HOH1198 2.4 5.0 1.0 O A:HOH1210 2.4 5.9 1.0 OD1 A:ASP81 2.5 5.1 1.0 CG A:ASP81 3.5 5.2 1.0 C A:GLY64 3.5 5.2 1.0 C A:PRO82 3.5 5.4 1.0 HD2 A:PRO82 3.8 6.9 1.0 OD2 A:ASP81 3.9 5.9 1.0 HA A:THR65 4.0 6.0 1.0 HE22 A:GLN68 4.0 6.3 1.0 HA2 A:GLY64 4.1 6.8 1.0 HA2 A:GLY83 4.1 7.2 1.0 O A:HOH1133 4.1 4.9 1.0 HB2 A:PRO82 4.2 10.1 1.0 CA A:GLY64 4.2 5.6 1.0 N A:PRO82 4.2 5.5 1.0 CA A:PRO82 4.4 6.3 1.0 C A:ASP81 4.4 5.5 1.0 OE1 A:GLN68 4.4 5.0 1.0 N A:GLY64 4.4 5.2 1.0 H A:GLY64 4.4 6.2 0.5 O A:GLY83 4.4 5.2 1.0 H A:GLY64 4.5 6.2 0.5 C A:GLY83 4.5 5.2 1.0 N A:THR65 4.5 5.2 1.0 CD A:PRO82 4.5 5.8 1.0 N A:GLY83 4.5 6.1 1.0 CA A:GLY83 4.6 6.0 1.0 NE2 A:GLN68 4.6 5.3 1.0 O A:ASP81 4.7 6.6 1.0 CA A:THR65 4.7 5.0 1.0 CB A:ASP81 4.8 5.5 1.0 CB A:PRO82 4.8 8.4 1.0 HG22 A:THR65 4.8 9.0 1.0 O A:HOH1336 4.8 12.4 1.0 OD1 A:ASP84 4.8 6.3 1.0 HA A:ASP81 4.8 6.5 1.0 O A:HOH1146 4.9 21.8 1.0 CD A:GLN68 4.9 4.6 1.0 CA A:ASP81 4.9 5.5 1.0

Calcium binding site 3 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:5.1 occ:0.98 OE1 A:GLN27 2.3 6.8 1.0 O A:GLN156 2.3 5.6 0.5 O A:GLN156 2.3 5.6 0.5 O A:HOH1272 2.4 6.8 1.0 O A:HOH1291 2.4 7.1 1.0 OD1 A:ASP87 2.4 5.1 1.0 O A:HOH1107 2.4 11.3 1.0 OD2 A:ASP87 2.5 5.2 1.0 CG A:ASP87 2.8 4.8 1.0 HA A:GLN27 3.3 7.2 1.0 HB2 A:GLN156 3.4 6.6 0.5 HB2 A:GLN156 3.4 6.5 0.5 C A:GLN156 3.4 5.0 0.5 C A:GLN156 3.4 5.0 0.5 CD A:GLN27 3.5 6.7 1.0 HA A:GLN156 3.7 5.7 0.5 HA A:GLN156 3.7 5.6 0.5 HG1 A:THR86 3.9 6.2 1.0 OE1 A:GLN156 4.0 6.3 0.5 CA A:GLN156 4.0 4.7 0.5 CA A:GLN156 4.0 4.6 0.5 H A:LEU28 4.0 6.4 1.0 CB A:GLN156 4.1 5.5 0.5 HB2 A:GLN27 4.1 8.2 1.0 CB A:GLN156 4.2 5.4 0.5 HE22 A:GLN27 4.2 9.4 1.0 CA A:GLN27 4.2 6.0 1.0 CB A:ASP87 4.3 4.9 1.0 NE2 A:GLN27 4.3 7.8 1.0 HB A:THR86 4.4 6.2 1.0 HA3 A:GLY157 4.4 6.0 1.0 OE1 A:GLN156 4.4 10.8 0.5 O A:HOH1365 4.4 24.9 1.0 CD A:GLN156 4.4 5.5 0.5 O A:HOH1170 4.4 6.7 1.0 O A:HOH1340 4.5 38.2 1.0 O A:HOH1164 4.5 8.2 1.0 CB A:GLN27 4.5 6.8 1.0 OG1 A:THR86 4.5 5.2 1.0 N A:GLY157 4.6 4.9 1.0 CG A:GLN27 4.6 7.2 1.0 O A:SER26 4.7 6.7 1.0 HG3 A:GLN156 4.7 7.9 0.5 HB3 A:ASP87 4.7 5.8 1.0 N A:LEU28 4.7 5.3 1.0 O A:THR86 4.8 5.2 1.0 HB2 A:ASP87 4.8 5.8 1.0 CG A:GLN156 4.8 6.6 0.5 HB3 A:GLN156 4.9 6.6 0.5 HA A:ASP87 4.9 5.2 1.0 HB3 A:GLN156 4.9 6.5 0.5 CG A:GLN156 4.9 6.0 0.5 CB A:THR86 5.0 5.2 1.0 CA A:GLY157 5.0 5.0 1.0

