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Sodium in PDB 6yt4: Crystal Structure of the N112A 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 N112A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6yt4 was solved by K.Kovalev, N.Maliar, R.Astashkin, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 129.840, 239.700, 134.580, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6yt4). 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 N112A Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6yt4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6yt4

Go back to Sodium Binding Sites List in 6yt4
Sodium binding site 1 out of 5 in the Crystal Structure of the N112A 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 N112A 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:Na312

b:32.2
occ:1.00
 O A:HOH436 2.2 26.9 1.0
O A:PHE86 2.3 39.2 1.0
OH A:TYR25 2.3 35.2 1.0
O A:THR83 2.4 33.9 1.0
OD1 E:ASP102 2.4 45.5 1.0
O A:HOH451 2.9 52.1 1.0
CG E:ASP102 3.1 42.6 1.0
OD2 E:ASP102 3.1 46.4 1.0
CZ A:TYR25 3.2 33.5 1.0
C A:THR83 3.4 30.8 1.0
C A:PHE86 3.5 34.5 1.0
O E:HOH529 3.6 28.3 1.0
CE1 A:TYR25 3.7 36.7 1.0
CA A:THR83 3.8 30.8 1.0
O A:HOH450 4.0 42.9 1.0
CA A:THR87 4.2 39.0 1.0
CE2 A:TYR25 4.2 34.8 1.0
N A:THR87 4.2 38.8 1.0
CB A:THR83 4.3 31.2 1.0
OG1 A:THR87 4.4 38.9 1.0
CD2 A:TYR95 4.6 32.7 1.0
CB E:ASP102 4.6 40.0 1.0
N A:SER84 4.6 29.3 1.0
CA A:PHE86 4.6 31.8 1.0
N A:PHE86 4.7 27.9 1.0
CE2 A:TYR95 4.8 37.2 1.0
CD1 A:TYR25 4.9 35.8 1.0
CB A:THR87 4.9 37.0 1.0

Sodium binding site 2 out of 5 in 6yt4

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Sodium binding site 2 out of 5 in the Crystal Structure of the N112A 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 N112A 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:Na314

b:33.2
occ:1.00
 O B:THR83 2.3 34.0 1.0
O B:PHE86 2.3 33.4 1.0
O B:HOH442 2.4 38.0 1.0
OH B:TYR25 2.4 31.1 1.0
OD1 A:ASP102 2.5 40.3 1.0
O A:HOH433 2.7 48.2 1.0
CG A:ASP102 3.3 38.5 1.0
CZ B:TYR25 3.3 32.5 1.0
C B:THR83 3.3 34.5 1.0
OD2 A:ASP102 3.4 40.5 1.0
C B:PHE86 3.5 29.4 1.0
O A:HOH428 3.7 24.1 1.0
CA B:THR83 3.8 31.8 1.0
CE1 B:TYR25 3.8 32.6 1.0
O B:HOH466 3.9 52.5 1.0
CA B:THR87 4.1 35.1 1.0
N B:THR87 4.2 30.5 1.0
CB B:THR83 4.3 28.7 1.0
OG1 B:THR87 4.3 38.7 1.0
CE2 B:TYR25 4.3 32.9 1.0
N B:SER84 4.5 27.2 1.0
CA B:PHE86 4.6 31.3 1.0
N B:PHE86 4.7 25.9 1.0
CD2 B:TYR95 4.7 33.2 1.0
CB A:ASP102 4.7 32.5 1.0
CB B:THR87 4.9 34.5 1.0
CE2 B:TYR95 5.0 36.1 1.0

Sodium binding site 3 out of 5 in 6yt4

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Sodium binding site 3 out of 5 in the Crystal Structure of the N112A 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 N112A 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:Na413

b:31.5
occ:1.00
 O D:THR83 2.3 29.0 1.0
O D:PHE86 2.3 39.1 1.0
O D:HOH537 2.3 29.6 1.0
OH D:TYR25 2.4 34.4 1.0
OD1 C:ASP102 2.5 31.1 1.0
O C:HOH1539 2.7 41.9 1.0
CG C:ASP102 3.3 37.3 1.0
CZ D:TYR25 3.3 28.0 1.0
C D:THR83 3.3 27.2 1.0
OD2 C:ASP102 3.4 36.3 1.0
C D:PHE86 3.5 35.1 1.0
O C:HOH1532 3.6 28.8 1.0
CA D:THR83 3.7 29.5 1.0
CE1 D:TYR25 3.8 32.0 1.0
O D:HOH547 3.8 47.9 1.0
CA D:THR87 4.2 35.2 1.0
O C:HOH1503 4.2 52.2 1.0
N D:THR87 4.2 35.4 1.0
CB D:THR83 4.3 29.2 1.0
OG1 D:THR87 4.3 35.5 1.0
CE2 D:TYR25 4.3 28.9 1.0
N D:SER84 4.5 28.1 1.0
CA D:PHE86 4.6 36.4 1.0
N D:PHE86 4.7 29.1 1.0
CD2 D:TYR95 4.7 38.4 1.0
CB C:ASP102 4.7 32.7 1.0
CB D:THR87 4.9 36.0 1.0
CE2 D:TYR95 5.0 36.1 1.0
O C:SER100 5.0 48.9 1.0

