Atomistry » Sodium » PDB 6c0l-6cgf » 6c1k
Atomistry »
  Sodium »
    PDB 6c0l-6cgf »
      6c1k »

Sodium in PDB 6c1k: Hypopp Mutant with LIGAND1

Protein crystallography data

The structure of Hypopp Mutant with LIGAND1, PDB code: 6c1k was solved by W.A.Catterall, N.Zheng, D.Jiang, T.M.Gamal El-Din, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.31 / 2.70
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 126.394, 126.235, 191.525, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Hypopp Mutant with LIGAND1 (pdb code 6c1k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Hypopp Mutant with LIGAND1, PDB code: 6c1k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6c1k

Go back to Sodium Binding Sites List in 6c1k
Sodium binding site 1 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hypopp Mutant with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1311

b:82.6
occ:1.00
O A:GLY1182 3.2 60.2 1.0
CE B:MET2181 3.7 28.4 1.0
CZ2 A:TRP1159 3.7 51.2 1.0
CH2 A:TRP1159 4.0 50.0 1.0
C A:GLY1182 4.0 52.7 1.0
CA A:GLY1182 4.0 40.7 1.0
CG A:PRO1186 4.4 37.9 1.0
O A:MET1181 4.9 64.0 1.0
CE2 A:TRP1159 4.9 49.7 1.0

Sodium binding site 2 out of 4 in 6c1k

Go back to Sodium Binding Sites List in 6c1k
Sodium binding site 2 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Hypopp Mutant with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1312

b:88.3
occ:1.00
OE2 A:GLU1158 2.6 83.6 1.0
NE1 A:TRP1159 2.7 51.8 1.0
CD A:GLU1158 3.5 76.1 1.0
CE B:MET2181 3.5 28.4 1.0
CE2 A:TRP1159 3.6 49.7 1.0
CD1 A:TRP1159 3.7 51.7 1.0
CD B:ARG2185 3.7 44.6 1.0
CZ2 A:TRP1159 3.9 51.2 1.0
OE1 A:GLU1158 4.0 75.7 1.0
SD B:MET2181 4.1 48.3 1.0
NE B:ARG2185 4.2 47.4 1.0
CG A:GLU1158 4.6 62.6 1.0
CZ B:ARG2185 4.7 46.0 1.0
CG B:ARG2185 4.8 44.8 1.0
CD2 A:TRP1159 4.8 60.7 1.0
CG A:TRP1159 4.9 48.2 1.0
NH1 B:ARG2185 4.9 45.8 1.0
CB B:ARG2185 5.0 29.9 1.0

Sodium binding site 3 out of 4 in 6c1k

Go back to Sodium Binding Sites List in 6c1k
Sodium binding site 3 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Hypopp Mutant with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2310

b:76.3
occ:1.00
O B:GLY2182 3.1 61.7 1.0
CZ2 B:TRP2159 3.6 51.1 1.0
CH2 B:TRP2159 3.9 50.9 1.0
C B:GLY2182 3.9 56.2 1.0
CA B:GLY2182 3.9 42.2 1.0
CG B:PRO2186 4.3 36.3 1.0
O B:MET2181 4.7 66.0 1.0
CE2 B:TRP2159 4.9 54.5 1.0

Sodium binding site 4 out of 4 in 6c1k

Go back to Sodium Binding Sites List in 6c1k
Sodium binding site 4 out of 4 in the Hypopp Mutant with LIGAND1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Hypopp Mutant with LIGAND1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2311

b:86.8
occ:1.00
NE1 B:TRP2159 2.6 50.0 1.0
OE2 B:GLU2158 2.7 80.0 1.0
CD B:GLU2158 3.4 81.7 1.0
CE2 B:TRP2159 3.6 54.5 1.0
CD1 B:TRP2159 3.6 48.5 1.0
OE1 B:GLU2158 3.8 92.5 1.0
CZ2 B:TRP2159 3.9 51.1 1.0
CG B:GLU2158 4.6 74.4 1.0
O B:HOH2403 4.8 47.6 1.0
CD2 B:TRP2159 4.8 54.2 1.0
CG B:TRP2159 4.8 47.2 1.0

Reference:

D.Jiang, T.M.Gamal El-Din, C.Ing, P.Lu, R.Pomes, N.Zheng, W.A.Catterall. Structural Basis For Gating Pore Current in Periodic Paralysis. Nature V. 557 590 2018.
ISSN: ESSN 1476-4687
PubMed: 29769724
DOI: 10.1038/S41586-018-0120-4
Page generated: Tue Dec 15 12:00:44 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy