Calcium in PDB 7c00: Crystal Structure of the Srcr Domain of Human SCARA5.

The structure of Crystal Structure of the Srcr Domain of Human SCARA5., PDB code: 7c00 was solved by B.Yu, Y.He, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.65 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.167, 48.802, 70.771, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17.5

The binding sites of Calcium atom in the Crystal Structure of the Srcr Domain of Human SCARA5. (pdb code 7c00). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Srcr Domain of Human SCARA5., PDB code: 7c00:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Srcr Domain of Human SCARA5.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Srcr Domain of Human SCARA5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:13.7 occ:1.00 OD1 A:ASP420 2.2 12.2 1.0 OD1 A:ASP419 2.4 11.2 1.0 O A:HOH754 2.4 17.3 1.0 OE2 A:GLU486 2.4 15.4 1.0 O A:HOH735 2.5 21.7 1.0 O A:HOH739 2.5 21.1 1.0 CG A:ASP419 3.4 11.9 1.0 CG A:ASP420 3.5 11.9 1.0 HG2 A:GLU486 3.5 17.8 1.0 CD A:GLU486 3.5 15.3 1.0 HA A:ASP420 3.5 12.9 1.0 HB3 A:GLU486 3.8 15.3 1.0 OD2 A:ASP419 3.9 12.6 1.0 CG A:GLU486 4.0 14.8 1.0 N A:ASP420 4.0 9.8 1.0 CA A:ASP420 4.1 10.8 1.0 H A:ASP420 4.1 11.8 1.0 C A:ASP419 4.2 9.8 1.0 OD2 A:ASP420 4.3 12.9 1.0 CB A:ASP420 4.4 11.0 1.0 CB A:GLU486 4.4 12.8 1.0 O A:HOH795 4.5 31.0 1.0 O A:ASP419 4.6 9.5 1.0 OE1 A:GLU486 4.6 16.0 1.0 CB A:ASP419 4.7 10.3 1.0 H A:ASP419 4.7 11.8 1.0 SG A:CYS418 4.7 13.5 1.0 HG3 A:GLU486 4.8 17.8 1.0 CA A:ASP419 4.9 9.2 1.0 HB3 A:ASP420 4.9 13.2 1.0 O A:HOH789 4.9 37.0 1.0 HD3 A:ARG444 5.0 31.9 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Srcr Domain of Human SCARA5.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Srcr Domain of Human SCARA5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:9.1 occ:1.00 O A:GLY421 2.3 10.8 1.0 OD2 A:ASP423 2.4 11.6 1.0 OD2 A:ASP426 2.4 11.3 1.0 O A:HOH729 2.4 13.2 1.0 O A:VAL460 2.4 10.8 1.0 O A:HOH770 2.4 13.4 1.0 OD1 A:ASP426 2.8 8.7 1.0 CG A:ASP426 2.9 9.6 1.0 HA A:ALA461 3.0 12.2 1.0 CG A:ASP423 3.1 12.4 1.0 OD1 A:ASP423 3.4 14.1 1.0 C A:VAL460 3.5 10.5 1.0 C A:GLY421 3.5 11.9 1.0 H A:ASP423 3.7 12.2 1.0 H A:CYS462 3.8 10.4 1.0 HA A:TRP422 3.8 12.1 1.0 CA A:ALA461 3.9 10.2 1.0 N A:ALA461 4.1 10.5 1.0 N A:ASP423 4.2 10.1 1.0 O A:HOH706 4.2 49.1 1.0 HA3 A:GLY421 4.2 14.2 1.0 O A:HOH734 4.3 22.1 1.0 H A:ASP426 4.3 9.1 1.0 CB A:ASP423 4.3 9.4 1.0 N A:CYS462 4.3 8.7 1.0 HG12 A:VAL460 4.4 13.1 1.0 HB3 A:ASP423 4.4 11.3 1.0 CB A:ASP426 4.4 8.5 1.0 N A:TRP422 4.4 11.6 1.0 O A:HOH777 4.4 20.0 1.0 CA A:GLY421 4.4 11.8 1.0 CA A:TRP422 4.4 10.1 1.0 HB A:VAL460 4.5 12.7 1.0 C A:ALA461 4.6 12.3 1.0 HA2 A:GLY421 4.6 14.2 1.0 C A:TRP422 4.7 11.2 1.0 HB2 A:ASP426 4.7 10.2 1.0 O A:HOH796 4.7 32.8 1.0 CA A:VAL460 4.7 9.4 1.0 CA A:ASP423 4.8 8.2 1.0 HB3 A:ASP426 4.8 10.2 1.0 O A:CYS462 4.9 11.6 1.0 H A:ALA461 4.9 12.6 1.0 N A:ASP426 4.9 7.7 1.0 CB A:ALA461 4.9 11.6 1.0 CB A:VAL460 5.0 10.5 1.0 HB2 A:CYS462 5.0 12.6 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Srcr Domain of Human SCARA5.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Srcr Domain of Human SCARA5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:13.1 occ:1.00 OD1 A:ASN481 2.4 14.6 1.0 OD2 A:ASP420 2.4 12.9 1.0 OD2 A:ASP458 2.4 12.5 1.0 OD1 A:ASP459 2.4 22.1 1.0 O A:HOH701 2.4 18.8 1.0 OD1 A:ASP458 2.5 11.9 1.0 CG A:ASP458 2.8 13.2 1.0 CG A:ASP459 3.0 18.4 1.0 OD2 A:ASP459 3.0 26.4 1.0 HB2 A:ASP420 3.2 13.2 1.0 CG A:ASP420 3.4 11.9 1.0 HB3 A:ASP420 3.4 13.2 1.0 CG A:ASN481 3.4 15.7 1.0 CB A:ASP420 3.5 11.0 1.0 H A:ASN481 3.6 18.6 1.0 ND2 A:ASN481 3.9 16.4 1.0 H A:ASP459 4.1 13.3 1.0 SG A:CYS482 4.1 14.9 1.0 CB A:ASP458 4.3 11.7 1.0 N A:ASN481 4.4 15.5 1.0 O A:HOH710 4.4 22.9 1.0 N A:ASP459 4.5 11.1 1.0 CB A:ASP459 4.5 13.5 1.0 OD1 A:ASP420 4.5 12.2 1.0 HB3 A:ASP458 4.5 14.0 1.0 CB A:ASN481 4.6 15.2 1.0 HA A:THR480 4.7 17.3 1.0 HB2 A:ASP458 4.8 14.0 1.0 HA A:ASP459 4.8 14.9 1.0 CA A:ASP459 4.9 12.4 1.0 HB A:THR480 4.9 15.6 1.0 HB2 A:ASP459 4.9 16.2 1.0 CA A:ASN481 5.0 15.4 1.0 SG A:CYS418 5.0 13.5 1.0

B.Yu, Y.He. Crystal Structure of the Srcr Domain of Human SCARA5. To Be Published.