Calcium in PDB 5e4k: Structure of Ligand Binding Region of Uparap at pH 7.4

The structure of Structure of Ligand Binding Region of Uparap at pH 7.4, PDB code: 5e4k 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)	37.47 / 2.58
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	74.940, 74.940, 224.570, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 25.7

The structure of Structure of Ligand Binding Region of Uparap at pH 7.4 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Calcium atom in the Structure of Ligand Binding Region of Uparap at pH 7.4 (pdb code 5e4k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Ligand Binding Region of Uparap at pH 7.4, PDB code: 5e4k:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Ligand Binding Region of Uparap at pH 7.4


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 7.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:68.3 occ:1.00 O A:HOH704 2.2 61.2 1.0 OD2 A:ASP446 2.3 71.8 1.0 O A:GLU479 2.3 69.5 1.0 OD1 A:ASN473 2.4 83.6 1.0 OE1 A:GLN450 2.4 83.1 1.0 OD1 A:ASP446 2.9 65.9 1.0 CG A:ASP446 2.9 66.1 1.0 OD1 A:ASP480 2.9 73.6 1.0 CG A:ASN473 3.2 83.6 1.0 C A:GLU479 3.2 71.1 1.0 ND2 A:ASN473 3.2 74.6 1.0 CD A:GLN450 3.3 80.8 1.0 NE2 A:GLN450 3.4 77.8 1.0 N A:GLU479 3.9 73.6 1.0 CA A:ASP480 3.9 69.1 1.0 N A:ASP480 3.9 71.1 1.0 CG A:ASP480 4.1 86.5 1.0 CA A:GLU479 4.1 69.6 1.0 CB A:ASP446 4.3 71.9 1.0 CB A:ASP480 4.6 82.2 1.0 CB A:ASN473 4.6 90.9 1.0 CG A:GLN450 4.7 73.7 1.0 OD2 A:ASP493 4.7 67.4 1.0 CB A:GLU479 4.7 69.5 1.0 N A:MET451 4.8 72.3 1.0 C A:LEU478 4.9 83.3 1.0 CA A:GLN450 5.0 63.8 1.0 C A:ASP480 5.0 61.8 1.0

Calcium binding site 2 out of 2 in the Structure of Ligand Binding Region of Uparap at pH 7.4


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 7.4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca602 b:77.1 occ:1.00 OD1 A:ASP493 2.3 66.7 1.0 OE1 A:GLU470 2.3 97.0 1.0 OD1 A:ASN492 2.4 67.2 1.0 OE1 A:GLU479 2.4 77.5 1.0 O A:ASP493 2.6 91.2 1.0 OD1 A:ASN472 2.8 0.7 1.0 O A:HOH726 3.0 76.8 1.0 O A:HOH708 3.1 77.2 1.0 CD A:GLU470 3.1 89.3 1.0 CG A:ASN492 3.3 76.2 1.0 OE2 A:GLU470 3.3 91.8 1.0 CD A:GLU479 3.3 80.6 1.0 CG A:ASP493 3.5 68.7 1.0 OE2 A:GLU479 3.6 88.3 1.0 ND2 A:ASN492 3.6 70.9 1.0 C A:ASP493 3.6 77.6 1.0 CG A:ASN472 3.6 0.5 1.0 N A:ASP493 3.8 76.7 1.0 ND2 A:ASN472 4.0 0.4 1.0 CA A:ASP493 4.1 78.5 1.0 N A:ASN472 4.3 95.2 1.0 OD2 A:ASP493 4.3 67.4 1.0 CB A:ASP493 4.4 70.2 1.0 CB A:PHE474 4.4 0.2 1.0 CG A:GLU470 4.5 80.6 1.0 CG A:GLU479 4.7 74.0 1.0 CB A:ASN492 4.7 73.3 1.0 N A:PHE474 4.7 0.4 1.0 N A:ASN473 4.7 0.6 1.0 C A:ASN492 4.7 80.6 1.0 N A:SER494 4.8 81.5 1.0 CB A:ASN472 4.9 0.4 1.0 CB A:GLU479 4.9 69.5 1.0 CA A:ASN492 4.9 75.7 1.0 CA A:ASN472 5.0 99.6 1.0

C.Yuan, H.J.Jurgensen, L.H.Engelholm, R.Li, M.Liu, L.Jiang, Z.Luo, N.Behrendt, M.Huang. Crystal Structures of the Ligand-Binding Region of Uparap: Effect of Calcium Ion Binding Biochem.J. V. 473 2359 2016.
ISSN: ESSN 1470-8728
PubMed: 27247422
DOI: 10.1042/BCJ20160276