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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

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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

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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

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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

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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

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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: Mon Aug 18 06:55:28 2025

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