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

Protein crystallography data

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

Other elements in 6o6j:

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

Calcium Binding Sites:

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 6o6j

Go back to Calcium Binding Sites List in 6o6j
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 6o6j

Go back to Calcium Binding Sites List in 6o6j
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 6o6j

Go back to Calcium Binding Sites List in 6o6j
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

Reference:

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
Page generated: Sat Dec 12 07:23:37 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy