Atomistry » Sodium » PDB 6r7k-6rjc » 6rf1
Atomistry »
  Sodium »
    PDB 6r7k-6rjc »
      6rf1 »

Sodium in PDB 6rf1: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form

Protein crystallography data

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form, PDB code: 6rf1 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) 48.17 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 130.628, 240.474, 135.614, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form (pdb code 6rf1). 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 "Wet" Form, PDB code: 6rf1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6rf1

Go back to Sodium Binding Sites List in 6rf1
Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form


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 "Wet" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:46.0
occ:1.00
 O A:THR83 2.3 52.4 1.0
O A:HOH421 2.3 47.8 1.0
OD1 B:ASP102 2.5 64.1 1.0
O A:PHE86 2.5 58.0 1.0
OH A:TYR25 2.6 50.2 1.0
O A:HOH429 3.1 58.2 1.0
CG B:ASP102 3.2 64.6 1.0
OD2 B:ASP102 3.3 62.4 1.0
C A:THR83 3.4 48.7 1.0
O B:HOH414 3.5 64.2 1.0
CZ A:TYR25 3.6 49.3 1.0
O A:HOH416 3.6 48.1 1.0
C A:PHE86 3.7 53.6 1.0
CA A:THR83 3.9 49.8 1.0
CA A:THR87 4.2 50.4 1.0
CE1 A:TYR25 4.2 51.5 1.0
OG1 A:THR87 4.2 52.2 1.0
CB A:THR83 4.3 44.7 1.0
N A:THR87 4.3 48.6 1.0
N A:SER84 4.5 43.4 0.5
N A:SER84 4.5 45.2 0.5
CE2 A:TYR25 4.5 46.2 1.0
CB B:ASP102 4.7 62.7 1.0
N A:PHE86 4.8 47.8 1.0
CA A:PHE86 4.8 49.7 1.0
CB A:THR87 4.8 43.7 1.0
O B:SER100 4.9 66.7 1.0
CD2 A:TYR95 4.9 43.3 1.0
CA A:SER84 4.9 50.5 0.5
CA A:SER84 4.9 47.2 0.5

Sodium binding site 2 out of 5 in 6rf1

Go back to Sodium Binding Sites List in 6rf1
Sodium binding site 2 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form


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 "Wet" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na314

b:48.5
occ:1.00
 O E:THR83 2.4 66.0 1.0
OD1 A:ASP102 2.4 61.4 1.0
O E:PHE86 2.4 44.6 1.0
OH E:TYR25 2.7 54.2 1.0
CG A:ASP102 3.3 54.3 1.0
OD2 A:ASP102 3.5 56.0 1.0
C E:THR83 3.5 62.6 1.0
C E:PHE86 3.6 45.2 1.0
O E:HOH417 3.6 45.5 1.0
CZ E:TYR25 3.7 48.3 1.0
CA E:THR87 4.0 53.1 1.0
OG1 E:THR87 4.1 53.3 1.0
CA E:THR83 4.1 54.4 1.0
N E:THR87 4.2 48.9 1.0
CE1 E:TYR25 4.3 50.0 1.0
CB E:THR83 4.5 47.0 1.0
N E:SER84 4.6 54.4 0.5
N E:SER84 4.6 56.2 0.5
CE2 E:TYR25 4.6 49.1 1.0
CB E:THR87 4.6 44.7 1.0
O A:SER100 4.7 66.0 1.0
CB A:ASP102 4.7 55.3 1.0
CA E:PHE86 4.7 42.6 1.0
N E:PHE86 4.7 48.4 1.0
CD2 E:TYR95 4.9 39.5 1.0
CA E:SER84 5.0 53.6 0.5
CA E:SER84 5.0 56.6 0.5
N A:ASP102 5.0 47.5 1.0

Sodium binding site 3 out of 5 in 6rf1

Go back to Sodium Binding Sites List in 6rf1
Sodium binding site 3 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form


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 "Wet" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na310

b:53.4
occ:1.00
 O B:HOH431 2.2 50.7 1.0
OD1 C:ASP102 2.3 59.9 1.0
OH B:TYR25 2.4 44.0 1.0
O B:THR83 2.4 72.7 1.0
O B:PHE86 2.6 45.3 1.0
CG C:ASP102 3.0 60.9 1.0
OD2 C:ASP102 3.1 70.7 1.0
CZ B:TYR25 3.4 48.1 1.0
C B:THR83 3.4 54.5 1.0
O C:HOH414 3.5 56.3 1.0
O C:HOH424 3.6 38.8 1.0
C B:PHE86 3.8 47.7 1.0
CA B:THR83 3.9 51.3 1.0
CE1 B:TYR25 4.0 47.3 1.0
CB B:THR83 4.3 56.1 1.0
CA B:THR87 4.3 48.9 1.0
CE2 B:TYR25 4.3 47.3 1.0
OG1 B:THR87 4.4 50.0 1.0
N B:THR87 4.5 48.2 1.0
CB C:ASP102 4.5 52.9 1.0
N B:SER84 4.6 53.6 0.5
N B:SER84 4.6 52.6 0.5
CD2 B:TYR95 4.8 46.9 1.0
O B:HOH435 4.8 55.3 1.0
O C:SER100 4.8 55.8 1.0
CA B:PHE86 4.9 48.4 1.0
CE2 B:TYR95 4.9 53.1 1.0
N B:PHE86 4.9 53.6 1.0
CG2 B:THR83 4.9 53.9 1.0
N C:ASP102 5.0 54.4 1.0
CB B:THR87 5.0 44.5 1.0

