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Calcium in PDB 5yby: Structure of Human Gliomedin

Protein crystallography data

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

Other elements in 5yby:

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

Sodium (Na) 4 atoms

Calcium Binding Sites:

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 5yby

Go back to Calcium Binding Sites List in 5yby
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 5yby

Go back to Calcium Binding Sites List in 5yby
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

Reference:

H.Liu, Z.Lin, F.Xu. High Resolution Structure of Human Gliomedin To Be Published.
Page generated: Wed Jul 9 11:56:20 2025

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