Calcium in PDB 4gvl: Crystal Structure of the Gsuk Rck Domain

The structure of Crystal Structure of the Gsuk Rck Domain, PDB code: 4gvl was solved by C.Kong, W.Zeng, S.Ye, L.Chen, D.B.Sauer, Y.Lam, M.G.Derebe, Y.Jiang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.45 / 3.00
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	110.648, 161.693, 310.127, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 26.2

The structure of Crystal Structure of the Gsuk Rck Domain also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of the Gsuk Rck Domain (pdb code 4gvl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Gsuk Rck Domain, PDB code: 4gvl:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Gsuk Rck Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca603 b:87.2 occ:1.00 O B:THR183 2.4 84.8 1.0 OD1 A:ASN450 2.7 85.0 1.0 OG1 B:THR214 2.7 75.5 1.0 O A:GLU449 2.9 91.0 1.0 OE1 A:GLN453 3.0 82.6 1.0 OD1 B:ASN210 3.0 77.8 1.0 CD A:GLN453 3.4 82.8 1.0 C B:THR183 3.6 84.8 1.0 CG A:GLN453 3.7 80.9 1.0 CG B:ASN210 3.8 75.4 1.0 CG2 B:THR214 3.9 75.2 1.0 CG A:ASN450 3.9 82.4 1.0 CB B:THR214 3.9 75.2 1.0 ND2 B:ASN210 4.1 73.3 1.0 C A:GLU449 4.1 89.8 1.0 CB B:THR183 4.1 83.2 1.0 NE2 A:GLN453 4.2 84.3 1.0 CA A:ASN450 4.3 81.3 1.0 CA B:THR183 4.3 83.7 1.0 O B:ASN210 4.5 76.2 1.0 CB A:GLN453 4.5 77.0 1.0 CB A:ASN450 4.6 79.6 1.0 N B:ASP184 4.7 85.8 1.0 N A:ASN450 4.7 98.2 1.0 ND2 A:ASN450 4.8 83.4 1.0 CA B:THR214 4.9 76.3 1.0 CA B:ASP184 4.9 87.5 1.0 CG2 B:THR183 5.0 82.4 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Gsuk Rck Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca604 b:0.4 occ:1.00 O A:THR183 2.6 98.6 1.0 O D:GLU449 2.7 0.0 1.0 OG1 A:THR214 2.9 84.1 1.0 OD1 A:ASN210 3.0 83.3 1.0 OE1 D:GLN453 3.1 95.9 1.0 OD1 D:ASN450 3.3 90.5 1.0 CD D:GLN453 3.6 96.6 1.0 C D:GLU449 3.8 0.1 1.0 CA D:ASN450 3.8 93.9 1.0 C A:THR183 3.8 97.2 1.0 CG D:GLN453 3.8 93.1 1.0 CG D:ASN450 3.9 91.2 1.0 CG A:ASN210 3.9 81.8 1.0 CG2 A:THR214 3.9 86.6 1.0 CB A:THR214 4.0 85.7 1.0 ND2 A:ASN210 4.0 81.1 1.0 N D:ASN450 4.2 0.0 1.0 CB A:THR183 4.4 94.2 1.0 CB D:ASN450 4.4 90.9 1.0 CB D:GLN453 4.4 90.1 1.0 NE2 D:GLN453 4.5 0.9 1.0 CA A:THR183 4.6 95.1 1.0 ND2 D:ASN450 4.7 92.6 1.0 O A:ASN210 4.8 83.3 1.0 C D:ASN450 4.8 93.6 1.0 N A:ASP184 4.9 97.9 1.0 CA A:THR214 5.0 87.8 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Gsuk Rck Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca603 b:0.6 occ:1.00 OD1 B:ASN450 2.5 97.8 1.0 O C:THR183 2.7 0.5 1.0 OD1 C:ASN210 2.8 94.5 1.0 OG1 C:THR214 2.8 98.7 1.0 O B:GLU449 3.0 0.1 1.0 OE1 B:GLN453 3.4 97.7 1.0 CG B:ASN450 3.7 95.4 1.0 CG C:ASN210 3.7 93.6 1.0 CD B:GLN453 3.8 97.8 1.0 CG B:GLN453 3.8 95.9 1.0 C C:THR183 3.9 1.0 1.0 ND2 C:ASN210 3.9 94.0 1.0 CA B:ASN450 4.0 96.8 1.0 C B:GLU449 4.1 0.8 1.0 CB C:THR214 4.1 99.4 1.0 CG2 C:THR214 4.3 99.3 1.0 CB C:THR183 4.3 0.0 1.0 CB B:ASN450 4.4 93.9 1.0 CB B:GLN453 4.4 92.1 1.0 N B:ASN450 4.5 0.8 1.0 CA C:THR183 4.6 0.1 1.0 NE2 B:GLN453 4.7 0.6 1.0 ND2 B:ASN450 4.8 93.2 1.0 CD1 B:ILE426 4.8 91.0 1.0 O C:ASN210 4.8 95.8 1.0 OG1 C:THR183 4.8 0.0 1.0 N C:ASP184 4.9 0.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Gsuk Rck Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Gsuk Rck Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca603 b:0.8 occ:1.00 OD1 C:ASN450 2.7 0.8 1.0 O C:GLU449 2.7 0.3 1.0 OE1 C:GLN453 2.8 0.2 1.0 O D:THR183 2.9 0.5 1.0 OG1 D:THR214 3.0 0.6 1.0 OD1 D:ASN210 3.1 0.3 1.0 CD C:GLN453 3.3 0.1 1.0 CG C:GLN453 3.7 0.3 1.0 CG C:ASN450 3.8 0.0 1.0 C C:GLU449 3.8 0.9 1.0 CG2 D:THR214 3.8 0.5 1.0 CA C:ASN450 3.9 0.9 1.0 CB D:THR214 4.0 0.6 1.0 C D:THR183 4.0 0.6 1.0 CG D:ASN210 4.1 0.3 1.0 NE2 C:GLN453 4.2 0.4 1.0 N C:ASN450 4.3 0.8 1.0 CB C:GLN453 4.3 0.4 1.0 CB D:THR183 4.3 0.8 1.0 CB C:ASN450 4.4 0.2 1.0 ND2 D:ASN210 4.5 0.2 1.0 O D:ASN210 4.6 0.0 1.0 CA D:THR183 4.7 0.6 1.0 ND2 C:ASN450 4.9 0.3 1.0 CG C:GLU449 4.9 0.3 1.0 CA D:THR214 4.9 0.4 1.0 C C:ASN450 5.0 0.6 1.0

C.Kong, W.Zeng, S.Ye, L.Chen, D.B.Sauer, Y.Lam, M.G.Derebe, Y.Jiang. Distinct Gating Mechanisms Revealed By the Structures of A Multi-Ligand Gated K(+) Channel. Elife V. 1 00184 2012.
PubMed: 23240087
DOI: 10.7554/ELIFE.00184