Calcium binding site 4 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:9.8 occ:0.50 O A:VAL38 2.3 8.5 1.0 O A:LYS41 2.3 8.9 1.0 O A:HOH1283 2.4 17.0 1.0 O A:HOH1280 2.5 15.5 1.0 OH A:TYR22 2.6 8.5 1.0 HE2 A:TYR22 3.1 8.3 1.0 CZ A:TYR22 3.5 7.1 1.0 C A:LYS41 3.5 9.2 1.0 C A:VAL38 3.5 7.8 1.0 HA A:GLU42 3.5 12.7 1.0 HG13 A:VAL38 3.5 9.5 1.0 H A:LYS41 3.6 10.9 1.0 CE2 A:TYR22 3.6 7.0 1.0 HG12 A:VAL38 4.0 9.5 1.0 O A:HOH1205 4.1 16.9 1.0 HA A:ASP39 4.1 11.6 1.0 HA A:VAL38 4.1 7.9 1.0 CG1 A:VAL38 4.2 7.9 1.0 CA A:GLU42 4.2 10.6 1.0 N A:GLU42 4.3 10.1 1.0 N A:LYS41 4.3 9.1 1.0 O A:HOH1245 4.3 16.8 1.0 CA A:VAL38 4.4 6.6 1.0 H A:ALA43 4.4 10.0 1.0 N A:ASP39 4.4 8.1 1.0 C A:ASP39 4.5 9.3 1.0 O A:HOH1188 4.5 19.1 1.0 CA A:ASP39 4.5 9.7 1.0 O A:HOH1228 4.5 23.7 1.0 CA A:LYS41 4.5 9.5 1.0 C A:GLU42 4.6 9.1 1.0 N A:ALA43 4.6 8.3 1.0 OE2 A:GLU42 4.6 29.3 1.0 OE1 A:GLU20 4.7 9.3 1.0 O A:ASP39 4.7 11.8 1.0 CE1 A:TYR22 4.7 6.5 1.0 CD2 A:TYR22 4.9 6.2 1.0 N A:SER40 4.9 9.0 1.0 O A:HOH1110 4.9 35.3 1.0 HG11 A:VAL38 4.9 9.5 1.0 CB A:VAL38 5.0 6.9 1.0 HE1 A:TYR22 5.0 7.8 1.0 H A:SER40 5.0 10.8 1.0

Calcium binding site 5 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:5.1 occ:0.65 O A:HOH1335 2.4 13.6 1.0 O A:HOH1367 2.4 14.4 1.0 O A:HOH1307 2.4 12.7 1.0 O A:HOH1232 2.4 7.2 1.0 O A:HOH1180 2.5 7.9 1.0 O A:HOH1254 2.5 7.4 1.0 O A:HOH1213 2.5 8.1 1.0 O A:HOH1275 2.7 11.8 1.0 HA3 A:GLY72 3.5 6.9 1.0 O A:SER53 4.1 5.2 1.0 H A:SER73 4.4 9.4 1.0 O A:HOH1308 4.4 16.9 1.0 H A:GLY55 4.4 6.5 1.0 CA A:GLY72 4.4 5.8 1.0 HA A:TYR54 4.5 4.8 1.0 O A:HOH1252 4.5 8.6 1.0 O A:GLY55 4.5 7.1 1.0 O A:HOH1371 4.5 22.8 1.0 O A:HOH1124 4.5 24.6 1.0 O A:HOH1300 4.6 19.3 1.0 O A:PHE70 4.6 4.3 1.0 HA2 A:GLY72 4.7 6.9 1.0 O A:GLU69 4.8 5.1 1.0 N A:GLY55 5.0 5.4 1.0 N A:GLY72 5.0 5.5 1.0

Calcium binding site 6 out of 6 in the Inositol-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 Inositol-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1008 b:29.0 occ:1.00 O A:HOH1106 2.4 30.1 1.0 O A:HOH1282 2.5 11.5 1.0 OG A:SER130 2.6 7.8 0.5 HB2 A:SER130 3.1 13.6 0.5 HG A:SER130 3.1 9.4 0.5 OG A:SER130 3.3 15.7 0.5 H A:SER130 3.4 8.7 0.5 H A:SER130 3.4 9.3 0.5 HB3 A:SER130 3.5 8.9 0.5 CB A:SER130 3.6 7.4 0.5 CB A:SER130 3.7 11.4 0.5 HO4 A:INS1006 3.7 18.5 0.4 H4 A:INS1006 3.9 16.6 0.4 HG A:SER130 4.0 18.8 0.5 HO4 A:INS1006 4.0 15.1 0.3 O4 A:INS1006 4.1 12.5 0.3 N A:SER130 4.2 7.3 0.5 N A:SER130 4.2 7.7 0.5 HB2 A:SER130 4.3 8.9 0.5 HB3 A:SER130 4.4 13.6 0.5 O A:HOH1239 4.4 12.1 1.0 O4 A:INS1006 4.4 15.4 0.4 O A:HOH1117 4.5 24.9 1.0 CA A:SER130 4.5 6.9 0.5 O A:HOH1102 4.6 16.8 1.0 O A:HOH1332 4.6 21.8 1.0 CA A:SER130 4.6 7.8 0.5 C4 A:INS1006 4.6 13.9 0.4 H5 A:INS1006 4.7 11.0 0.3 H4 A:INS1006 4.8 14.8 0.3 O A:HOH1169 4.9 14.4 1.0 HA A:GLN129 4.9 8.3 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