Calcium in PDB 5e4l: Structure of Ligand Binding Region of Uparap at pH 5.3

The structure of Structure of Ligand Binding Region of Uparap at pH 5.3, PDB code: 5e4l was solved by C.Yuan, M.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.43 / 2.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	74.270, 102.700, 87.760, 90.00, 94.54, 90.00
R / Rfree (%)	21.7 / 25.9

The binding sites of Calcium atom in the Structure of Ligand Binding Region of Uparap at pH 5.3 (pdb code 5e4l). 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 Ligand Binding Region of Uparap at pH 5.3, PDB code: 5e4l:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:61.7 occ:1.00 OD2 A:ASP446 2.3 77.9 1.0 OD1 A:ASP480 2.5 62.8 1.0 O A:GLU479 2.6 68.3 1.0 O A:HOH705 2.6 77.7 1.0 OD1 A:ASP446 2.9 75.9 1.0 OD1 A:ASN473 2.9 90.6 1.0 OE1 A:GLN450 2.9 95.3 1.0 CG A:ASP446 2.9 69.7 1.0 NE2 A:GLN450 3.0 95.2 1.0 C A:GLU479 3.2 73.4 1.0 CD A:GLN450 3.3 89.9 1.0 CA A:ASP480 3.5 69.5 1.0 CG A:ASN473 3.6 84.0 1.0 CG A:ASP480 3.7 60.9 1.0 ND2 A:ASN473 3.7 62.4 1.0 N A:ASP480 3.7 82.7 1.0 N A:GLU479 3.9 73.7 1.0 CB A:ASP480 4.1 62.8 1.0 CA A:GLU479 4.2 86.7 1.0 OD2 A:ASP493 4.3 80.2 1.0 CB A:ASP446 4.4 55.3 1.0 C A:ASP480 4.6 78.1 1.0 OD2 A:ASP480 4.7 64.8 1.0 C A:LEU478 4.8 92.1 1.0 CG A:GLN450 4.8 75.8 1.0 CA A:LEU478 4.9 82.5 1.0 CZ A:PHE453 4.9 68.5 1.0 N A:MET451 5.0 67.2 1.0 CB A:GLU479 5.0 0.6 1.0

Calcium binding site 2 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:0.1 occ:1.00 OD1 A:ASN472 2.2 0.7 1.0 OD1 A:ASN492 2.3 0.0 1.0 O A:ASP493 2.4 0.4 1.0 OE1 A:GLU470 2.5 1.0 1.0 ND2 A:ASN472 2.6 0.4 1.0 CG A:ASN472 2.6 0.9 1.0 O A:HOH722 2.7 0.2 1.0 OE1 A:GLU479 2.7 0.9 1.0 OD1 A:ASP493 2.8 90.7 1.0 O A:HOH758 2.9 0.2 1.0 OE2 A:GLU470 3.1 0.6 1.0 CD A:GLU470 3.1 0.3 1.0 CG A:ASN492 3.4 1.0 1.0 C A:ASP493 3.5 0.3 1.0 CG A:ASP493 3.7 80.1 1.0 ND2 A:ASN492 3.8 0.9 1.0 CD A:GLU479 3.8 0.8 1.0 CB A:ASN472 3.9 0.1 1.0 N A:ASP493 3.9 96.9 1.0 CA A:ASP493 4.2 94.6 1.0 N A:ASN472 4.3 84.2 1.0 OD2 A:ASP493 4.3 80.2 1.0 OE2 A:GLU479 4.4 0.3 1.0 CG A:GLU470 4.5 0.1 1.0 N A:ASN473 4.5 0.3 1.0 CB A:ASP493 4.6 77.2 1.0 N A:SER494 4.6 79.3 1.0 CA A:ASN472 4.6 91.7 1.0 CB A:ASN492 4.7 0.0 1.0 CD2 A:PHE474 4.7 0.8 1.0 C A:ASN492 4.8 81.5 1.0 CA A:SER494 4.8 96.0 1.0 N A:PHE474 4.8 0.8 1.0 CB A:GLU479 4.9 0.6 1.0 CG A:GLU479 5.0 0.3 1.0 CB A:PHE474 5.0 0.3 1.0

Calcium binding site 3 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:83.2 occ:1.00 OD1 A:ASP328 2.3 91.3 1.0 OD1 A:ASN348 2.4 84.0 1.0 OE1 A:GLN326 2.4 78.2 1.0 OE1 A:GLU333 2.4 82.1 1.0 O A:HOH788 2.5 74.7 1.0 O A:ASN348 2.6 61.8 1.0 NE2 A:GLN326 2.9 70.3 1.0 CD A:GLN326 3.0 74.5 1.0 CG A:ASP328 3.3 98.1 1.0 CD A:GLU333 3.3 73.5 1.0 CG A:ASN348 3.5 89.3 1.0 C A:ASN348 3.6 61.7 1.0 OE2 A:GLU333 3.7 68.3 1.0 OD2 A:ASP328 3.7 0.3 1.0 N A:ASN348 3.8 45.1 1.0 CA A:ASN348 4.1 54.4 1.0 ND2 A:ASN348 4.3 0.3 1.0 N A:ASP328 4.4 77.8 1.0 CB A:GLN347 4.4 64.4 1.0 CB A:ASN348 4.4 77.8 1.0 CG A:GLN326 4.5 70.6 1.0 O A:ASP328 4.5 97.5 1.0 CG A:GLU333 4.6 68.2 1.0 CB A:GLU333 4.6 72.7 1.0 CB A:ASP328 4.6 0.8 1.0 N A:ARG349 4.7 77.0 1.0 C A:ASP328 4.8 0.5 1.0 C A:GLN347 4.8 55.7 1.0 OE1 A:GLN347 4.8 92.4 1.0 CA A:ASP328 4.8 97.3 1.0 CD A:ARG349 4.9 54.7 1.0 CA A:GLN347 4.9 50.9 1.0

