Atomistry » Sodium » PDB 6r7p-6rjn » 6rex
Atomistry »
  Sodium »
    PDB 6r7p-6rjn »
      6rex »

Sodium in PDB 6rex: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0

Protein crystallography data

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0, PDB code: 6rex was solved by K.Kovalev, V.Polovinkin, I.Gushchin, V.Borshchevskiy, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.26 / 2.70
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.432, 240.787, 135.737, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 25

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 (pdb code 6rex). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0, PDB code: 6rex:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6rex

Go back to Sodium Binding Sites List in 6rex
Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0


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 Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:36.8
occ:1.00
 O A:HOH452 2.2 23.1 1.0
O A:THR83 2.3 26.0 1.0
O A:PHE86 2.4 30.0 1.0
OH A:TYR25 2.6 25.7 1.0
OD1 B:ASP102 2.6 39.3 1.0
O B:HOH448 2.8 37.9 1.0
CG B:ASP102 3.3 37.5 1.0
OD2 B:ASP102 3.4 35.6 1.0
C A:THR83 3.4 25.8 1.0
O A:HOH447 3.5 29.1 1.0
C A:PHE86 3.5 27.3 1.0
CZ A:TYR25 3.6 25.0 1.0
O B:HOH432 3.6 20.4 1.0
CA A:THR83 3.9 26.3 1.0
CA A:THR87 4.1 28.6 1.0
O B:HOH406 4.1 30.1 1.0
CE1 A:TYR25 4.1 23.3 1.0
N A:THR87 4.2 27.4 1.0
OG1 A:THR87 4.3 32.8 1.0
CB A:THR83 4.4 25.2 1.0
CE2 A:TYR25 4.5 24.9 1.0
N A:SER84 4.5 25.8 0.5
N A:SER84 4.5 25.6 0.5
CA A:PHE86 4.7 26.2 1.0
N A:PHE86 4.7 26.6 1.0
CB A:THR87 4.8 28.5 1.0
CB B:ASP102 4.8 37.4 1.0
CD2 A:TYR95 4.8 25.4 1.0
CA A:SER84 4.9 26.8 0.5
CA A:SER84 5.0 26.5 0.5

Sodium binding site 2 out of 5 in 6rex

Go back to Sodium Binding Sites List in 6rex
Sodium binding site 2 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0


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 Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na311

b:33.8
occ:1.00
 O B:HOH440 2.2 26.0 1.0
OD1 C:ASP102 2.3 45.1 1.0
O B:THR83 2.4 39.8 1.0
OH B:TYR25 2.6 24.5 1.0
O B:PHE86 2.7 28.4 1.0
CG C:ASP102 3.1 40.0 1.0
OD2 C:ASP102 3.2 39.1 1.0
O C:HOH443 3.4 14.8 1.0
C B:THR83 3.5 29.1 1.0
CZ B:TYR25 3.6 25.7 1.0
O C:HOH412 3.6 36.2 1.0
C B:PHE86 3.8 29.2 1.0
CA B:THR83 4.0 27.2 1.0
CE1 B:TYR25 4.2 23.6 1.0
CA B:THR87 4.3 31.9 1.0
CB B:THR83 4.3 26.6 1.0
OG1 B:THR87 4.4 29.2 1.0
CE2 B:TYR25 4.5 25.0 1.0
N B:THR87 4.5 29.7 1.0
CB C:ASP102 4.5 35.2 1.0
O B:HOH439 4.6 29.1 1.0
N B:SER84 4.6 30.1 0.5
N B:SER84 4.6 29.5 0.5
O C:SER100 4.8 38.0 1.0
N C:ASP102 4.9 32.3 1.0
CD2 B:TYR95 4.9 27.6 1.0
CB B:THR87 5.0 30.6 1.0
N B:PHE86 5.0 28.6 1.0
CA B:PHE86 5.0 30.1 1.0

Sodium binding site 3 out of 5 in 6rex

Go back to Sodium Binding Sites List in 6rex
Sodium binding site 3 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0


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 Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na316

