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Sodium in PDB 6yc3: 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: 6yc3 was solved by K.Kovalev, I.Gushchin, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.866, 240.323, 135.513, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 19.5

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 6yc3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 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: 6yc3:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6yc3

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Sodium binding site 1 out of 10 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:Na321

b:39.8
occ:1.00
 O A:PHE86 2.3 38.9 1.0
O A:HOH473 2.3 39.8 1.0
O A:THR83 2.3 40.1 1.0
OH A:TYR25 2.4 38.5 1.0
OD1 B:ASP102 2.5 41.9 1.0
O B:HOH473 2.8 61.6 1.0
CG B:ASP102 3.2 45.9 1.0
OD2 B:ASP102 3.3 46.1 1.0
CZ A:TYR25 3.3 38.6 1.0
C A:THR83 3.3 38.5 1.0
C A:PHE86 3.5 35.2 1.0
O B:HOH435 3.7 37.4 1.0
NA B:NA316 3.8 76.3 1.0
CA A:THR83 3.8 38.4 1.0
CE1 A:TYR25 3.8 39.7 1.0
O A:HOH489 4.0 58.6 1.0
CA A:THR87 4.2 40.5 1.0
N A:THR87 4.3 37.3 1.0
CB A:THR83 4.3 40.4 1.0
CE2 A:TYR25 4.3 36.4 1.0
OG1 A:THR87 4.4 46.4 1.0
N A:SER84 4.5 40.1 0.5
N A:SER84 4.5 36.5 0.2
N A:SER84 4.5 36.5 0.2
CA A:PHE86 4.6 33.0 1.0
N A:PHE86 4.7 36.0 1.0
CB B:ASP102 4.7 41.9 1.0
CD2 A:TYR95 4.7 35.1 1.0
O A:HOH492 4.8 71.9 1.0
CB A:THR87 4.9 39.1 1.0
CE2 A:TYR95 4.9 35.9 1.0

Sodium binding site 2 out of 10 in 6yc3

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Sodium binding site 2 out of 10 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
A:Na322

b:78.6
occ:1.00
 O A:HOH515 2.3 71.2 1.0
O E:HOH517 2.4 67.0 1.0
O A:SER100 2.5 44.0 1.0
O A:HOH451 2.5 59.3 1.0
O E:HOH479 2.5 42.2 1.0
O A:HOH497 2.7 53.6 1.0
C A:SER100 3.7 46.3 1.0
NA E:NA318 3.8 39.3 1.0
O E:HOH518 3.8 68.0 1.0
O A:HOH405 3.9 61.8 1.0
CA A:GLY101 4.1 38.5 1.0
OD1 A:ASP102 4.1 43.1 1.0
O E:HOH499 4.1 75.3 1.0
O E:THR83 4.2 39.0 1.0
C A:GLY101 4.3 37.7 1.0
N A:GLY101 4.3 40.3 1.0
O A:HOH514 4.3 69.5 1.0
O A:HOH435 4.5 35.1 1.0
O A:HOH521 4.5 87.2 1.0
O A:GLY101 4.6 44.5 1.0
CG A:ASP102 4.7 39.8 1.0
O E:HOH429 4.7 58.7 1.0
N A:ASP102 4.7 33.8 1.0
CA A:SER100 4.9 41.7 1.0
CG2 E:THR87 5.0 49.0 0.5
OD2 A:ASP102 5.0 43.4 1.0
OG1 E:THR87 5.0 41.3 0.5

