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Sodium in PDB 6yc1: Crystal Structure of the H30A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

Protein crystallography data

The structure of Crystal Structure of the H30A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6yc1 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 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.089, 239.733, 135.132, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 20.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the H30A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6yc1). 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 H30A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6yc1:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6yc1

Go back to Sodium Binding Sites List in 6yc1
Sodium binding site 1 out of 5 in the Crystal Structure of the H30A Mutant 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 H30A Mutant 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:Na314

b:41.1
occ:1.00
 O A:THR83 2.3 43.1 1.0
O A:HOH444 2.4 34.4 1.0
O A:PHE86 2.4 38.5 1.0
OH A:TYR25 2.4 39.5 1.0
OD1 B:ASP102 2.5 38.2 1.0
O B:HOH473 2.8 45.4 1.0
CG B:ASP102 3.3 37.5 1.0
OD2 B:ASP102 3.3 43.3 1.0
C A:THR83 3.4 37.8 1.0
CZ A:TYR25 3.4 37.1 1.0
O B:HOH448 3.6 36.9 1.0
C A:PHE86 3.6 39.3 1.0
CA A:THR83 3.8 40.3 1.0
O A:HOH503 3.9 54.3 1.0
CE1 A:TYR25 3.9 36.4 1.0
CA A:THR87 4.1 42.1 1.0
OG1 A:THR87 4.3 51.2 1.0
N A:THR87 4.3 38.6 1.0
CB A:THR83 4.3 40.7 1.0
CE2 A:TYR25 4.3 38.8 1.0
N A:SER84 4.5 35.4 0.5
N A:SER84 4.5 35.9 0.5
CA A:PHE86 4.7 34.1 1.0
CB B:ASP102 4.7 40.6 1.0
N A:PHE86 4.8 33.3 1.0
CD2 A:TYR95 4.8 35.9 1.0
CB A:THR87 4.8 41.2 1.0
O B:SER100 4.9 46.9 1.0
CE2 A:TYR95 5.0 38.6 1.0

Sodium binding site 2 out of 5 in 6yc1

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Sodium binding site 2 out of 5 in the Crystal Structure of the H30A Mutant 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 H30A Mutant 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:35.9
occ:1.00
 O B:THR83 2.3 42.7 1.0
O B:PHE86 2.3 37.7 1.0
OH B:TYR25 2.3 35.4 1.0
O B:HOH488 2.4 34.2 1.0
OD1 C:ASP102 2.5 41.0 1.0
O C:HOH458 2.6 46.3 1.0
CG C:ASP102 3.3 42.1 1.0
CZ B:TYR25 3.3 34.8 1.0
OD2 C:ASP102 3.3 39.0 1.0
C B:THR83 3.4 41.2 1.0
C B:PHE86 3.5 40.7 1.0
O C:HOH443 3.6 31.6 1.0
CA B:THR83 3.8 35.0 1.0
CE1 B:TYR25 3.8 35.0 1.0
O B:HOH484 3.9 49.2 1.0
CA B:THR87 4.1 41.9 1.0
O C:HOH404 4.1 44.8 1.0
N B:THR87 4.2 36.4 1.0
CE2 B:TYR25 4.3 37.6 1.0
CB B:THR83 4.3 36.4 1.0
OG1 B:THR87 4.3 44.2 1.0
N B:SER84 4.6 38.8 0.5
N B:SER84 4.6 38.7 0.5
CA B:PHE86 4.7 39.8 1.0
CB C:ASP102 4.7 39.3 1.0
CD2 B:TYR95 4.7 37.7 1.0
N B:PHE86 4.7 36.0 1.0
CB B:THR87 4.8 40.7 1.0
CE2 B:TYR95 4.9 40.3 1.0
O C:SER100 4.9 41.7 1.0

Sodium binding site 3 out of 5 in 6yc1

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Sodium binding site 3 out of 5 in the Crystal Structure of the H30A Mutant 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 H30A Mutant 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:38.2
occ:1.00
 O C:THR83 2.3 38.2 1.0
O C:HOH447 2.3 34.8 1.0
O C:PHE86 2.3 38.3 1.0
OH C:TYR25 2.4 39.3 1.0
OD1 D:ASP102 2.4 38.3 1.0
O D:HOH459 2.7 51.5 1.0
CG D:ASP102 3.2 43.0 1.0
OD2 D:ASP102 3.2 45.0 1.0
CZ C:TYR25 3.3 35.9 1.0
C C:THR83 3.4 37.2 1.0
O D:HOH424 3.5 32.4 1.0
C C:PHE86 3.5 41.5 1.0
CA C:THR83 3.8 38.7 1.0
O C:HOH503 3.8 50.2 1.0
CE1 C:TYR25 3.9 38.7 1.0
CA C:THR87 4.1 43.5 1.0
N C:THR87 4.2 39.2 1.0
CB C:THR83 4.3 35.4 1.0
OG1 C:THR87 4.3 47.3 1.0
CE2 C:TYR25 4.3 36.8 1.0
N C:SER84 4.5 35.5 0.5
N C:SER84 4.5 33.8 0.5
CB D:ASP102 4.7 36.3 1.0
CA C:PHE86 4.7 41.8 1.0
N C:PHE86 4.7 35.3 1.0
CD2 C:TYR95 4.8 37.5 1.0
CB C:THR87 4.8 44.8 1.0
O D:SER100 4.9 48.6 1.0
CE2 C:TYR95 5.0 32.6 1.0

Sodium binding site 4 out of 5 in 6yc1

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Sodium binding site 4 out of 5 in the Crystal Structure of the H30A Mutant 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 H30A Mutant 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:Na317

b:39.8
occ:1.00
 O D:THR83 2.3 43.5 1.0
O D:PHE86 2.3 40.8 1.0
O D:HOH453 2.4 32.9 1.0
OH D:TYR25 2.5 33.1 1.0
OD1 E:ASP102 2.5 46.5 1.0
CG E:ASP102 3.3 41.5 1.0
OD2 E:ASP102 3.3 44.8 1.0
C D:THR83 3.3 37.4 1.0
CZ D:TYR25 3.4 36.9 1.0
C D:PHE86 3.5 41.5 1.0
O E:HOH433 3.6 36.1 1.0
O D:HOH486 3.8 53.0 1.0
CA D:THR83 3.8 38.7 1.0
CE1 D:TYR25 3.9 35.1 1.0
CA D:THR87 4.1 41.6 1.0
O E:HOH404 4.2 42.1 1.0
OG1 D:THR87 4.2 49.9 1.0
N D:THR87 4.2 38.6 1.0
CB D:THR83 4.3 38.4 1.0
CE2 D:TYR25 4.4 40.7 1.0
N D:SER84 4.5 36.6 0.5
N D:SER84 4.5 37.3 0.5
CA D:PHE86 4.7 39.3 1.0
N D:PHE86 4.7 42.9 1.0
CB E:ASP102 4.7 41.5 1.0
CB D:THR87 4.8 42.4 1.0
CD2 D:TYR95 4.8 38.1 1.0
O E:SER100 4.9 45.6 1.0
CA D:SER84 5.0 38.9 0.5

Sodium binding site 5 out of 5 in 6yc1

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Sodium binding site 5 out of 5 in the Crystal Structure of the H30A Mutant 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 H30A Mutant 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:36.3
occ:1.00
 O E:THR83 2.3 41.8 1.0
OH E:TYR25 2.4 35.4 1.0
O E:PHE86 2.4 35.9 1.0
O E:HOH479 2.4 37.8 1.0
OD1 A:ASP102 2.5 38.3 1.0
O A:HOH463 2.6 55.5 1.0
CG A:ASP102 3.3 40.2 1.0
OD2 A:ASP102 3.3 36.2 1.0
C E:THR83 3.3 41.9 1.0
CZ E:TYR25 3.4 36.9 1.0
C E:PHE86 3.6 33.2 1.0
O A:HOH423 3.7 31.5 1.0
CA E:THR83 3.8 38.0 1.0
O E:HOH497 3.9 52.3 1.0
CE1 E:TYR25 3.9 34.7 1.0
CA E:THR87 4.1 39.0 1.0
CB E:THR83 4.2 37.1 1.0
OG1 E:THR87 4.3 48.1 1.0
N E:THR87 4.3 34.1 1.0
CE2 E:TYR25 4.3 35.6 1.0
N E:SER84 4.5 39.0 0.5
N E:SER84 4.5 38.2 0.5
CB A:ASP102 4.7 38.0 1.0
CA E:PHE86 4.7 35.6 1.0
N E:PHE86 4.8 34.4 1.0
CD2 E:TYR95 4.8 35.1 1.0
CB E:THR87 4.8 35.7 1.0
O A:SER100 4.9 43.2 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 15:02:23 2024

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