Calcium in PDB 6x7t: Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain

The structure of Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7t 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)	42.41 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.47, 50.27, 79.01, 90, 90, 90
R / Rfree (%)	12.7 / 13

The binding sites of Calcium atom in the Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain (pdb code 6x7t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain, PDB code: 6x7t:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Allose-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 Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:5.3 occ:1.00 OD1 A:ASP155 2.3 5.3 1.0 OD1 A:ASP110 2.3 5.8 1.0 O A:ASP159 2.4 6.2 1.0 H9 A:VDV208 2.4 37.4 0.3 O A:GLY157 2.4 6.3 1.0 OD2 A:ASP111 2.4 5.5 1.0 H9 A:VDS207 2.5 4.0 0.6 O4 A:VDS207 2.5 3.6 0.6 O3 A:VDS207 2.5 3.4 0.6 O4 A:VDV208 2.5 32.6 0.3 O3 A:VDV208 2.6 31.1 0.3 H10 A:VDV208 2.7 39.1 0.3 H6 A:VDV208 2.8 23.1 0.3 H10 A:VDS207 2.9 4.3 0.6 C5 A:VDV208 3.3 19.2 0.3 CG A:ASP110 3.3 5.9 1.0 H A:GLY157 3.3 7.1 1.0 CG A:ASP111 3.3 5.4 1.0 C5 A:VDS207 3.4 4.8 0.6 C4 A:VDS207 3.4 4.7 0.6 C4 A:VDV208 3.5 14.5 0.3 C A:GLY157 3.5 6.3 1.0 HG3 A:GLN156 3.5 8.8 1.0 C A:ASP159 3.5 6.1 1.0 CG A:ASP155 3.5 4.9 1.0 H7 A:VDS207 3.6 9.3 0.6 OD2 A:ASP110 3.6 6.8 1.0 OD1 A:ASP111 3.7 6.6 1.0 H A:GLN156 3.7 6.2 1.0 HE21 A:GLN156 3.7 11.6 1.0 HA A:ASP155 3.8 5.8 1.0 H A:ASP159 3.8 7.9 0.3 H A:ASP159 3.8 7.9 0.7 H5 A:VDV208 3.8 17.4 0.3 N A:ASP159 3.8 6.6 1.0 N A:GLY157 4.0 5.9 1.0 C6 A:VDS207 4.1 7.7 0.6 HA3 A:GLY158 4.1 8.0 1.0 C A:GLY158 4.2 6.3 1.0 HA A:TYR160 4.2 7.6 1.0 H5 A:VDS207 4.2 5.7 0.6 N A:GLN156 4.3 5.1 1.0 CA A:ASP159 4.3 7.0 0.7 CA A:ASP159 4.3 6.9 0.3 N A:GLY158 4.3 6.5 1.0 CA A:GLY157 4.3 6.6 1.0 OD2 A:ASP155 4.4 5.6 1.0 H6 A:VDS207 4.4 5.8 0.6 C6 A:VDV208 4.4 15.2 0.3 CA A:GLY158 4.4 6.7 1.0 HB3 A:TYR160 4.4 7.7 1.0 CB A:ASP155 4.4 5.1 1.0 CA A:ASP155 4.5 4.9 1.0 N A:ASP111 4.5 5.2 1.0 CG A:GLN156 4.5 7.3 1.0 C A:ASP110 4.5 5.2 1.0 H A:ASP111 4.5 6.2 1.0 NE2 A:GLN156 4.6 9.7 1.0 CB A:ASP111 4.6 5.5 1.0 HB2 A:ASP155 4.6 6.1 1.0 N A:TYR160 4.6 6.2 1.0 H8 A:VDS207 4.6 10.4 0.6 HB2 A:ASP159 4.6 9.7 0.3 O2 A:VDV208 4.6 29.1 0.3 CB A:ASP110 4.6 6.0 1.0 C3 A:VDS207 4.7 8.7 0.6 C3 A:VDV208 4.7 18.4 0.3 O2 A:VDS207 4.7 8.7 0.6 O A:ASP110 4.7 5.3 1.0 HB2 A:ASP111 4.7 6.6 1.0 HA A:ASP111 4.7 6.8 1.0 HB2 A:ASP159 4.7 10.4 0.7 H4 A:VDS207 4.8 10.4 0.6 CA A:TYR160 4.8 6.3 1.0 C A:ASP155 4.8 5.3 1.0 HG2 A:GLN156 4.8 8.8 1.0 O1 A:VDV208 4.8 34.7 0.3 O A:GLY158 4.8 7.0 1.0 O1 A:VDS207 4.9 8.9 0.6 HA2 A:GLY157 4.9 7.9 1.0 C A:GLN156 4.9 5.8 1.0 HD1 A:TYR160 4.9 7.3 1.0 HB3 A:ASP110 4.9 7.1 1.0 CA A:ASP111 4.9 5.6 1.0 O A:GLN129 4.9 8.1 1.0 H4 A:VDV208 4.9 22.1 0.3

Calcium binding site 2 out of 6 in the Allose-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 Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:5.7 occ:1.00 O A:PRO82 2.3 6.7 1.0 O A:HOH348 2.4 9.3 1.0 O A:HOH415 2.4 7.3 1.0 O A:GLY64 2.4 6.7 1.0 O A:HOH432 2.4 7.0 1.0 O A:HOH383 2.4 6.0 1.0 OD1 A:ASP81 2.5 6.1 1.0 CG A:ASP81 3.5 6.2 1.0 C A:GLY64 3.5 6.0 1.0 C A:PRO82 3.5 6.9 1.0 HD2 A:PRO82 3.8 8.8 1.0 HE22 A:GLN68 3.8 7.3 1.0 OD2 A:ASP81 3.9 6.9 1.0 HA A:THR65 4.0 7.2 1.0 HA2 A:GLY83 4.0 8.8 1.0 O A:HOH337 4.1 5.8 1.0 HA2 A:GLY64 4.2 8.2 1.0 N A:PRO82 4.2 6.5 1.0 CA A:GLY64 4.3 6.9 1.0 HB2 A:PRO82 4.4 11.4 1.0 C A:ASP81 4.4 6.7 1.0 OE1 A:GLN68 4.4 5.8 1.0 CA A:PRO82 4.4 7.6 1.0 N A:GLY64 4.4 6.5 1.0 O A:GLY83 4.5 6.5 1.0 H A:GLY64 4.5 7.8 0.7 CD A:PRO82 4.5 7.4 1.0 N A:GLY83 4.5 7.2 1.0 N A:THR65 4.5 5.9 1.0 H A:GLY64 4.5 7.8 0.3 C A:GLY83 4.5 6.4 1.0 CA A:GLY83 4.5 7.3 1.0 NE2 A:GLN68 4.6 6.1 1.0 O A:HOH536 4.6 34.1 1.0 O A:ASP81 4.7 7.8 1.0 CA A:THR65 4.7 6.0 1.0 HG22 A:THR65 4.8 10.0 1.0 CB A:ASP81 4.8 6.9 1.0 O A:HOH551 4.8 13.5 1.0 OD1 A:ASP84 4.8 7.8 1.0 CB A:PRO82 4.8 9.5 1.0 HA A:ASP81 4.9 8.0 1.0 CA A:ASP81 4.9 6.7 1.0 C A:LYS63 4.9 6.5 0.3 CD A:GLN68 5.0 5.5 1.0

Calcium binding site 3 out of 6 in the Allose-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 Allose-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 OE1 A:GLN27 2.3 7.4 1.0 O A:GLN156 2.3 6.5 1.0 O A:HOH487 2.4 7.5 1.0 O A:HOH501 2.4 8.0 1.0 OD1 A:ASP87 2.4 6.2 1.0 O A:HOH317 2.4 11.4 1.0 OD2 A:ASP87 2.5 6.0 1.0 CG A:ASP87 2.8 5.8 1.0 HA A:GLN27 3.3 7.9 1.0 HB2 A:GLN156 3.5 7.9 1.0 C A:GLN156 3.5 5.8 1.0 CD A:GLN27 3.5 7.0 1.0 HA A:GLN156 3.8 6.7 1.0 HG1 A:THR86 3.9 7.3 1.0 H A:LEU28 4.0 7.5 1.0 CA A:GLN156 4.0 5.6 1.0 OE1 A:GLN156 4.0 9.6 1.0 HB2 A:GLN27 4.1 8.4 1.0 HE22 A:GLN27 4.2 9.2 1.0 CB A:GLN156 4.2 6.6 1.0 CA A:GLN27 4.2 6.5 1.0 NE2 A:GLN27 4.3 7.7 1.0 CB A:ASP87 4.3 5.9 1.0 HA3 A:GLY157 4.4 7.9 1.0 HB A:THR86 4.4 7.3 1.0 O A:HOH368 4.4 7.4 1.0 CD A:GLN156 4.5 9.0 1.0 CB A:GLN27 4.5 7.0 1.0 OG1 A:THR86 4.5 6.0 1.0 O A:HOH377 4.5 9.5 1.0 N A:GLY157 4.6 5.9 1.0 CG A:GLN27 4.6 7.3 1.0 O A:SER26 4.7 7.8 1.0 HB3 A:ASP87 4.7 7.1 1.0 N A:LEU28 4.7 6.2 1.0 O A:THR86 4.8 6.1 1.0 HB2 A:ASP87 4.8 7.1 1.0 HA A:ASP87 4.8 6.6 1.0 HB3 A:GLN156 4.9 7.9 1.0 CG A:GLN156 4.9 7.3 1.0 CA A:GLY157 4.9 6.6 1.0 CB A:THR86 5.0 6.1 1.0

