Calcium in PDB 6x9p: 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain

The structure of 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x9p 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)	39.73 / 1.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.22, 50.53, 79.47, 90, 90, 90
R / Rfree (%)	12.9 / 14.2

The binding sites of Calcium atom in the 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain (pdb code 6x9p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain, PDB code: 6x9p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the 2-Deoxyribose-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 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:6.4 occ:1.00 H42 A:UZJ201 2.3 9.1 0.7 H42 A:UZJ201 2.3 9.4 0.3 OD1 A:ASP155 2.3 6.6 1.0 OD1 A:ASP110 2.3 6.8 1.0 O A:ASP159 2.4 7.4 0.5 O A:ASP159 2.4 7.3 0.5 O A:GLY157 2.4 7.5 1.0 OD2 A:ASP111 2.4 6.5 1.0 O3 A:UZJ201 2.6 7.6 0.7 O4 A:UZJ201 2.6 7.6 0.7 O3 A:UZJ201 2.6 7.9 0.3 O4 A:UZJ201 2.6 7.8 0.3 H32 A:UZJ201 3.1 9.5 0.3 H32 A:UZJ201 3.1 9.1 0.7 CG A:ASP110 3.3 7.2 1.0 H A:GLY157 3.3 8.5 0.5 CG A:ASP111 3.3 6.5 1.0 H A:GLY157 3.4 8.5 0.5 C4 A:UZJ201 3.4 8.5 0.7 C4 A:UZJ201 3.4 9.2 0.3 C3 A:UZJ201 3.4 8.4 0.7 C A:GLY157 3.5 7.3 1.0 H41 A:UZJ201 3.5 11.0 0.3 C3 A:UZJ201 3.5 9.2 0.3 H41 A:UZJ201 3.5 10.2 0.7 HG3 A:GLN156 3.5 10.5 0.5 CG A:ASP155 3.5 6.2 1.0 C A:ASP159 3.6 7.3 0.5 C A:ASP159 3.6 7.4 0.5 OD2 A:ASP110 3.6 8.1 1.0 H22 A:UZJ201 3.7 13.9 0.7 HE21 A:GLN156 3.7 14.1 0.5 H A:GLN156 3.7 7.5 0.5 OD1 A:ASP111 3.7 7.3 1.0 H A:GLN156 3.7 7.6 0.5 H22 A:UZJ201 3.7 15.2 0.3 HG3 A:GLN156 3.8 9.7 0.5 H A:ASP159 3.8 9.4 0.5 H A:ASP159 3.8 9.5 0.5 HA A:ASP155 3.8 7.2 1.0 N A:ASP159 3.9 7.9 0.5 HG2 A:GLN156 3.9 9.7 0.5 N A:ASP159 3.9 7.9 0.5 N A:GLY157 4.0 7.1 1.0 HA3 A:GLY158 4.1 9.5 1.0 C2 A:UZJ201 4.1 11.6 0.7 C2 A:UZJ201 4.2 12.7 0.3 HA A:TYR160 4.2 9.3 1.0 H31 A:UZJ201 4.2 10.1 0.7 C A:GLY158 4.2 7.6 1.0 N A:GLN156 4.2 6.3 0.5 N A:GLN156 4.2 6.3 0.5 H31 A:UZJ201 4.3 11.1 0.3 CG A:GLN156 4.3 8.1 0.5 N A:GLY158 4.3 7.7 1.0 CA A:ASP159 4.3 7.8 0.5 CA A:ASP159 4.3 8.0 0.5 CA A:GLY157 4.3 7.2 1.0 OD2 A:ASP155 4.3 6.9 1.0 HE21 A:GLN156 4.4 12.5 0.5 CA A:GLY158 4.4 7.9 1.0 HB3 A:TYR160 4.4 9.0 1.0 CB A:ASP155 4.5 6.2 1.0 CA A:ASP155 4.5 6.0 1.0 N A:ASP111 4.5 6.7 1.0 CG A:GLN156 4.5 8.8 0.5 C A:ASP110 4.5 6.2 1.0 NE2 A:GLN156 4.5 11.7 0.5 CB A:ASP111 4.6 6.7 1.0 H A:ASP111 4.6 8.1 1.0 HB2 A:ASP155 4.6 7.5 1.0 N A:TYR160 4.6 7.7 1.0 H23 A:UZJ201 4.6 13.9 0.7 CB A:ASP110 4.6 7.2 1.0 O A:ASP110 4.7 6.5 1.0 HB2 A:ASP159 4.7 12.0 0.5 HB2 A:ASP111 4.7 8.0 1.0 C A:ASP155 4.8 6.4 1.0 C5 A:UZJ201 4.8 11.8 0.7 CA A:TYR160 4.8 7.7 1.0 HB2 A:ASP159 4.8 10.9 0.5 C5 A:UZJ201 4.8 12.3 0.3 HG2 A:GLN156 4.8 10.5 0.5 HA A:ASP111 4.8 7.7 1.0 O A:GLY158 4.8 8.2 1.0 H23 A:UZJ201 4.8 15.2 0.3 C A:GLN156 4.9 7.2 0.5 HA2 A:GLY157 4.9 8.7 1.0 HB3 A:ASP110 4.9 8.7 1.0 C A:GLN156 4.9 6.9 0.5 HD1 A:TYR160 4.9 8.9 1.0 CA A:ASP111 4.9 6.4 1.0 O A:GLN129 5.0 8.4 1.0 H11 A:UZJ201 5.0 18.7 0.3 H51 A:UZJ201 5.0 14.1 0.7

Calcium binding site 2 out of 5 in the 2-Deoxyribose-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 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:7.0 occ:0.97 O A:PRO82 2.3 8.2 1.0 O A:HOH348 2.4 10.9 1.0 O A:HOH422 2.4 8.9 1.0 O A:GLY64 2.4 7.9 1.0 O A:HOH396 2.4 7.7 1.0 O A:HOH429 2.4 8.6 1.0 OD1 A:ASP81 2.5 7.6 1.0 CG A:ASP81 3.5 8.2 1.0 C A:GLY64 3.5 7.9 1.0 C A:PRO82 3.5 7.9 1.0 HE22 A:GLN68 3.8 9.5 1.0 HD2 A:PRO82 3.9 9.9 1.0 OD2 A:ASP81 3.9 8.3 1.0 HA A:THR65 4.0 9.0 1.0 HA2 A:GLY64 4.1 10.1 1.0 O A:HOH349 4.1 7.4 1.0 HA2 A:GLY83 4.1 10.8 1.0 CA A:GLY64 4.2 8.4 1.0 N A:PRO82 4.2 7.9 1.0 HB2 A:PRO82 4.3 13.1 1.0 OE1 A:GLN68 4.4 7.5 1.0 CA A:PRO82 4.4 8.6 1.0 C A:ASP81 4.4 7.8 1.0 N A:GLY64 4.4 8.0 1.0 H A:GLY64 4.4 9.6 0.5 O A:GLY83 4.5 7.9 1.0 N A:GLY83 4.5 8.7 1.0 N A:THR65 4.5 7.4 1.0 CD A:PRO82 4.5 8.3 1.0 H A:GLY64 4.5 9.6 0.5 C A:GLY83 4.5 7.7 1.0 CA A:GLY83 4.6 9.0 1.0 NE2 A:GLN68 4.6 7.9 1.0 O A:ASP81 4.7 9.2 1.0 O A:HOH447 4.7 28.6 1.0 HG22 A:THR65 4.7 12.9 1.0 CA A:THR65 4.7 7.5 1.0 O A:HOH559 4.8 15.9 1.0 CB A:ASP81 4.8 8.1 1.0 CB A:PRO82 4.8 10.9 1.0 OD1 A:ASP84 4.8 9.4 1.0 HA A:ASP81 4.8 9.6 1.0 C A:LYS63 4.9 5.9 0.5 CD A:GLN68 4.9 7.0 1.0 CA A:ASP81 5.0 8.0 1.0

Calcium binding site 3 out of 5 in the 2-Deoxyribose-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 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:7.5 occ:1.00 OE1 A:GLN27 2.3 8.8 1.0 O A:GLN156 2.3 7.8 0.5 O A:GLN156 2.4 8.0 0.5 O A:HOH495 2.4 9.4 1.0 O A:HOH510 2.4 9.3 1.0 OD1 A:ASP87 2.4 7.4 1.0 O A:HOH313 2.4 13.4 1.0 OD2 A:ASP87 2.5 7.2 1.0 CG A:ASP87 2.8 7.2 1.0 HA A:GLN27 3.3 9.7 1.0 HB2 A:GLN156 3.4 9.2 0.5 HB2 A:GLN156 3.4 8.6 0.5 C A:GLN156 3.5 6.9 0.5 C A:GLN156 3.5 7.2 0.5 CD A:GLN27 3.5 8.4 1.0 HA A:GLN156 3.7 8.1 0.5 HA A:GLN156 3.7 8.0 0.5 HG1 A:THR86 3.9 9.0 1.0 CA A:GLN156 4.0 6.8 0.5 CA A:GLN156 4.0 6.6 0.5 H A:LEU28 4.0 9.0 1.0 OE1 A:GLN156 4.0 9.5 0.5 HB2 A:GLN27 4.1 10.4 1.0 CB A:GLN156 4.1 7.7 0.5 CB A:GLN156 4.1 7.2 0.5 HE22 A:GLN27 4.2 11.0 1.0 CA A:GLN27 4.2 8.1 1.0 CB A:ASP87 4.3 7.1 1.0 NE2 A:GLN27 4.3 9.2 1.0 HB A:THR86 4.4 8.9 1.0 HA3 A:GLY157 4.4 8.7 1.0 O A:HOH377 4.5 9.1 1.0 O A:HOH360 4.5 10.4 1.0 O A:HOH595 4.5 23.7 1.0 O A:HOH533 4.5 30.1 0.5 CB A:GLN27 4.5 8.7 1.0 CD A:GLN156 4.5 9.4 0.5 OG1 A:THR86 4.5 7.5 1.0 OE1 A:GLN156 4.5 10.5 0.5 N A:GLY157 4.6 7.1 1.0 CG A:GLN27 4.6 9.2 1.0 HB3 A:ASP87 4.7 8.5 1.0 O A:SER26 4.7 9.2 1.0 N A:LEU28 4.7 7.5 1.0 HB2 A:ASP87 4.8 8.5 1.0 O A:THR86 4.8 7.3 1.0 HG3 A:GLN156 4.8 9.7 0.5 HB3 A:GLN156 4.8 9.2 0.5 HB3 A:GLN156 4.8 8.6 0.5 HA A:ASP87 4.9 7.9 1.0 CG A:GLN156 4.9 8.1 0.5 CG A:GLN156 4.9 8.8 0.5 CB A:THR86 5.0 7.4 1.0 CA A:GLY157 5.0 7.2 1.0

Calcium binding site 4 out of 5 in the 2-Deoxyribose-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 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:16.0 occ:0.47 O A:HOH512 2.3 29.7 1.0 O A:VAL38 2.4 11.6 1.0 O A:LYS41 2.4 11.2 1.0 O A:HOH503 2.5 24.6 1.0 OH A:TYR22 2.7 13.5 1.0 HE2 A:TYR22 3.1 12.2 1.0 HH A:TYR22 3.2 16.2 1.0 HG13 A:VAL38 3.5 12.7 1.0 HA A:GLU42 3.5 15.6 1.0 CZ A:TYR22 3.5 10.3 1.0 C A:LYS41 3.6 11.3 1.0 C A:VAL38 3.6 10.5 1.0 CE2 A:TYR22 3.6 10.1 1.0 H A:LYS41 3.7 13.1 1.0 O A:HOH490 3.9 29.9 1.0 HG12 A:VAL38 3.9 12.7 1.0 HA A:VAL38 4.1 11.2 1.0 CG1 A:VAL38 4.2 10.6 1.0 HA A:ASP39 4.2 14.2 1.0 CA A:GLU42 4.2 13.0 1.0 N A:GLU42 4.3 12.2 1.0 O A:HOH417 4.4 28.6 1.0 N A:LYS41 4.4 10.9 1.0 H A:ALA43 4.4 12.8 1.0 CA A:VAL38 4.4 9.3 1.0 O A:HOH507 4.5 40.8 1.0 N A:ASP39 4.5 10.4 1.0 C A:GLU42 4.6 11.2 1.0 N A:ALA43 4.6 10.7 1.0 CA A:ASP39 4.6 11.8 1.0 CA A:LYS41 4.6 11.5 1.0 C A:ASP39 4.6 11.2 1.0 OE1 A:GLU20 4.7 14.8 1.0 OE2 A:GLU42 4.8 35.9 1.0 CE1 A:TYR22 4.8 9.7 1.0 O A:ASP39 4.9 14.3 1.0 HG11 A:VAL38 4.9 12.7 1.0 CD2 A:TYR22 4.9 9.1 1.0 CB A:VAL38 5.0 9.6 1.0

Calcium binding site 5 out of 5 in the 2-Deoxyribose-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 2-Deoxyribose-Bound Structure of Marinomonas Primoryensis PA14 Carbohydrate-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:14.6 occ:0.96 O A:SER73 2.3 11.8 1.0 O A:HOH511 2.4 20.3 1.0 O A:HOH455 2.5 14.0 1.0 O A:HOH525 2.5 27.7 1.0 O A:HOH441 2.6 12.2 1.0 OG A:SER76 2.6 10.1 1.0 O A:HOH413 2.7 28.4 0.5 C A:SER73 3.4 10.7 1.0 HA A:SER73 3.5 12.9 1.0 HB3 A:SER76 3.5 11.0 1.0 CB A:SER76 3.6 9.2 1.0 H A:SER76 3.7 9.3 1.0 CA A:SER73 4.0 10.8 1.0 HB2 A:SER73 4.0 13.9 1.0 HB2 A:SER76 4.3 11.0 1.0 HA A:ASP74 4.3 9.0 1.0 O A:HOH413 4.4 28.5 0.5 O A:HOH378 4.4 13.3 1.0 N A:SER76 4.4 7.8 1.0 N A:ASP74 4.5 8.3 1.0 CB A:SER73 4.6 11.6 1.0 CA A:SER76 4.6 7.8 1.0 O A:HOH574 4.7 17.7 1.0 HG23 A:THR77 4.7 11.3 1.0 CA A:ASP74 4.8 7.5 1.0 O A:HOH364 4.9 13.2 1.0 C A:ASP74 5.0 7.9 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