Calcium binding site 4 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:0.5 occ:1.00 OE1 B:GLN450 2.4 0.7 1.0 OD2 B:ASP446 2.5 0.1 1.0 ND2 B:ASN473 2.8 0.7 1.0 OD1 B:ASN473 2.8 0.1 1.0 CG B:ASP446 2.9 0.9 1.0 OD1 B:ASP446 2.9 0.7 1.0 O B:GLU479 3.1 0.0 1.0 CG B:ASN473 3.2 0.2 1.0 OD1 B:ASP480 3.2 0.5 1.0 CD B:GLN450 3.4 0.4 1.0 NE2 B:GLN450 3.9 0.2 1.0 C B:GLU479 3.9 0.7 1.0 CA B:ASP480 4.1 0.9 1.0 CB B:ASP446 4.1 96.9 1.0 CG B:ASP480 4.4 0.4 1.0 N B:ASP480 4.4 0.1 1.0 N B:MET451 4.4 0.3 1.0 OD2 B:ASP493 4.5 0.5 1.0 CG B:GLN450 4.5 0.7 1.0 N B:GLU479 4.7 0.1 1.0 CB B:ASN473 4.7 0.4 1.0 SD B:MET451 4.7 0.1 1.0 CB B:ASP480 4.8 0.5 1.0 CZ B:PHE453 4.8 0.5 1.0 CA B:GLU479 4.9 0.8 1.0 CG B:MET451 5.0 0.2 1.0

Calcium binding site 5 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:0.8 occ:1.00 OD1 B:ASN492 2.3 0.8 1.0 OD1 B:ASN472 2.3 0.8 1.0 O B:ASP493 2.4 0.9 1.0 ND2 B:ASN472 2.5 0.7 1.0 CG B:ASN472 2.8 0.4 1.0 CG B:ASN492 2.8 0.6 1.0 ND2 B:ASN492 2.8 0.7 1.0 OE1 B:GLU479 3.0 0.9 1.0 OD1 B:ASP493 3.1 0.8 1.0 OE1 B:GLU470 3.2 0.5 1.0 C B:ASP493 3.4 0.8 1.0 N B:ASP493 3.4 0.0 1.0 CD B:GLU479 3.7 0.5 1.0 CD2 B:PHE474 3.7 0.3 1.0 CG B:ASP493 3.8 0.9 1.0 OE2 B:GLU479 3.8 0.3 1.0 CE2 B:PHE474 3.8 0.9 1.0 OE2 B:GLU470 3.9 0.1 1.0 CA B:ASP493 3.9 0.1 1.0 CD B:GLU470 4.0 0.4 1.0 CB B:ASN492 4.1 0.2 1.0 C B:ASN492 4.3 0.4 1.0 CG B:PHE474 4.3 0.8 1.0 CB B:ASN472 4.3 0.3 1.0 OD2 B:ASP493 4.4 0.5 1.0 CB B:ASP493 4.4 0.4 1.0 CA B:ASN492 4.5 0.0 1.0 CZ B:PHE474 4.5 0.2 1.0 N B:SER494 4.6 0.0 1.0 N B:ASN473 4.6 0.4 1.0 N B:PHE474 4.7 0.5 1.0 N B:ASN472 4.8 0.8 1.0 CD1 B:PHE474 4.8 0.2 1.0 CB B:PHE474 4.9 0.0 1.0 CG B:GLU479 4.9 0.6 1.0 CB B:GLU479 4.9 0.5 1.0 CE1 B:PHE474 4.9 0.5 1.0

Calcium binding site 6 out of 6 in the Structure of Ligand Binding Region of Uparap at pH 5.3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Ligand Binding Region of Uparap at pH 5.3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:0.4 occ:1.00 OE1 B:GLU333 2.4 98.0 1.0 OE1 B:GLN326 2.7 90.8 1.0 OE2 B:GLU333 3.1 83.4 1.0 CD B:GLU333 3.1 90.8 1.0 O B:ASN348 3.1 75.0 1.0 OD1 B:ASN348 3.3 0.2 1.0 CD B:GLN326 3.8 95.2 1.0 CB B:ASP328 4.0 0.3 1.0 ND2 B:ASN329 4.1 0.5 1.0 NE2 B:GLN326 4.2 96.6 1.0 CG B:ASN348 4.2 0.9 1.0 C B:ASN348 4.3 71.7 1.0 OD2 B:ASP328 4.4 0.7 1.0 CG B:ASP328 4.5 0.3 1.0 CG B:GLU333 4.5 87.1 1.0 OE1 B:GLN347 4.6 90.3 1.0 N B:ASN348 4.6 74.0 1.0 CB B:GLN347 4.7 79.7 1.0 ND2 B:ASN348 4.8 0.1 1.0 CD B:ARG349 4.9 70.3 1.0 CA B:ASN348 4.9 74.9 1.0

C.Yuan, M.Huang. Crystal Structures of Uparap, A Member of Mannose Receptor Family To Be Published.