Sodium binding site 3 out of 10 in 6yc3

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Sodium binding site 3 out of 10 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
B:Na315

b:39.1
occ:1.00
 O B:THR83 2.3 43.5 1.0
O B:PHE86 2.3 38.2 1.0
O B:HOH490 2.4 40.9 1.0
OH B:TYR25 2.4 36.8 1.0
OD1 C:ASP102 2.5 39.7 1.0
O C:HOH456 2.7 61.9 1.0
CG C:ASP102 3.2 43.3 1.0
OD2 C:ASP102 3.3 46.6 1.0
C B:THR83 3.3 39.6 1.0
CZ B:TYR25 3.3 38.8 1.0
C B:PHE86 3.5 36.3 1.0
O C:HOH441 3.7 35.1 1.0
CA B:THR83 3.8 41.4 1.0
CE1 B:TYR25 3.9 36.3 1.0
NA C:NA320 3.9 70.9 1.0
O B:HOH506 4.0 57.0 1.0
CA B:THR87 4.2 37.4 1.0
N B:THR87 4.2 36.2 1.0
CB B:THR83 4.3 38.9 1.0
OG1 B:THR87 4.3 42.9 1.0
CE2 B:TYR25 4.3 36.1 1.0
N B:SER84 4.5 36.9 0.2
N B:SER84 4.5 40.3 0.5
N B:SER84 4.5 38.2 0.2
CA B:PHE86 4.6 37.6 1.0
N B:PHE86 4.7 37.5 1.0
CB C:ASP102 4.7 41.4 1.0
CD2 B:TYR95 4.8 37.6 1.0
CB B:THR87 4.9 38.5 1.0
CE2 B:TYR95 5.0 39.4 1.0

Sodium binding site 4 out of 10 in 6yc3

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Sodium binding site 4 out of 10 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
B:Na316

b:76.3
occ:1.00
 O B:HOH502 2.1 69.5 1.0
O A:HOH473 2.4 39.8 1.0
O A:HOH489 2.4 58.6 1.0
O B:SER100 2.4 44.1 1.0
O B:HOH473 2.5 61.6 1.0
O B:HOH485 2.9 60.4 1.0
C B:SER100 3.6 43.0 1.0
NA A:NA321 3.8 39.8 1.0
OD1 B:ASP102 4.0 41.9 1.0
O B:HOH411 4.1 62.1 1.0
O A:HOH492 4.1 71.9 1.0
CA B:GLY101 4.1 37.5 1.0
O B:HOH435 4.2 37.4 1.0
O A:THR83 4.2 40.1 1.0
C B:GLY101 4.3 36.4 1.0
N B:GLY101 4.3 38.2 1.0
O B:HOH503 4.5 88.9 1.0
O B:GLY101 4.6 40.5 1.0
CG B:ASP102 4.6 45.9 1.0
N B:ASP102 4.6 35.3 1.0
CA B:SER100 4.7 44.2 1.0
OG1 A:THR87 4.8 46.4 1.0
OD2 B:ASP102 4.9 46.1 1.0
O A:HOH404 5.0 61.0 1.0

Sodium binding site 5 out of 10 in 6yc3

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Sodium binding site 5 out of 10 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
C:Na319

b:39.1
occ:1.00
 O C:THR83 2.3 38.1 1.0
O C:PHE86 2.3 37.4 1.0
O C:HOH466 2.4 40.7 1.0
OH C:TYR25 2.4 39.6 1.0
OD1 D:ASP102 2.5 38.2 1.0
O D:HOH435 2.8 55.1 1.0
CG D:ASP102 3.2 40.7 1.0
OD2 D:ASP102 3.3 48.3 1.0
C C:THR83 3.3 39.7 1.0
CZ C:TYR25 3.4 35.0 1.0
C C:PHE86 3.5 38.7 1.0
O D:HOH425 3.7 35.9 1.0
CA C:THR83 3.8 39.9 1.0
CE1 C:TYR25 3.9 35.9 1.0
O C:HOH499 4.0 61.6 1.0
NA D:NA319 4.1 71.5 1.0
CA C:THR87 4.2 41.7 1.0
N C:THR87 4.2 38.7 1.0
CB C:THR83 4.2 36.3 1.0
OG1 C:THR87 4.3 48.4 1.0
CE2 C:TYR25 4.3 34.8 1.0
N C:SER84 4.5 36.2 0.5
N C:SER84 4.5 37.3 0.5
CA C:PHE86 4.6 36.6 1.0
N C:PHE86 4.7 34.5 1.0
CB D:ASP102 4.7 39.3 1.0
CD2 C:TYR95 4.8 34.8 1.0
CB C:THR87 4.9 44.6 1.0
CE2 C:TYR95 5.0 36.4 1.0

Sodium binding site 6 out of 10 in 6yc3

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Sodium binding site 6 out of 10 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 6 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:Na320

b:70.9
occ:1.00
 O C:HOH456 2.4 61.9 1.0
O C:HOH512 2.5 67.2 1.0
O C:SER100 2.5 38.9 1.0
O B:HOH490 2.5 40.9 1.0
O B:HOH506 2.6 57.0 1.0
O C:HOH484 2.8 63.3 1.0
C C:SER100 3.7 42.3 1.0
O C:HOH503 3.7 66.8 1.0
NA B:NA315 3.9 39.1 1.0
CA C:GLY101 4.0 37.8 1.0
OD1 C:ASP102 4.1 39.7 1.0
C C:GLY101 4.2 37.7 1.0
N C:GLY101 4.3 38.6 1.0
O C:HOH465 4.3 77.9 1.0
O B:THR83 4.3 43.5 1.0
O C:GLY101 4.5 45.7 1.0
O C:HOH441 4.5 35.1 1.0
N C:ASP102 4.7 36.3 1.0
CG C:ASP102 4.7 43.3 1.0
CA C:SER100 4.9 43.0 1.0
OD2 C:ASP102 4.9 46.6 1.0

Sodium binding site 7 out of 10 in 6yc3

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Sodium binding site 7 out of 10 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 7 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:Na318

b:38.8
occ:1.00
 O D:THR83 2.2 39.3 1.0
O D:PHE86 2.3 37.7 1.0
O D:HOH469 2.3 39.4 1.0
OH D:TYR25 2.5 37.4 1.0
OD1 E:ASP102 2.5 40.5 1.0
O E:HOH465 2.9 60.1 1.0
CG E:ASP102 3.3 41.0 1.0
C D:THR83 3.3 37.8 1.0
OD2 E:ASP102 3.3 47.5 1.0
CZ D:TYR25 3.4 36.0 1.0
C D:PHE86 3.5 36.5 1.0
O E:HOH426 3.7 39.4 1.0
O D:HOH474 3.7 62.0 1.0
CA D:THR83 3.8 37.9 1.0
CE1 D:TYR25 3.9 38.8 1.0
CA D:THR87 4.0 43.3 0.5
NA E:NA319 4.1 66.1 1.0
CA D:THR87 4.1 35.8 0.5
N D:THR87 4.2 38.4 0.5
N D:THR87 4.2 34.0 0.5
OG1 D:THR87 4.2 36.5 0.5
CB D:THR83 4.2 37.7 1.0
CG2 D:THR87 4.3 50.0 0.5
CE2 D:TYR25 4.4 36.9 1.0
N D:SER84 4.5 36.8 0.5
N D:SER84 4.5 35.0 0.2
N D:SER84 4.5 34.0 0.2
CA D:PHE86 4.6 37.8 1.0
N D:PHE86 4.6 38.4 1.0
CB D:THR87 4.7 44.2 0.5
CB E:ASP102 4.8 39.4 1.0
CD2 D:TYR95 4.8 35.6 1.0
CB D:THR87 4.8 31.5 0.5
CA D:SER84 5.0 34.7 0.2

Sodium binding site 8 out of 10 in 6yc3

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Sodium binding site 8 out of 10 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 8 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:Na319

b:71.5
occ:1.00
 O D:HOH500 2.3 69.8 1.0
O C:HOH499 2.3 61.6 1.0
O D:SER100 2.4 43.0 1.0
O C:HOH466 2.6 40.7 1.0
O D:HOH435 2.8 55.1 1.0
O D:HOH478 2.9 62.6 1.0
C D:SER100 3.6 44.1 1.0
NA C:NA319 4.1 39.1 1.0
CA D:GLY101 4.1 38.6 1.0
O D:HOH498 4.1 67.0 1.0
N D:GLY101 4.3 38.3 1.0
OD1 D:ASP102 4.3 38.2 1.0
C D:GLY101 4.4 35.9 1.0
O C:THR83 4.4 38.1 1.0
O D:HOH425 4.6 35.9 1.0
O C:HOH431 4.6 58.9 1.0
O D:GLY101 4.7 43.4 1.0
CA D:SER100 4.8 44.2 1.0
N D:ASP102 4.8 35.3 1.0
O D:HOH428 4.9 62.0 1.0
CG D:ASP102 4.9 40.7 1.0
OG1 C:THR87 5.0 48.4 1.0

