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Sodium in PDB 6xyt: Crystal Structure of the O-State of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

Protein crystallography data

The structure of Crystal Structure of the O-State of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6xyt 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 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 131.157, 240.629, 135.039, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the O-State of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6xyt). 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 O-State of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6xyt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6xyt

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Sodium binding site 1 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na313

b:53.2
occ:1.00
 O A:HOH436 2.2 58.2 1.0
O A:THR83 2.3 53.1 1.0
O A:PHE86 2.3 50.8 1.0
OH A:TYR25 2.4 45.8 1.0
OD1 B:ASP102 2.6 58.6 1.0
O B:HOH428 2.7 62.2 1.0
CG B:ASP102 3.3 63.8 1.0
OD2 B:ASP102 3.3 55.8 1.0
CZ A:TYR25 3.3 48.5 1.0
C A:THR83 3.4 46.9 1.0
C A:PHE86 3.5 51.6 1.0
CE1 A:TYR25 3.8 45.9 1.0
O B:HOH411 3.9 51.2 1.0
CA A:THR83 3.9 46.1 1.0
CE2 A:TYR25 4.3 48.3 1.0
CA A:THR87 4.3 51.5 1.0
N A:THR87 4.3 50.6 1.0
CB A:THR83 4.5 46.6 1.0
OG1 A:THR87 4.5 56.2 1.0
N A:SER84 4.5 43.0 1.0
CA A:PHE86 4.6 49.5 1.0
N A:PHE86 4.6 48.5 1.0
CB B:ASP102 4.8 53.0 1.0
CD2 A:TYR95 4.8 46.5 1.0
CE2 A:TYR95 5.0 44.5 1.0
CA A:SER84 5.0 45.1 1.0

Sodium binding site 2 out of 10 in 6xyt

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Sodium binding site 2 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na319

b:56.5
occ:1.00
 OG A:SER70 2.2 49.4 1.0
OD1 A:ASN112 2.3 49.0 1.0
OD1 A:ASP116 2.3 51.2 1.0
O A:VAL67 2.5 49.4 1.0
OD2 A:ASP116 2.6 61.0 1.0
CG A:ASP116 2.7 56.6 1.0
N A:ALA71 2.8 45.2 1.0
CB A:SER70 3.3 47.9 1.0
CG A:ASN112 3.3 48.9 1.0
C A:SER70 3.4 46.1 1.0
CA A:ALA71 3.5 48.4 1.0
C A:VAL67 3.5 45.6 1.0
CB A:ALA71 3.6 45.1 1.0
ND2 A:ASN112 3.7 49.8 1.0
CA A:SER70 3.7 48.2 1.0
CA A:VAL67 3.9 51.2 1.0
O A:HOH406 4.1 51.0 1.0
N A:SER70 4.1 48.9 1.0
O A:SER70 4.2 45.2 1.0
O A:HOH435 4.2 49.7 1.0
CB A:ASP116 4.2 52.4 1.0
CG1 A:VAL67 4.3 51.6 1.0
O A:ASN112 4.3 53.9 1.0
CD1 A:ILE115 4.5 69.2 1.0
CG1 A:ILE115 4.5 63.1 1.0
CB A:ASN112 4.6 49.5 1.0
CB A:VAL67 4.6 50.2 1.0
O A:VAL66 4.7 51.2 1.0
N A:MET68 4.7 46.9 1.0
CA A:ASN112 4.8 47.7 1.0
CA A:ASP116 4.9 48.9 1.0
C A:ASN112 4.9 49.9 1.0
C A:ALA71 4.9 49.0 1.0

Sodium binding site 3 out of 10 in 6xyt

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Sodium binding site 3 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na311

b:52.1
occ:1.00
 O B:THR83 2.2 47.9 1.0
O B:PHE86 2.3 53.7 1.0
O B:HOH424 2.4 66.9 1.0
OH B:TYR25 2.4 46.4 1.0
OD1 C:ASP102 2.5 53.9 1.0
O C:HOH412 2.6 61.5 1.0
OD2 C:ASP102 3.1 55.5 1.0
CG C:ASP102 3.2 57.5 1.0
CZ B:TYR25 3.3 47.0 1.0
C B:THR83 3.4 52.1 1.0
C B:PHE86 3.6 46.6 1.0
CE1 B:TYR25 3.8 49.3 1.0
O C:HOH407 3.9 47.6 1.0
CA B:THR83 3.9 47.0 1.0
CE2 B:TYR25 4.3 46.9 1.0
CA B:THR87 4.3 51.7 1.0
N B:THR87 4.3 51.1 1.0
CB B:THR83 4.4 43.9 1.0
OG1 B:THR87 4.5 61.4 1.0
N B:SER84 4.5 44.8 0.3
N B:SER84 4.5 45.4 0.7
CA B:PHE86 4.6 49.2 1.0
N B:PHE86 4.6 48.2 1.0
CB C:ASP102 4.7 55.8 1.0
CD2 B:TYR95 4.8 47.4 1.0
CA B:SER84 4.9 43.2 0.3
CA B:SER84 5.0 46.4 0.7

Sodium binding site 4 out of 10 in 6xyt

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Sodium binding site 4 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na318

b:56.8
occ:1.00
 OG B:SER70 2.2 51.2 1.0
OD1 B:ASN112 2.2 50.7 1.0
OD1 B:ASP116 2.2 56.4 1.0
O B:VAL67 2.5 45.3 1.0
OD2 B:ASP116 2.6 61.8 1.0
CG B:ASP116 2.7 58.6 1.0
N B:ALA71 2.9 46.1 1.0
CG B:ASN112 3.2 53.4 1.0
CB B:SER70 3.3 47.0 1.0
C B:SER70 3.4 46.6 1.0
CA B:ALA71 3.5 48.7 1.0
C B:VAL67 3.6 46.5 1.0
CB B:ALA71 3.6 49.8 1.0
ND2 B:ASN112 3.6 49.0 1.0
CA B:SER70 3.8 49.7 1.0
CA B:VAL67 3.9 51.3 1.0
O B:HOH406 4.1 55.6 1.0
N B:SER70 4.2 48.6 1.0
CB B:ASP116 4.2 55.0 1.0
O B:ASN112 4.2 57.2 1.0
O B:SER70 4.2 46.1 1.0
CG1 B:VAL67 4.3 50.6 1.0
O B:HOH441 4.3 55.4 1.0
CG1 B:ILE115 4.5 57.7 1.0
CD1 B:ILE115 4.5 61.9 1.0
CB B:ASN112 4.5 54.9 1.0
CB B:VAL67 4.6 53.7 1.0
O B:VAL66 4.7 49.6 1.0
CA B:ASN112 4.8 53.0 1.0
N B:MET68 4.8 45.2 1.0
C B:ASN112 4.8 53.8 1.0
CA B:ASP116 4.9 54.6 1.0
C B:ALA71 5.0 47.1 1.0

Sodium binding site 5 out of 10 in 6xyt

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Sodium binding site 5 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na310

b:48.1
occ:1.00
 O C:THR83 2.2 47.7 1.0
O C:HOH429 2.2 56.9 1.0
O C:PHE86 2.3 50.0 1.0
OH C:TYR25 2.5 50.4 1.0
OD1 D:ASP102 2.5 53.5 1.0
O D:HOH521 2.6 61.3 1.0
CG D:ASP102 3.3 58.4 1.0
OD2 D:ASP102 3.3 53.7 1.0
C C:THR83 3.4 47.3 1.0
CZ C:TYR25 3.4 44.8 1.0
C C:PHE86 3.5 52.4 1.0
O D:HOH531 3.9 51.0 1.0
CA C:THR83 3.9 46.1 1.0
CE1 C:TYR25 3.9 48.0 1.0
CA C:THR87 4.3 49.1 1.0
N C:THR87 4.3 52.7 1.0
CE2 C:TYR25 4.4 50.1 1.0
OG1 C:THR87 4.4 60.4 1.0
CB C:THR83 4.4 42.5 1.0
N C:SER84 4.5 44.8 1.0
N C:PHE86 4.6 50.7 1.0
CA C:PHE86 4.6 48.7 1.0
CB D:ASP102 4.7 48.4 1.0
CD2 C:TYR95 4.9 47.3 1.0
CA C:SER84 4.9 43.9 1.0

Sodium binding site 6 out of 10 in 6xyt

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Sodium binding site 6 out of 10 in the Crystal Structure of the O-State 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 O-State 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:54.4
occ:1.00
 OG C:SER70 2.1 49.8 1.0
OD1 C:ASP116 2.2 50.8 1.0
OD1 C:ASN112 2.3 52.9 1.0
O C:VAL67 2.4 45.4 1.0
OD2 C:ASP116 2.6 62.9 1.0
CG C:ASP116 2.7 55.7 1.0
N C:ALA71 2.9 45.4 1.0
CB C:SER70 3.3 48.3 1.0
CG C:ASN112 3.3 51.9 1.0
C C:SER70 3.4 46.2 1.0
C C:VAL67 3.5 46.5 1.0
CA C:ALA71 3.5 49.6 1.0
CB C:ALA71 3.6 47.3 1.0
CA C:SER70 3.7 47.3 1.0
ND2 C:ASN112 3.7 47.5 1.0
CA C:VAL67 3.8 50.2 1.0
N C:SER70 4.1 48.2 1.0
O C:HOH416 4.1 57.2 1.0
O C:HOH438 4.1 53.5 1.0
O C:SER70 4.2 47.0 1.0
CB C:ASP116 4.2 52.0 1.0
CG1 C:VAL67 4.2 48.8 1.0
O C:ASN112 4.3 52.1 1.0
CD1 C:ILE115 4.5 70.3 1.0
CG1 C:ILE115 4.5 66.7 1.0
CB C:VAL67 4.6 51.0 1.0
O C:VAL66 4.6 51.1 1.0
CB C:ASN112 4.6 50.5 1.0
N C:MET68 4.7 47.3 1.0
CA C:ASN112 4.9 52.7 1.0
CA C:ASP116 4.9 50.4 1.0
C C:ALA71 5.0 50.4 1.0
C C:ASN112 5.0 50.2 1.0

Sodium binding site 7 out of 10 in 6xyt

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Sodium binding site 7 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na415

b:51.5
occ:1.00
 O D:THR83 2.2 49.0 1.0
O D:PHE86 2.3 52.1 1.0
O D:HOH545 2.4 62.0 1.0
OH D:TYR25 2.4 45.3 1.0
OD1 E:ASP102 2.6 55.1 1.0
O E:HOH420 2.8 65.7 1.0
OD2 E:ASP102 3.2 53.8 1.0
CG E:ASP102 3.2 60.9 1.0
C D:THR83 3.3 46.6 1.0
CZ D:TYR25 3.4 45.7 1.0
C D:PHE86 3.5 47.0 1.0
O E:HOH408 3.8 51.0 1.0
CE1 D:TYR25 3.9 45.5 1.0
CA D:THR83 3.9 47.9 1.0
CA D:THR87 4.3 50.5 1.0
CE2 D:TYR25 4.3 48.5 1.0
N D:THR87 4.3 49.5 1.0
CB D:THR83 4.4 47.6 1.0
OG1 D:THR87 4.4 61.0 1.0
N D:SER84 4.5 44.2 0.3
N D:SER84 4.5 43.4 0.7
N D:PHE86 4.6 49.4 1.0
CA D:PHE86 4.6 48.8 1.0
CB E:ASP102 4.7 49.1 1.0
CD2 D:TYR95 4.8 46.1 1.0
CA D:SER84 4.9 43.9 0.3
CA D:SER84 4.9 44.9 0.7

Sodium binding site 8 out of 10 in 6xyt

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Sodium binding site 8 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na418

b:56.8
occ:1.00
 OG D:SER70 2.1 47.0 1.0
OD1 D:ASP116 2.2 52.5 1.0
OD1 D:ASN112 2.3 53.9 1.0
O D:VAL67 2.5 50.2 1.0
OD2 D:ASP116 2.6 57.5 1.0
CG D:ASP116 2.7 54.5 1.0
N D:ALA71 2.8 41.6 1.0
CB D:SER70 3.2 49.1 1.0
CG D:ASN112 3.3 58.0 1.0
C D:SER70 3.4 45.3 1.0
CA D:ALA71 3.5 46.0 1.0
C D:VAL67 3.5 42.7 1.0
CB D:ALA71 3.6 45.5 1.0
CA D:SER70 3.7 48.6 1.0
ND2 D:ASN112 3.7 48.6 1.0
CA D:VAL67 3.9 47.6 1.0
N D:SER70 4.1 46.2 1.0
O D:HOH511 4.1 56.1 1.0
O D:HOH533 4.1 54.4 1.0
O D:SER70 4.2 41.6 1.0
CB D:ASP116 4.2 51.6 1.0
CG1 D:VAL67 4.3 43.6 1.0
O D:ASN112 4.3 53.3 1.0
CD1 D:ILE115 4.4 67.5 1.0
CG1 D:ILE115 4.5 61.4 1.0
CB D:ASN112 4.6 52.4 1.0
CB D:VAL67 4.6 46.8 1.0
O D:VAL66 4.6 48.6 1.0
N D:MET68 4.7 45.8 1.0
CA D:ASN112 4.9 54.3 1.0
CA D:ASP116 4.9 51.8 1.0
C D:ASN112 4.9 52.0 1.0
C D:ALA71 5.0 50.6 1.0

Sodium binding site 9 out of 10 in 6xyt

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Sodium binding site 9 out of 10 in the Crystal Structure of the O-State 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 O-State 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:Na314

b:49.0
occ:1.00
 O E:HOH415 2.3 64.0 1.0
O E:THR83 2.3 47.9 1.0
O E:PHE86 2.4 49.6 1.0
OH E:TYR25 2.4 46.9 1.0
OD1 A:ASP102 2.5 61.4 1.0
O A:HOH409 2.6 67.4 1.0
OD2 A:ASP102 3.1 56.2 1.0
CG A:ASP102 3.2 58.4 1.0
CZ E:TYR25 3.3 48.0 1.0
C E:THR83 3.4 50.2 1.0
C E:PHE86 3.6 46.9 1.0
CE1 E:TYR25 3.9 45.6 1.0
O A:HOH410 3.9 49.1 1.0
CA E:THR83 4.0 48.3 1.0
CE2 E:TYR25 4.3 46.6 1.0
CA E:THR87 4.3 48.5 1.0
N E:THR87 4.4 52.4 1.0
CB E:THR83 4.4 46.4 1.0
OG1 E:THR87 4.5 55.4 1.0
N E:SER84 4.6 39.1 1.0
CB A:ASP102 4.6 48.5 1.0
CA E:PHE86 4.7 49.5 1.0
N E:PHE86 4.7 45.4 1.0
CD2 E:TYR95 4.8 45.7 1.0

Sodium binding site 10 out of 10 in 6xyt

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Sodium binding site 10 out of 10 in the Crystal Structure of the O-State 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 O-State 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:61.8
occ:1.00
 OD1 E:ASP116 2.1 61.6 1.0
OG E:SER70 2.2 51.7 1.0
OD1 E:ASN112 2.2 56.4 1.0
OD2 E:ASP116 2.5 66.8 1.0
O E:VAL67 2.6 49.6 1.0
CG E:ASP116 2.6 65.3 1.0
N E:ALA71 2.9 45.0 1.0
CG E:ASN112 3.2 50.6 1.0
CB E:SER70 3.3 53.5 1.0
C E:SER70 3.4 49.5 1.0
CA E:ALA71 3.5 46.9 1.0
C E:VAL67 3.6 45.1 1.0
CB E:ALA71 3.6 45.8 1.0
ND2 E:ASN112 3.7 56.8 1.0
CA E:SER70 3.8 52.9 1.0
CA E:VAL67 3.9 50.8 1.0
CB E:ASP116 4.1 55.6 1.0
O E:HOH409 4.1 60.0 1.0
O E:ASN112 4.1 53.1 1.0
N E:SER70 4.2 47.6 1.0
O E:SER70 4.2 44.3 1.0
O E:HOH449 4.2 59.1 1.0
CG1 E:VAL67 4.3 46.8 1.0
CG1 E:ILE115 4.4 63.8 1.0
CD1 E:ILE115 4.5 60.3 1.0
CB E:ASN112 4.5 47.8 1.0
CB E:VAL67 4.6 46.7 1.0
O E:VAL66 4.7 51.7 1.0
CA E:ASN112 4.8 54.2 1.0
CA E:ASP116 4.8 54.5 1.0
C E:ASN112 4.8 53.4 1.0
N E:MET68 4.8 46.5 1.0
N E:ASP116 5.0 50.5 1.0

Reference:

K.Kovalev, R.Astashkin, I.Gushchin, V.Gordeliy. KR2 Rhodopsin: New Mechanism of A Light-Driven Ion Translocation To Be Published.
Page generated: Tue Oct 8 14:56:43 2024

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