Calcium in PDB 6w12: Structure of the Crd of CLEC10A

The structure of Structure of the Crd of CLEC10A, PDB code: 6w12 was solved by G.Birrane, P.V.Murphy, A.Gabba, J.G.Luz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.58 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.155, 52.155, 112.667, 90, 90, 120
R / Rfree (%)	16.8 / 19.6

The structure of Structure of the Crd of CLEC10A also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Zinc	(Zn)	1 atom

The binding sites of Calcium atom in the Structure of the Crd of CLEC10A (pdb code 6w12). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Crd of CLEC10A, PDB code: 6w12:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:11.1 occ:1.00 OD1 A:ASP293 2.3 10.1 1.0 OE1 A:GLU280 2.4 13.9 1.0 OD1 A:ASN292 2.5 12.6 1.0 O A:ASP293 2.5 10.0 1.0 OD1 A:ASP269 2.5 19.9 1.0 OE1 A:GLN267 2.5 10.8 1.0 O4 A:A2G414 2.5 13.7 1.0 O3 A:A2G414 2.6 12.7 1.0 CG A:ASP293 3.3 9.8 1.0 CD A:GLN267 3.4 12.8 1.0 CD A:GLU280 3.4 14.0 1.0 CG A:ASN292 3.4 10.8 1.0 C4 A:A2G414 3.4 15.8 1.0 CG A:ASP269 3.4 15.8 1.0 C A:ASP293 3.5 9.5 1.0 C3 A:A2G414 3.5 12.0 1.0 OE2 A:GLU280 3.8 12.6 1.0 NE2 A:GLN267 3.8 11.0 1.0 ND2 A:ASN292 3.8 9.5 1.0 N A:ASP293 3.8 8.2 1.0 OD2 A:ASP269 3.9 16.7 1.0 CA A:ASP293 4.0 7.8 1.0 OD2 A:ASP293 4.0 9.1 1.0 CB A:ASP293 4.2 8.9 1.0 N A:ASP269 4.3 15.2 1.0 C2 A:A2G414 4.3 14.8 1.0 CG A:GLN267 4.5 11.6 1.0 CG A:GLU280 4.6 13.7 1.0 CB A:ASP269 4.7 17.4 1.0 N A:ASP294 4.7 8.6 1.0 CB A:GLU280 4.7 12.1 1.0 CB A:ASN292 4.7 9.4 1.0 C A:ASN292 4.8 8.5 1.0 CB A:TRP271 4.8 13.9 1.0 N A:ASP270 4.8 15.1 1.0 N A:TRP271 4.8 13.1 1.0 C5 A:A2G414 4.9 16.5 1.0 CB A:GLN267 4.9 11.5 1.0 CA A:ASP269 4.9 15.5 1.0 CA A:ASN292 5.0 8.1 1.0 N2 A:A2G414 5.0 16.5 1.0

Calcium binding site 2 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca402 b:11.9 occ:1.00 OE2 A:GLU224 2.4 12.1 1.0 OD1 A:ASN220 2.4 15.4 1.0 O A:HOH559 2.4 13.9 1.0 O A:HOH570 2.4 13.9 1.0 O A:VAL218 2.4 10.1 1.0 OE2 A:GLU305 2.4 13.0 1.0 OE1 A:GLU305 2.6 11.6 1.0 OE1 A:GLU224 2.7 13.2 1.0 CD A:GLU224 2.9 15.2 1.0 CD A:GLU305 2.9 15.3 1.0 CG A:ASN220 3.6 15.4 1.0 C A:VAL218 3.6 9.5 1.0 CB A:VAL218 4.2 12.0 1.0 OH A:TYR193 4.3 9.8 1.0 CA A:VAL218 4.3 10.0 1.0 CB A:ASN220 4.3 16.4 1.0 N A:ASN220 4.3 11.7 1.0 CG A:GLU224 4.4 13.3 1.0 N A:VAL218 4.4 7.6 1.0 CG A:GLU305 4.4 13.1 1.0 ND2 A:ASN220 4.5 19.9 1.0 N A:ILE219 4.6 9.5 1.0 O A:HOH525 4.6 17.0 1.0 CG1 A:VAL218 4.6 10.6 1.0 CA A:ILE219 4.7 11.2 1.0 OG A:SER191 4.7 19.4 1.0 CL A:CL409 4.9 17.3 1.0 C A:ILE219 4.9 11.7 1.0 O A:HOH515 5.0 35.1 1.0 O A:HOH551 5.0 18.3 1.0 CA A:ASN220 5.0 14.1 1.0