Sodium binding site 9 out of 10 in 6yc3

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Sodium binding site 9 out of 10 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 9 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:Na318

b:39.3
occ:1.00
 O E:THR83 2.2 39.0 1.0
O E:HOH479 2.3 42.2 1.0
O E:PHE86 2.4 38.0 1.0
OH E:TYR25 2.4 37.1 1.0
OD1 A:ASP102 2.5 43.1 1.0
O A:HOH451 2.7 59.3 1.0
CG A:ASP102 3.2 39.8 1.0
OD2 A:ASP102 3.3 43.4 1.0
C E:THR83 3.3 38.4 1.0
CZ E:TYR25 3.4 38.3 1.0
C E:PHE86 3.6 38.1 1.0
CA E:THR83 3.8 36.9 1.0
O A:HOH435 3.8 35.1 1.0
NA A:NA322 3.8 78.6 1.0
CE1 E:TYR25 3.9 36.4 1.0
O E:HOH517 4.1 67.0 1.0
CA E:THR87 4.1 42.8 0.5
CA E:THR87 4.2 37.3 0.5
CB E:THR83 4.2 33.8 1.0
N E:THR87 4.3 38.5 0.5
N E:THR87 4.3 35.0 0.5
CG2 E:THR87 4.3 49.0 0.5
OG1 E:THR87 4.3 41.3 0.5
CE2 E:TYR25 4.4 36.0 1.0
N E:SER84 4.5 36.0 0.2
N E:SER84 4.5 34.0 0.2
N E:SER84 4.5 36.3 0.5
CB E:THR87 4.6 44.3 0.5
CA E:PHE86 4.7 34.1 1.0
N E:PHE86 4.7 37.0 1.0
CB A:ASP102 4.7 40.3 1.0
CD2 E:TYR95 4.9 37.0 1.0
CB E:THR87 4.9 35.5 0.5
O E:HOH499 5.0 75.3 1.0
CA E:SER84 5.0 35.6 0.2
CA E:SER84 5.0 32.4 0.2

Sodium binding site 10 out of 10 in 6yc3

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Sodium binding site 10 out of 10 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 10 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:Na319

b:66.1
occ:1.00
 O E:HOH523 2.3 72.1 1.0
O E:SER100 2.4 41.5 1.0
O D:HOH474 2.5 62.0 1.0
O E:HOH465 2.5 60.1 1.0
O D:HOH469 2.6 39.4 1.0
O E:HOH453 2.7 56.1 1.0
C E:SER100 3.5 44.7 1.0
O E:HOH510 4.0 71.8 1.0
CA E:GLY101 4.0 41.8 1.0
O E:HOH403 4.0 57.7 1.0
NA D:NA318 4.1 38.8 1.0
N E:GLY101 4.2 41.0 1.0
C E:GLY101 4.3 39.6 1.0
OD1 E:ASP102 4.3 40.5 1.0
O E:HOH426 4.4 39.4 1.0
O D:THR83 4.5 39.3 1.0
O E:GLY101 4.6 41.9 1.0
CA E:SER100 4.7 42.7 1.0
N E:ASP102 4.7 38.0 1.0
CG E:ASP102 4.8 41.0 1.0
O E:HOH519 4.9 75.6 1.0
O D:HOH408 5.0 58.8 1.0

Reference:

K.Kovalev, R.Astashkin, I.Gushchin, V.Gordeliy. Molecular Mechanism of Light-Driven Sodium Pumping To Be Published.
Page generated: Tue Oct 8 15:02:41 2024

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