Sodium binding site 4 out of 5 in 6yt4

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Sodium binding site 4 out of 5 in the Crystal Structure of the N112A 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 N112A 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:Na415

b:36.2
occ:1.00
 O E:HOH545 2.3 34.5 1.0
O E:THR83 2.3 40.3 1.0
OD1 D:ASP102 2.4 40.7 1.0
OH E:TYR25 2.4 36.7 1.0
O E:PHE86 2.4 36.7 1.0
CG D:ASP102 3.1 42.4 1.0
OD2 D:ASP102 3.1 43.0 1.0
CZ E:TYR25 3.3 33.2 1.0
C E:THR83 3.4 30.2 1.0
O D:HOH524 3.6 19.9 1.0
C E:PHE86 3.6 30.4 1.0
CA E:THR83 3.8 28.4 1.0
O D:HOH510 3.8 47.4 1.0
CE1 E:TYR25 3.8 32.2 1.0
O E:HOH555 4.2 42.4 1.0
CA E:THR87 4.2 35.3 1.0
CB E:THR83 4.3 27.4 1.0
CE2 E:TYR25 4.3 33.4 1.0
N E:THR87 4.4 32.6 1.0
OG1 E:THR87 4.4 37.3 1.0
CB D:ASP102 4.6 34.9 1.0
N E:SER84 4.6 31.8 1.0
CD2 E:TYR95 4.7 34.8 1.0
CA E:PHE86 4.8 31.6 1.0
N E:PHE86 4.8 31.1 1.0
O D:SER100 4.9 41.7 1.0
CE2 E:TYR95 4.9 33.2 1.0
CB E:THR87 5.0 31.9 1.0

Sodium binding site 5 out of 5 in 6yt4

Go back to Sodium Binding Sites List in 6yt4
Sodium binding site 5 out of 5 in the Crystal Structure of the N112A 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 N112A 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:Na1410

b:33.0
occ:1.00
 O C:THR83 2.3 31.1 1.0
O C:PHE86 2.3 37.4 1.0
O C:HOH1531 2.4 31.9 1.0
OH C:TYR25 2.4 31.8 1.0
OD1 B:ASP102 2.5 31.7 1.0
CG B:ASP102 3.3 33.7 1.0
CZ C:TYR25 3.3 31.3 1.0
C C:THR83 3.3 30.5 1.0
OD2 B:ASP102 3.4 34.1 1.0
C C:PHE86 3.5 32.5 1.0
O C:HOH1543 3.6 46.6 1.0
O B:HOH433 3.7 27.3 1.0
CA C:THR83 3.7 30.5 1.0
CE1 C:TYR25 3.8 30.4 1.0
CA C:THR87 4.1 32.3 1.0
CB C:THR83 4.2 31.2 1.0
N C:THR87 4.2 31.4 1.0
OG1 C:THR87 4.3 36.6 1.0
CE2 C:TYR25 4.3 34.0 1.0
N C:SER84 4.5 31.8 1.0
O B:HOH411 4.5 48.9 1.0
CA C:PHE86 4.6 30.7 1.0
N C:PHE86 4.7 30.9 1.0
CD2 C:TYR95 4.7 37.1 1.0
CB B:ASP102 4.7 30.3 1.0
CB C:THR87 4.9 32.5 1.0
CE2 C:TYR95 4.9 35.0 1.0
CG2 C:THR83 5.0 28.8 1.0

Reference:

N.Maliar, K.Kovalev, C.Baeken, T.Balandin, R.Astashkin, M.Rulev, A.Alekseev, N.Ilyinsky, A.Rogachev, V.Chupin, D.Dolgikh, M.Kirpichnikov, V.Gordeliy. Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2 Crystals 2020.
ISSN: ESSN 2073-4352
DOI: 10.3390/CRYST10060496
Page generated: Tue Oct 8 15:12:33 2024

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