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Sodium in PDB 6rez: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0

Protein crystallography data

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0, PDB code: 6rez 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) 48.13 / 2.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 130.241, 241.392, 135.109, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 22.5

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 5.0 (pdb code 6rez). 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 5.0, PDB code: 6rez:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6rez

Go back to Sodium Binding Sites List in 6rez
Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0


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 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:71.1
occ:1.00
 O A:HOH413 2.2 79.4 1.0
OH A:TYR25 2.4 65.7 1.0
O A:THR83 2.4 60.4 1.0
OD1 B:ASP102 2.4 95.8 1.0
O A:PHE86 2.6 75.6 1.0
OD2 B:ASP102 3.1 72.7 1.0
CG B:ASP102 3.1 79.5 1.0
CZ A:TYR25 3.4 62.7 1.0
C A:THR83 3.4 59.8 1.0
CA A:THR83 3.8 58.9 1.0
C A:PHE86 3.8 68.5 1.0
CE1 A:TYR25 4.0 61.2 1.0
CB A:THR83 4.2 53.3 1.0
CE2 A:TYR25 4.3 61.3 1.0
CA A:THR87 4.4 73.4 1.0
CB B:ASP102 4.6 79.8 1.0
N A:THR87 4.6 72.6 1.0
N A:SER84 4.6 59.4 0.5
N A:SER84 4.6 54.6 0.5
OG1 A:THR87 4.6 89.3 1.0
CD2 A:TYR95 4.8 56.6 1.0
CG2 A:THR83 4.8 54.9 1.0
CE2 A:TYR95 4.8 64.2 1.0
N A:PHE86 4.9 62.4 1.0
CA A:PHE86 5.0 65.3 1.0

Sodium binding site 2 out of 5 in 6rez

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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 5.0


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 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na308

b:67.0
occ:1.00
 O B:HOH416 2.3 72.8 1.0
O B:THR83 2.4 64.4 1.0
O B:PHE86 2.4 62.0 1.0
OD1 C:ASP102 2.5 75.2 1.0
OH B:TYR25 2.6 64.2 1.0
CG C:ASP102 3.3 75.5 1.0
OD2 C:ASP102 3.4 70.5 1.0
O C:HOH417 3.4 57.2 1.0
C B:THR83 3.4 57.6 1.0
CZ B:TYR25 3.5 64.6 1.0
C B:PHE86 3.6 60.5 1.0
CA B:THR83 3.9 59.8 1.0
CE1 B:TYR25 4.0 67.0 1.0
CA B:THR87 4.2 77.1 1.0
CB B:THR83 4.3 55.1 1.0
N B:THR87 4.3 64.6 1.0
OG1 B:THR87 4.4 80.6 1.0
CE2 B:TYR25 4.4 64.0 1.0
N B:SER84 4.6 55.6 0.5
N B:SER84 4.6 62.3 0.5
CD2 B:TYR95 4.7 64.9 1.0
CB C:ASP102 4.7 67.8 1.0
CA B:PHE86 4.7 61.2 1.0
N B:PHE86 4.8 63.1 1.0
CE2 B:TYR95 4.8 66.3 1.0
CB B:THR87 4.9 65.8 1.0
O C:SER100 4.9 0.3 1.0

Sodium binding site 3 out of 5 in 6rez

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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 5.0


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 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na309

b:69.3
occ:1.00
 O C:HOH421 2.3 86.7 1.0
OH C:TYR25 2.4 65.1 1.0
O C:PHE86 2.4 68.9 1.0
O C:THR83 2.4 58.9 1.0
OD1 D:ASP102 2.5 79.2 1.0
CG D:ASP102 3.2 84.5 1.0
CZ C:TYR25 3.3 63.2 1.0
OD2 D:ASP102 3.3 79.9 1.0
C C:THR83 3.4 57.9 1.0
C C:PHE86 3.6 68.0 1.0
O C:HOH416 3.7 62.0 1.0
CE1 C:TYR25 3.8 60.9 1.0
CA C:THR83 3.8 60.3 1.0
CE2 C:TYR25 4.2 56.1 1.0
CA C:THR87 4.2 68.7 1.0
CB C:THR83 4.2 56.0 1.0
N C:THR87 4.4 67.4 1.0
OG1 C:THR87 4.5 85.4 1.0
CD2 C:TYR95 4.6 64.4 1.0
N C:SER84 4.6 55.3 0.5
N C:SER84 4.6 62.0 0.5
CE2 C:TYR95 4.7 73.2 1.0
CB D:ASP102 4.7 69.0 1.0
CA C:PHE86 4.7 64.1 1.0
N C:PHE86 4.7 63.1 1.0
CG2 C:THR83 4.9 55.6 1.0

Sodium binding site 4 out of 5 in 6rez

Go back to Sodium Binding Sites List in 6rez
Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0


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 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na307

b:71.4
occ:1.00
 O D:THR83 2.3 65.0 1.0
O D:HOH403 2.4 89.3 1.0
OD1 E:ASP102 2.4 88.9 1.0
O D:PHE86 2.5 69.0 1.0
OH D:TYR25 2.7 62.5 1.0
CG E:ASP102 3.2 74.2 1.0
OD2 E:ASP102 3.3 82.7 1.0
C D:THR83 3.4 63.0 1.0
O E:HOH413 3.6 63.9 1.0
CZ D:TYR25 3.6 61.7 1.0
C D:PHE86 3.7 59.0 1.0
CA D:THR83 4.0 57.9 1.0
CE1 D:TYR25 4.2 65.0 1.0
CA D:THR87 4.2 69.8 1.0
OG1 D:THR87 4.3 89.7 1.0
CB D:THR83 4.4 57.3 1.0
N D:THR87 4.4 63.4 1.0
CE2 D:TYR25 4.6 70.3 1.0
N D:SER84 4.6 65.6 0.5
N D:SER84 4.6 59.7 0.5
CB E:ASP102 4.7 69.9 1.0
N D:PHE86 4.8 58.2 1.0
CA D:PHE86 4.8 59.8 1.0
O E:SER100 4.8 96.6 1.0
CD2 D:TYR95 4.9 66.5 1.0
CB D:THR87 4.9 71.2 1.0
CE2 D:TYR95 5.0 65.9 1.0

Sodium binding site 5 out of 5 in 6rez

Go back to Sodium Binding Sites List in 6rez
Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 5.0


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 5.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na309

b:70.8
occ:1.00
 O E:THR83 2.4 72.5 1.0
OD1 A:ASP102 2.5 81.6 1.0
O E:PHE86 2.6 67.1 1.0
OH E:TYR25 2.6 65.2 1.0
CG A:ASP102 3.3 73.4 1.0
OD2 A:ASP102 3.4 66.8 1.0
C E:THR83 3.5 59.1 1.0
CZ E:TYR25 3.6 58.9 1.0
C E:PHE86 3.8 65.2 1.0
CA E:THR83 4.0 63.3 1.0
CE1 E:TYR25 4.1 62.9 1.0
CA E:THR87 4.3 73.6 1.0
CB E:THR83 4.3 59.3 1.0
OG1 E:THR87 4.4 85.3 1.0
N E:THR87 4.5 65.0 1.0
CE2 E:TYR25 4.5 57.0 1.0
N E:SER84 4.6 57.9 0.5
N E:SER84 4.6 62.8 0.5
CB A:ASP102 4.7 77.7 1.0
CD2 E:TYR95 4.8 69.5 1.0
O A:SER100 4.9 0.9 1.0
N E:PHE86 4.9 52.7 1.0
CA E:PHE86 4.9 62.7 1.0
CE2 E:TYR95 4.9 69.2 1.0
CB E:THR87 5.0 72.8 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 Oct 8 13:07:33 2024

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