Calcium binding site 3 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca403 b:11.0 occ:1.00 ND1 A:HIS286 2.0 12.2 1.0 O A:HOH586 2.2 7.7 1.0 O A:HOH585 2.3 9.1 1.0 O A:HOH587 2.3 7.0 1.0 CE1 A:HIS286 3.0 20.3 1.0 CG A:HIS286 3.1 12.3 1.0 CB A:HIS286 3.5 11.0 1.0 NZ A:LYS264 3.9 26.5 1.0 CE A:LYS264 3.9 29.5 1.0 NE2 A:HIS286 4.1 14.8 1.0 CD A:PRO287 4.2 25.6 1.0 CD2 A:HIS286 4.2 14.9 1.0 CA A:HIS286 4.6 11.1 1.0 CE1 A:TYR236 4.7 15.9 1.0 OH A:TYR236 4.7 16.4 1.0 N A:PRO287 4.9 19.9 1.0 OD1 A:ASP288 5.0 20.8 1.0

Calcium binding site 4 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca404 b:30.9 occ:1.00 O A:HOH548 2.0 24.4 1.0 CE1 A:HIS188 2.2 37.7 1.0 O A:HOH590 2.2 23.3 1.0 ND1 A:HIS188 3.1 31.0 1.0 NE2 A:HIS188 3.2 30.1 1.0 O A:HOH504 3.4 29.7 1.0 CG A:HIS188 4.3 24.9 1.0 CD2 A:HIS188 4.3 25.0 1.0 CD1 A:PHE227 4.7 21.4 1.0 NZ A:LYS230 4.8 95.8 1.0 CB A:PHE227 4.8 18.4 1.0

Calcium binding site 5 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:38.5 occ:1.00 ND1 A:HIS197 2.4 22.9 1.0 O A:HOH595 2.8 21.5 1.0 CG A:HIS197 3.3 15.7 1.0 CE1 A:HIS197 3.3 21.9 1.0 CB A:HIS197 3.5 11.7 1.0 NE2 A:HIS197 4.5 24.4 1.0 CD2 A:HIS197 4.5 21.5 1.0 O A:HOH574 4.9 9.0 1.0 CA A:HIS197 5.0 11.7 1.0

Calcium binding site 6 out of 6 in the Structure of the Crd of CLEC10A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Crd of CLEC10A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:18.0 occ:1.00 O A:HOH546 2.3 11.1 1.0 OD1 A:ASP270 2.3 15.1 1.0 O A:GLU280 2.4 12.1 1.0 OD1 A:ASP281 2.4 12.8 1.0 O A:HOH568 2.5 27.1 1.0 OD1 A:ASP243 2.7 17.7 1.0 OD2 A:ASP243 2.7 19.0 1.0 CG A:ASP243 3.1 18.6 1.0 CG A:ASP270 3.2 21.1 1.0 C A:GLU280 3.4 11.6 1.0 CG A:ASP281 3.6 13.8 1.0 CA A:ASP281 3.7 10.7 1.0 CB A:ASP270 3.9 17.6 1.0 OD2 A:ASP270 4.0 19.1 1.0 N A:ASP281 4.0 10.3 1.0 O A:HOH508 4.1 22.7 1.0 N A:GLU280 4.1 11.9 1.0 CB A:ASP281 4.2 11.0 1.0 CA A:ASP270 4.3 15.2 1.0 CA A:GLU280 4.4 12.2 1.0 O A:ASP243 4.4 20.6 1.0 CB A:ASP243 4.6 13.2 1.0 OD2 A:ASP281 4.6 18.7 1.0 OD2 A:ASP293 4.6 9.1 1.0 CZ2 A:TRP248 4.6 13.4 1.0 O A:HOH524 4.8 38.3 1.0 O A:HOH591 4.8 8.4 1.0 O A:HOH510 4.8 29.6 1.0 C A:ASP281 4.9 11.1 1.0

G.Birrane, P.V.Murphy. Structure of the Carbohydrate Recognition Domain of CLEC10A To Be Published.