b:25.5
occ:1.00
 O C:THR83 2.3 24.8 1.0
O C:HOH414 2.3 16.8 1.0
OD1 D:ASP102 2.4 37.3 1.0
OH C:TYR25 2.5 26.2 1.0
O C:PHE86 2.6 25.2 1.0
O C:HOH455 2.8 37.8 1.0
CG D:ASP102 3.1 34.9 1.0
OD2 D:ASP102 3.2 37.7 1.0
C C:THR83 3.4 27.6 1.0
O D:HOH405 3.4 22.7 1.0
CZ C:TYR25 3.6 24.8 1.0
O D:HOH416 3.6 19.0 1.0
C C:PHE86 3.8 28.0 1.0
O C:HOH466 3.9 31.0 1.0
CA C:THR83 3.9 27.5 1.0
CE1 C:TYR25 4.2 24.2 1.0
CA C:THR87 4.2 29.4 1.0
CB C:THR83 4.3 25.6 1.0
CE2 C:TYR25 4.4 25.1 1.0
OG1 C:THR87 4.4 36.8 1.0
N C:THR87 4.5 29.3 1.0
N C:SER84 4.6 27.8 0.5
N C:SER84 4.6 27.6 0.5
CB D:ASP102 4.6 31.2 1.0
CD2 C:TYR95 4.9 28.1 1.0
N C:PHE86 4.9 25.7 1.0
O D:SER100 4.9 34.5 1.0
CA C:PHE86 4.9 25.7 1.0
CB C:THR87 4.9 31.8 1.0
CE2 C:TYR95 5.0 28.9 1.0
CG2 C:THR83 5.0 25.5 1.0

Sodium binding site 4 out of 5 in 6rex

Go back to Sodium Binding Sites List in 6rex
Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na313

b:35.0
occ:1.00
 O D:HOH424 2.1 46.2 1.0
OD1 E:ASP102 2.3 31.7 1.0
O D:THR83 2.4 27.6 1.0
OH D:TYR25 2.5 26.3 1.0
O D:PHE86 2.5 29.3 1.0
CG E:ASP102 3.1 34.3 1.0
OD2 E:ASP102 3.2 34.9 1.0
O E:HOH414 3.2 20.2 1.0
CZ D:TYR25 3.5 25.7 1.0
C D:THR83 3.5 27.8 1.0
C D:PHE86 3.7 24.4 1.0
O E:HOH407 3.9 31.1 1.0
CA D:THR83 4.0 28.6 1.0
CE1 D:TYR25 4.1 24.1 1.0
CA D:THR87 4.2 27.9 1.0
CE2 D:TYR25 4.3 28.0 1.0
CB D:THR83 4.4 28.4 1.0
N D:THR87 4.4 24.9 1.0
OG1 D:THR87 4.4 38.5 1.0
CB E:ASP102 4.5 33.1 1.0
N D:SER84 4.7 25.9 0.5
N D:SER84 4.7 25.6 0.5
CD2 D:TYR95 4.7 26.8 1.0
CA D:PHE86 4.8 22.4 1.0
CE2 D:TYR95 4.9 27.7 1.0
N D:PHE86 4.9 21.6 1.0
CB D:THR87 4.9 29.0 1.0
N E:ASP102 4.9 31.1 1.0
O E:SER100 5.0 37.7 1.0

Sodium binding site 5 out of 5 in 6rex

Go back to Sodium Binding Sites List in 6rex
Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 6.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na311

b:34.5
occ:1.00
 O E:THR83 2.4 31.2 1.0
OD1 A:ASP102 2.5 36.9 1.0
O E:PHE86 2.5 22.8 1.0
OH E:TYR25 2.7 27.5 1.0
CG A:ASP102 3.2 35.5 1.0
OD2 A:ASP102 3.3 33.0 1.0
C E:THR83 3.5 28.9 1.0
O E:HOH427 3.6 23.4 1.0
CZ E:TYR25 3.6 28.9 1.0
C E:PHE86 3.7 24.0 1.0
CA E:THR83 4.0 27.7 1.0
CA E:THR87 4.1 24.1 1.0
CE1 E:TYR25 4.3 27.5 1.0
OG1 E:THR87 4.3 25.4 1.0
N E:THR87 4.3 23.5 1.0
CB E:THR83 4.4 25.1 1.0
O E:HOH466 4.4 37.6 1.0
CE2 E:TYR25 4.5 28.8 1.0
N E:SER84 4.6 28.1 0.5
N E:SER84 4.6 27.4 0.5
CB A:ASP102 4.7 32.2 1.0
N E:PHE86 4.8 22.3 1.0
CA E:PHE86 4.8 23.8 1.0
CB E:THR87 4.8 22.6 1.0
O A:SER100 4.8 45.1 1.0
CD2 E:TYR95 4.9 25.0 1.0
CA E:SER84 5.0 28.3 0.5

Reference:

K.Kovalev, V.Polovinkin, I.Gushchin, A.Alekseev, V.Shevchenko, V.Borshchevskiy, R.Astashkin, T.Balandin, D.Bratanov, S.Vaganova, A.Popov, V.Chupin, G.Buldt, E.Bamberg, V.Gordeliy. Structure and Mechanisms of Sodium-Pumping KR2 Rhodopsin. Sci Adv V. 5 V2671 2019.
ISSN: ESSN 2375-2548
PubMed: 30989112
DOI: 10.1126/SCIADV.AAV2671
Page generated: Tue Oct 8 13:07:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy