Calcium in PDB 6o6j: Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition

The structure of Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition, PDB code: 6o6j was solved by Y.Jiang, S.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 1.60
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	125.234, 125.234, 81.512, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.8

The structure of Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition (pdb code 6o6j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition, PDB code: 6o6j:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition


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 Ljcastor Gating Ring in the CA2+ and Na+ Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:19.3 occ:1.00 OD2 A:ASP444 2.3 25.2 1.0 O A:HOH1513 2.4 23.7 1.0 O A:HOH1257 2.4 31.5 1.0 OD2 A:ASP591 2.5 20.8 1.0 OD2 A:ASP442 2.5 19.6 1.0 OD1 A:ASP591 2.5 25.2 1.0 OD1 A:ASP442 2.5 16.4 1.0 O A:HOH1516 2.6 25.1 1.0 CG A:ASP591 2.8 21.8 1.0 CG A:ASP442 2.8 17.5 1.0 CG A:ASP444 3.4 23.5 1.0 CB A:ASP444 3.9 18.4 1.0 O A:HOH1245 4.0 28.9 1.0 CB A:ASP442 4.4 15.0 1.0 CB A:ASP591 4.4 13.7 1.0 O A:HOH1206 4.4 26.8 1.0 O A:HOH1136 4.5 23.6 1.0 O A:HOH1187 4.5 42.4 1.0 OD1 A:ASP444 4.5 22.1 1.0 O A:HOH1525 4.6 41.8 1.0 CG A:ARG590 4.6 17.6 1.0 O A:HOH1117 4.7 33.6 1.0 N A:ASP444 4.7 15.9 1.0 O A:HOH1198 4.8 17.0 1.0 CD A:ARG590 4.8 18.8 1.0 NH1 A:ARG590 5.0 17.6 1.0 CA A:ASP444 5.0 17.7 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition


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 Ljcastor Gating Ring in the CA2+ and Na+ Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:12.1 occ:1.00 O A:PHE489 2.3 11.2 1.0 O A:GLU552 2.3 11.6 1.0 O A:ASN491 2.3 13.2 1.0 O A:HOH1523 2.4 15.1 1.0 OE2 A:GLU493 2.4 12.8 1.0 O A:HOH1521 2.5 15.7 1.0 OE1 A:GLU493 2.6 11.7 1.0 CD A:GLU493 2.9 10.8 1.0 C A:PHE489 3.5 11.2 1.0 C A:ASN491 3.5 13.9 1.0 C A:GLU552 3.5 11.8 1.0 C A:GLU490 4.0 13.8 1.0 N A:ASN491 4.0 15.0 1.0 O A:GLU490 4.2 15.8 1.0 CA A:PHE489 4.2 9.6 1.0 N A:CYS492 4.3 13.7 0.3 CA A:GLU552 4.3 10.8 1.0 CA A:CYS492 4.3 13.2 0.3 N A:CYS492 4.3 13.5 0.7 CA A:ASN491 4.4 13.8 1.0 CA A:GLU490 4.4 14.0 1.0 N A:GLU490 4.4 11.4 1.0 CG A:GLU493 4.4 12.7 1.0 CA A:CYS492 4.4 13.2 0.7 O A:HOH1450 4.4 26.9 1.0 N A:ASP553 4.5 12.0 1.0 NA A:NA1005 4.5 12.9 1.0 OH A:TYR495 4.5 12.8 1.0 O A:HOH1452 4.5 23.7 1.0 CG A:GLU552 4.6 17.2 1.0 CA A:ASP553 4.6 10.3 1.0 CB A:PHE489 4.7 14.0 1.0 O A:HOH1204 4.7 34.8 1.0 O A:HOH1608 4.7 34.5 1.0 C A:CYS492 4.8 12.1 0.3 O A:ALA551 4.8 12.5 1.0 C A:CYS492 4.8 12.0 0.7 CB A:ASP553 4.9 10.3 1.0 CG A:ASP553 4.9 16.1 1.0 CD1 A:PHE489 5.0 12.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition


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 Ljcastor Gating Ring in the CA2+ and Na+ Condition within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:13.8 occ:1.00 O A:HOH1369 2.4 14.7 1.0 OD1 A:ASP554 2.4 18.0 1.0 O A:ALA342 2.4 12.9 1.0 OG A:SER345 2.4 15.8 1.0 O A:HOH1319 2.4 16.4 1.0 OD1 A:ASP553 2.4 14.8 1.0 O A:HOH1140 2.5 14.6 1.0 CG A:ASP553 3.4 16.1 1.0 CB A:SER345 3.5 16.4 1.0 C A:ALA342 3.5 12.9 1.0 CG A:ASP554 3.6 19.9 1.0 OD2 A:ASP553 3.7 19.8 1.0 CA A:ALA342 4.1 11.4 1.0 O A:HOH1141 4.2 24.5 1.0 N A:SER345 4.3 15.7 1.0 O A:HOH1190 4.3 17.4 1.0 OD2 A:ASP554 4.4 20.4 1.0 N A:ASP554 4.4 12.5 1.0 CA A:SER345 4.5 19.5 1.0 CB A:ASP554 4.6 13.1 1.0 O A:HOH1504 4.6 30.3 1.0 N A:ASN343 4.6 12.1 1.0 OH A:TYR495 4.7 12.8 1.0 O A:ILE341 4.7 13.1 1.0 O A:HOH1205 4.7 16.4 1.0 CB A:ASP553 4.8 10.3 1.0 O A:HOH1521 4.8 15.7 1.0 CA A:ASN343 4.9 12.7 1.0 O A:HOH1582 4.9 34.8 1.0 C A:ASN343 4.9 13.2 1.0 CB A:ALA342 4.9 12.5 1.0 N A:GLU344 5.0 13.0 1.0

S.Kim, W.Zeng, S.Bernard, J.Liao, M.Venkateshwaran, J.M.Ane, Y.Jiang. CA2+-Regulated CA2+Channels with An Rck Gating Ring Control Plant Symbiotic Associations. Nat Commun V. 10 3703 2019.
ISSN: ESSN 2041-1723
PubMed: 31420535
DOI: 10.1038/S41467-019-11698-5