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Sodium in PDB 6rew: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

Protein crystallography data

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rew 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) 48.03 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.360, 239.590, 135.250, 90.00, 90.00, 90.00
R / Rfree (%) 14.9 / 17.2

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 8.0 (pdb code 6rew). 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 8.0, PDB code: 6rew:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6rew

Go back to Sodium Binding Sites List in 6rew
Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


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 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:26.3
occ:1.00
O A:HOH450 2.3 21.6 1.0
O A:PHE86 2.3 26.2 1.0
O A:THR83 2.3 27.4 1.0
OH A:TYR25 2.5 24.4 1.0
OD1 B:ASP102 2.5 29.9 1.0
O B:HOH451 2.9 43.3 1.0
CG B:ASP102 3.3 32.9 1.0
OD2 B:ASP102 3.3 34.3 1.0
C A:THR83 3.3 24.1 1.0
CZ A:TYR25 3.4 24.5 1.0
C A:PHE86 3.5 22.9 1.0
O B:HOH425 3.7 22.1 1.0
CA A:THR83 3.8 25.8 1.0
CE1 A:TYR25 3.9 24.5 1.0
CA A:THR87 4.1 26.9 1.0
OG1 A:THR87 4.2 37.8 1.0
CB A:THR83 4.2 28.2 1.0
N A:THR87 4.2 25.2 1.0
CE2 A:TYR25 4.4 24.2 1.0
N A:SER84 4.5 21.6 0.5
N A:SER84 4.5 22.1 0.5
CA A:PHE86 4.6 21.9 1.0
N A:PHE86 4.6 23.5 1.0
CB B:ASP102 4.7 32.9 1.0
CD2 A:TYR95 4.8 24.5 1.0
CB A:THR87 4.8 28.7 1.0
CE2 A:TYR95 4.9 24.1 1.0
CA A:SER84 4.9 23.4 0.5
CA A:SER84 5.0 24.4 0.5

Sodium binding site 2 out of 5 in 6rew

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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 8.0


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 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na313

b:24.7
occ:1.00
O B:PHE86 2.3 24.2 1.0
O B:HOH472 2.3 27.7 1.0
O B:THR83 2.3 25.6 1.0
OH B:TYR25 2.4 24.2 1.0
OD1 C:ASP102 2.5 27.3 1.0
O C:HOH478 2.9 45.0 1.0
CG C:ASP102 3.3 29.5 1.0
CZ B:TYR25 3.3 24.6 1.0
OD2 C:ASP102 3.3 31.0 1.0
C B:THR83 3.4 23.7 1.0
C B:PHE86 3.5 21.7 1.0
O C:HOH441 3.7 21.6 1.0
CA B:THR83 3.8 24.3 1.0
CE1 B:TYR25 3.8 25.2 1.0
O C:HOH404 4.1 44.3 1.0
CA B:THR87 4.1 25.9 1.0
OG1 B:THR87 4.2 32.2 1.0
CB B:THR83 4.2 24.9 1.0
N B:THR87 4.2 22.9 1.0
O B:HOH499 4.2 46.8 1.0
CE2 B:TYR25 4.3 25.2 1.0
N B:SER84 4.5 23.1 0.5
N B:SER84 4.5 23.0 0.5
CA B:PHE86 4.6 22.2 1.0
N B:PHE86 4.6 22.5 1.0
CD2 B:TYR95 4.7 23.7 1.0
CB C:ASP102 4.7 26.8 1.0
CB B:THR87 4.8 27.7 1.0
CE2 B:TYR95 4.9 25.6 1.0
O B:TRP82 4.9 22.1 1.0
CA B:SER84 5.0 24.2 0.5
CA B:SER84 5.0 24.0 0.5

Sodium binding site 3 out of 5 in 6rew

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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 8.0


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 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na316

b:26.1
occ:1.00
O C:HOH451 2.3 24.1 1.0
O C:PHE86 2.3 24.2 1.0
O C:THR83 2.3 22.7 1.0
OH C:TYR25 2.5 25.4 1.0
OD1 D:ASP102 2.5 26.0 1.0
O D:HOH444 2.9 43.5 1.0
CG D:ASP102 3.3 28.3 1.0
OD2 D:ASP102 3.3 33.6 1.0
C C:THR83 3.4 22.7 1.0
CZ C:TYR25 3.4 24.2 1.0
C C:PHE86 3.5 23.9 1.0
O D:HOH415 3.7 23.2 1.0
CA C:THR83 3.8 25.8 1.0
CE1 C:TYR25 3.9 24.1 1.0
O C:HOH497 4.1 51.0 1.0
CA C:THR87 4.1 29.2 1.0
OG1 C:THR87 4.2 37.0 1.0
N C:THR87 4.2 23.7 1.0
CB C:THR83 4.2 24.4 1.0
CE2 C:TYR25 4.3 20.8 1.0
N C:SER84 4.5 23.5 0.5
N C:SER84 4.5 22.0 0.5
CA C:PHE86 4.6 24.0 1.0
N C:PHE86 4.6 22.6 1.0
CB D:ASP102 4.7 26.3 1.0
CD2 C:TYR95 4.7 22.7 1.0
CB C:THR87 4.8 31.8 1.0
CE2 C:TYR95 4.9 24.5 1.0
CA C:SER84 5.0 26.5 0.5
CA C:SER84 5.0 23.9 0.5
O C:TRP82 5.0 24.5 1.0

Sodium binding site 4 out of 5 in 6rew

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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 8.0


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 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na316

b:25.5
occ:1.00
O D:PHE86 2.3 25.6 1.0
O D:THR83 2.3 25.6 1.0
O D:HOH438 2.4 24.1 1.0
OH D:TYR25 2.4 23.4 1.0
OD1 E:ASP102 2.5 25.4 1.0
CG E:ASP102 3.2 27.6 1.0
OD2 E:ASP102 3.3 30.9 1.0
C D:THR83 3.3 24.5 1.0
CZ D:TYR25 3.4 26.0 1.0
C D:PHE86 3.5 23.4 1.0
O E:HOH409 3.7 22.2 1.0
CA D:THR83 3.8 25.1 1.0
CE1 D:TYR25 3.9 26.9 1.0
CA D:THR87 4.0 30.3 0.5
CA D:THR87 4.1 23.3 0.5
O D:HOH487 4.1 46.0 1.0
OG1 D:THR87 4.2 26.2 0.5
CB D:THR83 4.2 26.3 1.0
N D:THR87 4.2 24.2 0.5
O E:HOH402 4.2 42.7 1.0
N D:THR87 4.2 20.5 0.5
CG2 D:THR87 4.3 38.1 0.5
CE2 D:TYR25 4.3 25.7 1.0
N D:SER84 4.5 22.0 0.5
N D:SER84 4.5 21.5 0.5
CA D:PHE86 4.6 23.7 1.0
N D:PHE86 4.6 22.2 1.0
CB D:THR87 4.6 32.1 0.5
CB E:ASP102 4.7 24.4 1.0
CD2 D:TYR95 4.7 22.3 1.0
CB D:THR87 4.8 20.6 0.5
CE2 D:TYR95 4.9 24.2 1.0
CA D:SER84 5.0 25.3 0.5
O D:TRP82 5.0 22.6 1.0

Sodium binding site 5 out of 5 in 6rew

Go back to Sodium Binding Sites List in 6rew
Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


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 8.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na315

b:25.5
occ:1.00
O E:HOH453 2.3 28.2 1.0
O E:THR83 2.3 24.1 1.0
O E:PHE86 2.3 24.8 1.0
OH E:TYR25 2.4 24.4 1.0
OD1 A:ASP102 2.5 28.4 1.0
CG A:ASP102 3.3 27.6 1.0
OD2 A:ASP102 3.3 30.1 1.0
C E:THR83 3.3 22.6 1.0
CZ E:TYR25 3.4 24.1 1.0
C E:PHE86 3.5 23.5 1.0
O A:HOH428 3.8 23.3 1.0
CA E:THR83 3.8 22.4 1.0
CE1 E:TYR25 3.9 23.8 1.0
CA E:THR87 4.1 26.6 0.5
O E:HOH501 4.1 49.6 1.0
CA E:THR87 4.2 22.4 0.5
CB E:THR83 4.2 20.9 1.0
OG1 E:THR87 4.2 26.6 0.5
N E:THR87 4.2 24.2 0.5
N E:THR87 4.3 21.6 0.5
CG2 E:THR87 4.3 32.9 0.5
CE2 E:TYR25 4.3 25.2 1.0
N E:SER84 4.5 22.2 0.5
N E:SER84 4.5 21.5 0.5
N E:PHE86 4.6 24.0 1.0
CA E:PHE86 4.6 22.5 1.0
CB E:THR87 4.7 28.2 0.5
CB A:ASP102 4.7 26.4 1.0
CD2 E:TYR95 4.8 22.2 1.0
CB E:THR87 4.8 21.3 0.5
CA E:SER84 4.9 23.7 0.5
CA E:SER84 5.0 22.6 0.5
CE2 E:TYR95 5.0 21.2 1.0
O E:TRP82 5.0 22.0 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 12:52:24 2020

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