Sodium binding site 4 out of 5 in 6rf1

Go back to Sodium Binding Sites List in 6rf1
Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form


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 "Wet" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na315

b:44.8
occ:1.00
 O C:HOH409 2.1 40.0 1.0
O C:THR83 2.3 45.6 1.0
OD1 D:ASP102 2.4 50.4 1.0
O C:PHE86 2.5 48.0 1.0
OH C:TYR25 2.6 58.0 1.0
O D:HOH427 2.9 64.5 1.0
CG D:ASP102 3.2 54.6 1.0
OD2 D:ASP102 3.3 62.3 1.0
C C:THR83 3.4 47.4 1.0
O D:HOH421 3.4 33.6 1.0
CZ C:TYR25 3.6 53.6 1.0
O D:HOH401 3.6 69.0 1.0
C C:PHE86 3.7 54.3 1.0
O C:HOH441 3.7 49.9 1.0
CA C:THR83 4.0 45.0 1.0
CA C:THR87 4.1 51.1 1.0
CE1 C:TYR25 4.2 56.1 1.0
OG1 C:THR87 4.2 55.7 1.0
N C:THR87 4.3 51.5 1.0
CB C:THR83 4.4 45.7 1.0
CE2 C:TYR25 4.5 51.3 1.0
N C:SER84 4.6 48.1 0.5
N C:SER84 4.6 48.6 0.5
CB D:ASP102 4.6 48.1 1.0
CB C:THR87 4.8 55.3 1.0
N C:PHE86 4.8 42.8 1.0
O D:SER100 4.8 61.7 1.0
CA C:PHE86 4.8 47.8 1.0
CD2 C:TYR95 4.9 50.7 1.0
CA C:SER84 5.0 54.8 0.5
CA C:SER84 5.0 55.8 0.5
N D:ASP102 5.0 51.8 1.0

Sodium binding site 5 out of 5 in 6rf1

Go back to Sodium Binding Sites List in 6rf1
Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form


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 "Wet" Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na314

b:58.7
occ:1.00
 O D:HOH414 2.1 67.3 1.0
O D:PHE86 2.3 51.6 1.0
OD1 E:ASP102 2.3 64.5 1.0
OH D:TYR25 2.6 48.6 1.0
O D:THR83 2.6 46.3 1.0
CG E:ASP102 3.2 62.5 1.0
O E:HOH420 3.3 38.2 1.0
O E:HOH404 3.3 68.2 1.0
C D:PHE86 3.4 52.1 1.0
OD2 E:ASP102 3.4 71.2 1.0
CZ D:TYR25 3.5 51.1 1.0
C D:THR83 3.7 49.0 1.0
CA D:THR87 3.9 47.5 1.0
CE1 D:TYR25 4.0 51.8 1.0
N D:THR87 4.1 48.0 1.0
OG1 D:THR87 4.1 56.8 1.0
CA D:THR83 4.2 53.0 1.0
CE2 D:TYR25 4.4 57.1 1.0
CD2 D:TYR95 4.5 50.6 1.0
CB E:ASP102 4.6 59.2 1.0
CB D:THR83 4.6 50.9 1.0
CB D:THR87 4.6 46.4 1.0
CA D:PHE86 4.6 52.6 1.0
CE2 D:TYR95 4.7 52.2 1.0
N D:PHE86 4.7 48.5 1.0
N D:SER84 4.8 45.3 0.5
N D:SER84 4.8 46.0 0.5
C D:THR87 4.9 50.0 1.0
N D:PHE88 4.9 50.2 1.0
O E:SER100 4.9 61.6 1.0
N E:ASP102 4.9 49.5 1.0

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 Dec 15 12:52:41 2020

Last articles

Zn in 8PFC
Zn in 8SF0
Zn in 8SOJ
Zn in 8SOK
Zn in 8SYI
Zn in 8SLG
Zn in 8SEX
Zn in 8SEZ
Zn in 8SJG
Zn in 8SEY
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy