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Sodium in PDB 4xto: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Red Form, pH 5.6

Protein crystallography data

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Red Form, pH 5.6, PDB code: 4xto was solved by I.Gushchin, V.Shevchenko, V.Polovinkin, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.30 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 127.100, 238.980, 132.480, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 28

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Red Form, pH 5.6 (pdb code 4xto). 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 Red Form, pH 5.6, PDB code: 4xto:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4xto

Go back to Sodium Binding Sites List in 4xto
Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Red Form, pH 5.6


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 Red Form, pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:81.4
occ:1.00
 O A:THR83 2.2 63.7 1.0
O A:PHE86 2.3 65.5 1.0
OH A:TYR25 2.5 66.6 1.0
OD1 B:ASP102 2.6 90.0 1.0
OD2 B:ASP102 2.8 72.2 1.0
CG B:ASP102 3.0 81.1 1.0
C A:THR83 3.2 64.7 1.0
CZ A:TYR25 3.4 63.9 1.0
C A:PHE86 3.5 62.5 1.0
CA A:THR83 3.7 62.7 1.0
CE1 A:TYR25 4.0 64.2 1.0
CB A:THR83 4.2 65.6 1.0
CA A:THR87 4.2 69.5 1.0
N A:THR87 4.3 62.4 1.0
CE2 A:TYR25 4.4 59.0 1.0
N A:SER84 4.4 58.9 1.0
N A:PHE86 4.4 53.2 1.0
CA A:PHE86 4.5 59.5 1.0
CB B:ASP102 4.5 70.1 1.0
OG1 A:THR87 4.8 73.5 1.0
CA A:SER84 4.8 56.2 1.0
O B:SER100 4.9 0.0 1.0
C A:SER84 4.9 60.2 1.0
O A:TRP82 4.9 84.0 1.0
CD2 A:TYR95 4.9 68.6 1.0
O A:SER84 5.0 70.2 1.0
CG2 A:THR83 5.0 68.6 1.0
CB A:PHE86 5.0 63.4 1.0

Sodium binding site 2 out of 5 in 4xto

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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 Red Form, pH 5.6


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 Red Form, pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:62.0
occ:1.00
 O B:THR83 2.1 85.4 1.0
O B:PHE86 2.3 63.7 1.0
OH B:TYR25 2.7 62.6 1.0
OD1 C:ASP102 2.8 0.9 1.0
OD2 C:ASP102 3.2 81.7 1.0
C B:THR83 3.2 70.3 1.0
CG C:ASP102 3.4 90.8 1.0
C B:PHE86 3.5 62.9 1.0
CZ B:TYR25 3.6 67.8 1.0
CA B:THR83 3.9 67.9 1.0
CE1 B:TYR25 4.1 67.4 1.0
CA B:THR87 4.3 69.6 1.0
N B:SER84 4.3 64.8 1.0
N B:THR87 4.4 65.2 1.0
CB B:THR83 4.4 62.6 1.0
N B:PHE86 4.4 60.9 1.0
CA B:PHE86 4.5 61.2 1.0
OG1 B:THR87 4.5 82.9 1.0
CE2 B:TYR25 4.6 70.4 1.0
CA B:SER84 4.7 65.6 1.0
CB C:ASP102 4.9 77.4 1.0
C B:SER84 4.9 63.0 1.0
CD2 B:TYR95 4.9 60.1 1.0
CB B:THR87 4.9 68.7 1.0
O B:TRP82 5.0 72.4 1.0
CE2 B:TYR95 5.0 63.4 1.0

Sodium binding site 3 out of 5 in 4xto

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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 Red Form, pH 5.6


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 Red Form, pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:0.3
occ:1.00
 O C:THR83 2.3 78.9 1.0
O C:PHE86 2.5 74.2 1.0
OD1 D:ASP102 2.5 0.1 1.0
OH C:TYR25 3.1 67.2 1.0
OD2 D:ASP102 3.2 87.5 1.0
CG D:ASP102 3.2 97.5 1.0
C C:THR83 3.5 69.0 1.0
C C:PHE86 3.6 65.5 1.0
CZ C:TYR25 4.1 68.5 1.0
CA C:THR87 4.1 69.4 1.0
N C:THR87 4.3 66.0 1.0
CA C:THR83 4.3 70.1 1.0
O D:SER100 4.4 98.8 1.0
OG1 C:THR87 4.4 78.4 1.0
N C:SER84 4.5 61.8 1.0
CA C:SER84 4.6 63.9 1.0
N C:PHE86 4.6 58.1 1.0
CE1 C:TYR25 4.7 64.6 1.0
CB D:ASP102 4.7 80.3 1.0
CA C:PHE86 4.7 64.9 1.0
CB C:THR83 4.8 69.0 1.0
C C:SER84 4.8 66.5 1.0
CB C:THR87 4.8 73.8 1.0
O C:SER84 4.9 78.1 1.0

Sodium binding site 4 out of 5 in 4xto

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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 Red Form, pH 5.6


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 Red Form, pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:75.3
occ:1.00
 O D:THR83 2.2 62.6 1.0
OD1 E:ASP102 2.4 0.5 1.0
O D:PHE86 2.4 73.2 1.0
OH D:TYR25 2.7 67.1 1.0
OD2 E:ASP102 2.8 87.8 1.0
CG E:ASP102 2.9 96.8 1.0
C D:THR83 3.4 59.8 1.0
CZ D:TYR25 3.6 62.8 1.0
C D:PHE86 3.6 63.6 1.0
CE2 D:TYR25 4.0 65.1 1.0
CA D:THR83 4.1 55.3 1.0
CA D:THR87 4.2 58.5 1.0
N D:THR87 4.3 63.1 1.0
CB E:ASP102 4.4 85.7 1.0
OG1 D:THR87 4.5 63.2 1.0
N D:SER84 4.5 61.0 1.0
CE1 D:TYR25 4.5 58.1 1.0
CB D:THR83 4.6 51.1 1.0
O E:SER100 4.6 0.4 1.0
N D:PHE86 4.6 62.2 1.0
CA D:PHE86 4.7 60.5 1.0
CA D:SER84 4.7 66.5 1.0
CB D:THR87 4.9 60.0 1.0
CD2 D:TYR95 5.0 63.1 1.0

Sodium binding site 5 out of 5 in 4xto

Go back to Sodium Binding Sites List in 4xto
Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Red Form, pH 5.6


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 Red Form, pH 5.6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:81.6
occ:1.00
 O E:THR83 2.2 67.0 1.0
O E:PHE86 2.3 60.7 1.0
OD1 A:ASP102 2.6 0.4 1.0
OH E:TYR25 3.0 53.9 1.0
OD2 A:ASP102 3.3 92.6 1.0
CG A:ASP102 3.3 95.8 1.0
C E:THR83 3.4 61.5 1.0
C E:PHE86 3.4 59.7 1.0
CZ E:TYR25 4.0 62.2 1.0
CA E:THR87 4.1 66.2 1.0
CA E:THR83 4.2 60.9 1.0
N E:THR87 4.2 61.1 1.0
OG1 E:THR87 4.3 74.5 1.0
N E:SER84 4.4 64.3 1.0
O A:SER100 4.4 0.6 1.0
N E:PHE86 4.4 62.5 1.0
CE1 E:TYR25 4.5 61.0 1.0
CA E:PHE86 4.5 60.1 1.0
CA E:SER84 4.5 65.1 1.0
CB E:THR83 4.7 62.5 1.0
CB A:ASP102 4.8 78.7 1.0
CB E:THR87 4.8 65.6 1.0
C E:SER84 4.9 59.0 1.0
CE2 E:TYR25 4.9 61.3 1.0

Reference:

I.Gushchin, V.Shevchenko, V.Polovinkin, K.Kovalev, A.Alekseev, E.Round, V.Borshchevskiy, T.Balandin, A.Popov, T.Gensch, C.Fahlke, C.Bamann, D.Willbold, G.Buldt, E.Bamberg, V.Gordeliy. Crystal Structure of A Light-Driven Sodium Pump Nat.Struct.Mol.Biol. 2015.
ISSN: ESSN 1545-9985
Page generated: Mon Oct 7 19:25:38 2024

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