Calcium binding site 4 out of 6 in the Allose-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 Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:14.1 occ:0.39 O A:HOH510 2.3 31.8 1.0 O A:HOH502 2.4 38.9 1.0 O A:VAL38 2.4 11.4 1.0 O A:LYS41 2.5 10.2 1.0 O A:HOH504 2.6 37.5 1.0 OH A:TYR22 2.6 13.6 1.0 HE2 A:TYR22 3.1 12.0 1.0 HG13 A:VAL38 3.4 12.4 1.0 CZ A:TYR22 3.5 10.8 1.0 HA A:GLU42 3.5 13.5 1.0 C A:VAL38 3.6 10.0 1.0 CE2 A:TYR22 3.6 10.0 1.0 C A:LYS41 3.6 10.1 1.0 H A:LYS41 3.8 12.3 1.0 HG12 A:VAL38 3.9 12.4 1.0 HA A:ASP39 3.9 15.2 1.0 O A:HOH426 4.0 24.9 1.0 CG1 A:VAL38 4.1 10.3 1.0 HA A:VAL38 4.1 10.5 1.0 O A:HOH467 4.2 18.9 1.0 CA A:GLU42 4.3 11.3 1.0 H A:ALA43 4.4 10.6 1.0 N A:GLU42 4.4 10.7 1.0 CA A:VAL38 4.4 8.8 1.0 O A:HOH499 4.4 31.6 1.0 N A:LYS41 4.5 10.2 1.0 N A:ASP39 4.5 10.4 1.0 CA A:ASP39 4.6 12.7 1.0 N A:ALA43 4.6 8.8 1.0 C A:GLU42 4.6 9.4 1.0 CA A:LYS41 4.7 10.3 1.0 CE1 A:TYR22 4.7 9.5 1.0 C A:ASP39 4.8 12.1 1.0 OE1 A:GLU20 4.8 15.2 1.0 HG11 A:VAL38 4.8 12.4 1.0 CD2 A:TYR22 4.9 8.0 1.0 CB A:VAL38 4.9 9.2 1.0

Calcium binding site 5 out of 6 in the Allose-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 Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:6.9 occ:0.31 O A:SER73 2.2 13.4 0.6 O A:SER73 2.2 9.6 0.4 HG A:SER76 2.2 11.3 1.0 O A:HOH520 2.4 27.3 1.0 O A:HOH514 2.5 59.1 1.0 O A:HOH388 2.6 26.2 1.0 O A:HOH413 2.6 14.9 1.0 OG A:SER76 2.7 9.4 1.0 HB2 A:SER73 3.2 14.8 0.4 C A:SER73 3.2 10.4 0.4 C A:SER73 3.2 11.8 0.6 HA A:SER73 3.3 13.6 0.4 HA A:SER73 3.4 14.7 0.6 HB3 A:SER76 3.5 9.4 1.0 HB2 A:SER73 3.5 16.0 0.6 CB A:SER76 3.7 7.8 1.0 CA A:SER73 3.7 11.3 0.4 H A:SER76 3.7 7.5 1.0 CA A:SER73 3.8 12.2 0.6 CB A:SER73 3.9 12.4 0.4 CB A:SER73 4.2 13.3 0.6 HA A:ASP74 4.2 8.1 1.0 HB2 A:SER76 4.3 9.4 1.0 N A:ASP74 4.4 8.4 1.0 N A:SER76 4.5 6.3 1.0 HB3 A:SER73 4.5 14.8 0.4 HG A:SER73 4.5 16.1 0.4 HB3 A:SER73 4.6 16.0 0.6 CA A:SER76 4.7 6.4 1.0 CA A:ASP74 4.7 6.7 1.0 O A:HOH323 4.7 11.9 1.0 HG23 A:THR77 4.7 9.7 1.0 OG A:SER73 4.8 13.4 0.4

Calcium binding site 6 out of 6 in the Allose-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 Allose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate- Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:8.0 occ:0.49 O A:HOH556 2.4 28.9 1.0 O A:HOH523 2.4 32.2 1.0 O A:HOH463 2.4 12.4 1.0 O A:HOH373 2.4 12.7 1.0 O A:HOH414 2.5 11.7 1.0 O A:HOH494 2.7 27.6 1.0 HA3 A:GLY72 3.5 10.0 1.0 O A:SER53 4.0 6.6 1.0 CA A:GLY72 4.3 8.3 1.0 O A:HOH579 4.4 53.7 1.0 HA2 A:GLY72 4.4 10.0 1.0 O A:GLY55 4.5 9.3 1.0 O A:HOH338 4.5 18.4 1.0 HA A:TYR54 4.5 6.2 1.0 H A:GLY55 4.6 8.7 1.0 H A:SER73 4.6 13.1 0.6 H A:SER73 4.6 12.4 0.4 O A:HOH444 4.7 14.4 1.0 O A:HOH507 4.7 21.9 1.0 O A:PHE70 4.7 5.7 1.0 O A:GLU69 4.8 6.5 1.0 N A:GLY72 4.9 7.5 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