Sodium in PDB 3v6i: Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution

The structure of Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution, PDB code: 3v6i was solved by A.G.Stewart, L.K.Lee, M.Donohoe, J.J.Chaston, D.Stock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.67 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	102.510, 208.690, 36.900, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 26.3

The structure of Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution also contains other interesting chemical elements:

Calcium

(Ca)

5 atoms

The binding sites of Sodium atom in the Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution (pdb code 3v6i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution, PDB code: 3v6i:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution


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 Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ X:Na201 b:37.6 occ:1.00 O X:HOH313 2.3 13.4 1.0 OE2 X:GLU117 2.5 31.7 1.0 OE1 X:GLU117 2.6 26.6 1.0 CD X:GLU117 2.9 27.3 1.0 NZ Y:LYS181 4.2 18.0 1.0 CG X:GLU117 4.4 22.6 1.0 O X:HOH312 4.5 14.8 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution


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 Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ X:Na202 b:43.7 occ:1.00 OE1 X:GLU93 2.1 23.9 1.0 O X:HOH315 2.3 15.5 1.0 OE1 X:GLU90 2.5 17.4 1.0 O X:HOH316 2.6 19.7 1.0 CD X:GLU93 3.2 18.7 1.0 CD X:GLU90 3.3 17.9 1.0 OE2 X:GLU90 3.3 21.6 1.0 OE2 X:GLU93 3.7 19.8 1.0 CG X:GLU93 4.5 13.1 1.0 CB X:GLU93 4.6 7.8 1.0 CG X:GLU90 4.7 13.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Peripheral Stalk of Thermus Thermophilus H+- Atpase/Synthase at 2.25 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ Y:Na201 b:13.4 occ:0.50 OE2 Y:GLU22 2.2 27.3 1.0 O Y:HOH312 2.4 19.6 1.0 O Y:HOH317 2.5 23.1 1.0 OE1 Y:GLU22 2.7 21.1 1.0 CD Y:GLU22 2.8 20.4 1.0 O A:HOH333 2.9 23.9 1.0 CG Y:GLU22 4.3 15.2 1.0 NH2 A:ARG58 4.9 15.2 1.0

A.G.Stewart, L.K.Lee, M.Donohoe, J.J.Chaston, D.Stock. The Dynamic Stator Stalk of Rotary Atpases Nat Commun V. 3 687 2012.
ISSN: ESSN 2041-1723
PubMed: 22353718
DOI: 10.1038/NCOMMS1693