Calcium in PDB 5yby: Structure of Human Gliomedin

The structure of Structure of Human Gliomedin, PDB code: 5yby was solved by H.Liu, Z.Lin, F.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.26 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.880, 81.573, 66.194, 90.00, 90.00, 90.00
R / Rfree (%)	15 / 16.9

The structure of Structure of Human Gliomedin also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Calcium atom in the Structure of Human Gliomedin (pdb code 5yby). 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 Human Gliomedin, PDB code: 5yby:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca511 b:45.6 occ:1.00 HZ1 A:LYS345 2.9 25.6 1.0 HA A:LYS291 3.6 21.6 1.0 O A:HOH792 3.6 28.9 1.0 O A:HOH796 3.7 24.6 1.0 HG2 A:LYS291 3.7 26.8 1.0 NZ A:LYS345 3.8 21.3 1.0 O2 A:EDO509 3.9 37.1 1.0 HZ2 A:LYS345 3.9 25.6 1.0 H21 A:EDO509 4.0 39.1 1.0 HO2 A:EDO509 4.1 44.5 1.0 H11 A:EDO509 4.2 35.8 1.0 HZ3 A:LYS345 4.3 25.6 1.0 C2 A:EDO509 4.4 32.6 1.0 HE3 A:LYS345 4.5 21.3 1.0 CA A:LYS291 4.5 18.0 1.0 O A:ARG290 4.5 21.5 1.0 HB3 A:LYS291 4.6 21.8 1.0 CG A:LYS291 4.6 22.3 1.0 CE A:LYS345 4.7 17.8 1.0 C1 A:EDO509 4.7 29.8 1.0 O1 A:EDO509 4.7 28.4 1.0 HD3 A:LYS291 4.8 31.4 1.0 HE2 A:LYS345 4.8 21.3 1.0 CB A:LYS291 4.8 18.1 1.0 H A:TYR292 4.8 19.5 1.0

Calcium binding site 2 out of 2 in the Structure of Human Gliomedin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Human Gliomedin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca512 b:71.2 occ:1.00 H21 A:EDO509 3.3 39.1 1.0 HB2 A:SER346 3.4 20.2 1.0 H22 A:EDO509 3.5 39.1 1.0 O A:HOH649 3.7 42.9 1.0 C2 A:EDO509 4.0 32.6 1.0 HB3 A:SER346 4.2 20.2 1.0 CB A:SER346 4.3 16.8 1.0 HO2 A:EDO509 4.6 44.5 1.0 O2 A:EDO509 4.9 37.1 1.0 HA A:SER346 5.0 19.0 1.0 H12 A:EDO509 5.0 35.8 1.0 O A:HOH850 5.0 30.6 1.0 C1 A:EDO509 5.0 29.8 1.0

H.Liu, Z.Lin, F.Xu. High Resolution Structure of Human Gliomedin To Be Published.