Calcium in PDB 9qy1: ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside

The structure of ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside, PDB code: 9qy1 was solved by K.Drickamer, H.Feinberg, W.I.Weis, M.E.Taylor, S.A.F.Jegouzo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.65 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	45.65, 66.56, 37.23, 90, 90, 90
R / Rfree (%)	18.4 / 23.9

The binding sites of Calcium atom in the ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside (pdb code 9qy1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside, PDB code: 9qy1:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:30.6 occ:1.00 OD1 A:ASP481 2.2 33.6 1.0 O A:HOH740 2.3 31.6 1.0 OE1 A:GLN451 2.4 37.8 1.0 OD2 A:ASP447 2.4 31.9 1.0 OD1 A:ASN474 2.4 38.0 1.0 O A:GLU480 2.4 32.7 1.0 OD1 A:ASP447 2.5 30.4 1.0 CG A:ASP447 2.8 32.4 1.0 CD A:GLN451 3.2 38.2 1.0 NE2 A:GLN451 3.4 41.3 1.0 CG A:ASP481 3.4 33.9 1.0 C A:GLU480 3.5 33.0 1.0 CG A:ASN474 3.5 39.9 1.0 CA A:ASP481 3.7 30.3 1.0 N A:ASP481 4.0 29.5 1.0 CB A:ASP481 4.0 31.8 1.0 CB A:ASN474 4.2 39.7 1.0 CB A:ASP447 4.3 27.8 1.0 OD2 A:ASP481 4.4 34.8 1.0 ND2 A:ASN474 4.4 46.9 1.0 CZ A:PHE454 4.5 27.3 1.0 O A:HOH761 4.6 37.5 1.0 CA A:GLU480 4.6 31.1 1.0 OD2 A:ASP494 4.6 30.7 1.0 CG A:GLN451 4.6 37.0 1.0 O A:ASP447 4.7 31.5 1.0 CA A:ASN474 4.7 35.2 1.0 N A:MET452 4.8 35.2 1.0 N A:GLU480 4.8 36.1 1.0 C A:ASP481 4.9 29.0 1.0 CA A:GLN451 4.9 35.3 1.0 CB A:GLU480 5.0 31.8 1.0

Calcium binding site 2 out of 2 in the ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of ENDO180 (Uparap) Carbohydrate-Recognition Domain 2 with Bound Methyl Fucoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:29.5 occ:1.00 O2 A:MFU603 2.2 30.8 0.5 OD1 A:ASN493 2.4 30.6 1.0 OD1 A:ASP494 2.4 29.4 1.0 O A:ASP494 2.4 26.6 1.0 OD1 A:ASN473 2.4 29.7 1.0 O3 A:MFU603 2.5 31.9 0.5 OE1 A:GLU480 2.5 28.5 1.0 O3 A:MFU603 2.6 31.9 0.5 O4 A:MFU603 2.6 30.9 0.5 OE1 A:GLU471 2.6 30.5 1.0 C2 A:MFU603 3.2 32.3 0.5 C3 A:MFU603 3.2 32.7 0.5 CG A:ASP494 3.4 27.3 1.0 C3 A:MFU603 3.4 32.6 0.5 CD A:GLU471 3.4 31.7 1.0 CG A:ASN493 3.4 28.3 1.0 CG A:ASN473 3.4 31.4 1.0 C4 A:MFU603 3.5 32.7 0.5 C A:ASP494 3.5 27.8 1.0 CD A:GLU480 3.5 34.6 1.0 OE2 A:GLU471 3.7 30.7 1.0 N A:ASP494 3.7 24.9 1.0 OE2 A:GLU480 3.8 38.7 1.0 C2 A:MFU603 3.8 33.4 0.5 ND2 A:ASN493 3.9 29.4 1.0 ND2 A:ASN473 4.0 32.0 1.0 CA A:ASP494 4.0 24.6 1.0 OD2 A:ASP494 4.1 30.7 1.0 CB A:ASP494 4.3 26.2 1.0 N A:ASN473 4.3 29.8 1.0 C1 A:MFU603 4.5 32.7 0.5 O2 A:MFU603 4.5 35.3 0.5 O1 A:MFU603 4.6 32.3 0.5 C A:ASN493 4.6 24.6 1.0 N A:SER495 4.6 26.4 1.0 CB A:ASN473 4.6 32.8 1.0 C4 A:MFU603 4.7 32.8 0.5 CG A:GLU471 4.7 26.4 1.0 N A:ASN474 4.7 33.3 1.0 CB A:ASN493 4.7 25.7 1.0 CG A:GLU480 4.8 35.8 1.0 C5 A:MFU603 4.8 32.3 0.5 CA A:ASN473 4.8 32.4 1.0 N A:PHE475 4.9 38.5 1.0 CA A:ASN493 4.9 25.7 1.0 CB A:PHE475 4.9 38.6 1.0 CB A:GLU480 5.0 31.8 1.0

S.A.F.Jegouzo, H.Feinberg, Y.Lasanajak, D.H.Smith, W.I.Weis, K.Drickamer, M.E.Taylor. Sugar Binding Activity of the Endothelial Receptor ENDO180 To Be Published.