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Sodium 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
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the Ljcastor Gating Ring in the CA2+ and Na+ Condition, PDB code: 6o6j:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6o6j

Go back to Sodium Binding Sites List in 6o6j
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na1005

b:12.9
occ:1.00
O A:GLY488 2.2 14.0 1.0
O A:GLU490 2.2 15.8 1.0
O A:CYS492 2.3 12.9 0.7
O A:ASP485 2.3 15.7 1.0
O A:CYS492 2.3 13.0 0.3
OE1 A:GLU493 2.4 11.7 1.0
C A:CYS492 3.0 12.0 0.7
C A:CYS492 3.0 12.1 0.3
C A:GLY488 3.3 14.2 1.0
N A:CYS492 3.4 13.5 0.7
C A:GLU490 3.4 13.8 1.0
N A:CYS492 3.4 13.7 0.3
CB A:GLU493 3.5 11.2 1.0
C A:ASP485 3.5 16.1 1.0
CD A:GLU493 3.5 10.8 1.0
C A:ASN491 3.6 13.9 1.0
CA A:CYS492 3.7 13.2 0.3
CA A:CYS492 3.7 13.2 0.7
N A:GLU493 3.8 11.9 1.0
C A:PHE489 3.8 11.2 1.0
O A:HOH1221 3.9 24.2 1.0
O A:ASN491 3.9 13.2 1.0
O A:ILE486 3.9 16.5 1.0
CA A:PHE489 3.9 9.6 1.0
CA A:ILE486 4.0 11.7 1.0
CA A:GLU493 4.0 11.7 1.0
N A:GLU490 4.0 11.4 1.0
CG A:GLU493 4.0 12.7 1.0
N A:PHE489 4.1 11.8 1.0
O A:PHE489 4.1 11.2 1.0
C A:ILE486 4.1 15.2 1.0
O A:HOH1359 4.2 29.8 1.0
N A:ASN491 4.2 15.0 1.0
N A:ILE486 4.2 13.1 1.0
CA A:ASN491 4.2 13.8 1.0
CB A:ASN491 4.3 19.6 1.0
N A:GLY488 4.3 15.5 1.0
CA A:GLU490 4.4 14.0 1.0
CA A:GLY488 4.4 14.9 1.0
CA A:CA1002 4.5 12.1 1.0
CA A:ASP485 4.6 14.4 1.0
OE2 A:GLU493 4.6 12.8 1.0
N A:LEU487 4.9 12.7 1.0
CE A:MET763 5.0 16.4 1.0

Sodium binding site 2 out of 2 in 6o6j

Go back to Sodium Binding Sites List in 6o6j
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na 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:Na1006

b:16.9
occ:1.00
O A:ASN783 2.3 15.3 1.0
O A:GLU776 2.3 15.9 1.0
O A:GLU781 2.3 19.7 1.0
O A:ALA779 2.4 21.3 1.0
O A:HOH1422 2.4 19.0 1.0
C A:ASN783 3.3 14.7 1.0
C A:ALA779 3.3 21.8 1.0
C A:GLU781 3.4 23.9 1.0
C A:GLU776 3.5 14.1 1.0
C A:GLY782 3.7 17.3 1.0
N A:ASN783 3.8 15.2 1.0
N A:ALA779 3.9 14.7 1.0
O A:GLY782 3.9 18.1 1.0
CA A:ALA779 4.0 16.3 1.0
CB A:ALA779 4.1 18.7 1.0
CB A:GLU784 4.1 17.6 1.0
N A:GLU781 4.1 19.7 1.0
C A:GLU780 4.1 20.2 1.0
N A:GLU784 4.1 13.8 1.0
CA A:ASN783 4.1 14.5 1.0
O A:LEU777 4.1 18.1 1.0
CA A:LEU777 4.2 13.8 1.0
C A:LEU777 4.2 18.6 1.0
CG A:GLU776 4.2 14.7 1.0
N A:GLY782 4.2 24.3 1.0
CA A:GLY782 4.3 20.7 1.0
N A:LEU777 4.3 13.1 1.0
O A:GLU780 4.3 28.2 1.0
N A:GLU780 4.3 20.4 1.0
CA A:GLU784 4.4 14.7 1.0
CA A:GLU781 4.4 27.9 1.0
O A:HOH1153 4.4 29.1 1.0
CA A:GLU776 4.5 13.8 1.0
CA A:GLU780 4.5 20.6 1.0
N A:PHE778 4.8 15.0 1.0
C A:PHE778 4.9 18.1 1.0
CG A:GLU784 5.0 18.9 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: Tue Dec 15 12:41:00 2020

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