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Sodium in PDB 4oyf: Crystal Structure of Gltph R397A in Sodium-Bound State

Protein crystallography data

The structure of Crystal Structure of Gltph R397A in Sodium-Bound State, PDB code: 4oyf was solved by O.Boudker, S.Oh, G.Verdon, R.Serio, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.41
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 110.579, 110.579, 306.923, 90.00, 90.00, 120.00
R / Rfree (%) 28.4 / 29.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Gltph R397A in Sodium-Bound State (pdb code 4oyf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Crystal Structure of Gltph R397A in Sodium-Bound State, PDB code: 4oyf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 1 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:0.1
occ:1.00
 OD2 A:ASP405 2.8 0.2 1.0
O A:ASN310 2.8 0.9 1.0
O A:GLY306 2.9 1.0 1.0
O A:ASN401 3.5 0.3 1.0
OD1 A:ASP405 3.5 0.8 1.0
CG A:ASP405 3.5 0.2 1.0
C A:GLY306 3.7 0.1 1.0
CA A:ALA307 3.8 0.8 1.0
C A:ASN401 3.8 0.6 1.0
CB A:ASN401 3.8 0.2 1.0
OG A:SER278 4.0 0.2 1.0
C A:ASN310 4.0 0.2 1.0
ND2 A:ASN310 4.1 0.8 1.0
CB A:SER278 4.1 0.5 1.0
O A:ALA307 4.1 0.5 1.0
N A:ALA307 4.1 0.8 1.0
C A:ALA307 4.1 0.9 1.0
CA A:ASN401 4.3 0.7 1.0
N A:VAL402 4.5 1.0 1.0
CG A:ASN401 4.6 0.9 1.0
ND2 A:ASN401 4.6 1.0 1.0
CG A:MET311 4.7 0.7 1.0
CB A:ASN310 4.8 0.4 1.0
CA A:VAL402 4.8 0.2 1.0
CA A:GLY306 4.9 0.0 1.0
CA A:ASN310 4.9 0.6 1.0
CG A:ASN310 4.9 0.4 1.0
CA A:MET311 4.9 0.9 1.0
N A:MET311 5.0 0.3 1.0
CB A:ASP405 5.0 0.3 1.0

Sodium binding site 2 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 2 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na501

b:91.7
occ:1.00
 OD2 B:ASP405 2.7 0.7 1.0
O B:ASN310 3.0 0.5 1.0
O B:GLY306 3.0 0.3 1.0
OD1 B:ASP405 3.4 0.7 1.0
CG B:ASP405 3.4 0.4 1.0
O B:ASN401 3.5 0.6 1.0
C B:GLY306 3.8 0.6 1.0
C B:ASN401 3.8 0.7 1.0
CA B:ALA307 3.8 0.2 1.0
CB B:ASN401 3.8 0.3 1.0
OG B:SER278 3.9 0.4 1.0
CB B:SER278 4.0 0.9 1.0
N B:ALA307 4.1 0.4 1.0
ND2 B:ASN310 4.2 0.9 1.0
C B:ASN310 4.2 0.9 1.0
O B:ALA307 4.2 0.9 1.0
C B:ALA307 4.2 0.6 1.0
CA B:ASN401 4.3 0.6 1.0
N B:VAL402 4.4 0.9 1.0
CG B:ASN401 4.6 0.9 1.0
CA B:VAL402 4.7 0.3 1.0
ND2 B:ASN401 4.7 0.3 1.0
CG B:MET311 4.8 0.3 1.0
CB B:ASN310 4.9 0.6 1.0
CA B:GLY306 4.9 0.8 1.0
CB B:ASP405 4.9 0.7 1.0
CB B:ALA307 5.0 0.5 1.0

Sodium binding site 3 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 3 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na501

b:98.0
occ:1.00
 O C:ASN310 2.7 0.6 1.0
OD2 C:ASP405 2.8 0.1 1.0
O C:GLY306 2.8 0.4 1.0
O C:ASN401 3.5 0.8 1.0
OD1 C:ASP405 3.5 0.9 1.0
CG C:ASP405 3.5 0.2 1.0
C C:GLY306 3.7 0.8 1.0
CB C:ASN401 3.8 0.5 1.0
C C:ASN401 3.8 0.3 1.0
CA C:ALA307 3.8 0.1 1.0
C C:ASN310 3.9 0.4 1.0
OG C:SER278 4.0 0.7 1.0
ND2 C:ASN310 4.0 0.2 1.0
CB C:SER278 4.1 0.3 1.0
O C:ALA307 4.1 0.5 1.0
N C:ALA307 4.2 0.9 1.0
C C:ALA307 4.2 0.9 1.0
CA C:ASN401 4.3 0.9 1.0
N C:VAL402 4.5 0.1 1.0
CG C:ASN401 4.5 0.7 1.0
ND2 C:ASN401 4.5 0.8 1.0
CG C:MET311 4.6 0.3 1.0
CB C:ASN310 4.7 0.8 1.0
CA C:ASN310 4.8 0.7 1.0
CA C:VAL402 4.8 0.9 1.0
CA C:MET311 4.8 0.8 1.0
CA C:GLY306 4.8 0.6 1.0
N C:MET311 4.9 0.2 1.0
CG C:ASN310 4.9 0.6 1.0
CB C:ASP405 5.0 0.4 1.0

Sodium binding site 4 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 4 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na501

b:0.6
occ:1.00
 OD2 D:ASP405 2.7 0.8 1.0
O D:ASN310 2.8 0.2 1.0
O D:GLY306 2.9 0.1 1.0
O D:ASN401 3.4 0.6 1.0
OD1 D:ASP405 3.4 0.8 1.0
CG D:ASP405 3.5 0.1 1.0
C D:GLY306 3.7 0.4 1.0
C D:ASN401 3.8 0.0 1.0
CB D:ASN401 3.8 1.0 1.0
CA D:ALA307 3.9 0.4 1.0
C D:ASN310 4.0 0.1 1.0
ND2 D:ASN310 4.0 0.2 1.0
OG D:SER278 4.0 0.6 1.0
CB D:SER278 4.1 0.3 1.0
N D:ALA307 4.2 0.4 1.0
O D:ALA307 4.2 0.6 1.0
C D:ALA307 4.2 0.2 1.0
CA D:ASN401 4.3 0.6 1.0
N D:VAL402 4.4 0.8 1.0
CG D:ASN401 4.5 0.1 1.0
ND2 D:ASN401 4.6 0.0 1.0
CG D:MET311 4.7 0.5 1.0
CB D:ASN310 4.8 0.8 1.0
CA D:VAL402 4.8 0.6 1.0
CA D:GLY306 4.8 0.5 1.0
CA D:ASN310 4.9 0.6 1.0
CA D:MET311 4.9 0.4 1.0
CG D:ASN310 4.9 0.7 1.0
N D:MET311 4.9 0.9 1.0
CB D:ASP405 4.9 0.4 1.0

Sodium binding site 5 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 5 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na501

b:0.8
occ:1.00
 OD2 E:ASP405 2.8 0.3 1.0
O E:ASN310 2.8 0.1 1.0
O E:GLY306 2.9 0.2 1.0
O E:ASN401 3.4 0.2 1.0
OD1 E:ASP405 3.5 0.8 1.0
CG E:ASP405 3.5 0.2 1.0
C E:GLY306 3.7 0.3 1.0
C E:ASN401 3.8 0.6 1.0
CA E:ALA307 3.8 0.1 1.0
CB E:ASN401 3.8 0.3 1.0
OG E:SER278 4.0 0.5 1.0
ND2 E:ASN310 4.0 0.7 1.0
C E:ASN310 4.0 0.3 1.0
CB E:SER278 4.1 0.7 1.0
O E:ALA307 4.1 0.8 1.0
N E:ALA307 4.1 0.1 1.0
C E:ALA307 4.2 0.3 1.0
CA E:ASN401 4.3 0.7 1.0
N E:VAL402 4.5 0.9 1.0
CG E:ASN401 4.6 0.0 1.0
ND2 E:ASN401 4.7 0.1 1.0
CG E:MET311 4.7 0.0 1.0
CB E:ASN310 4.7 0.4 1.0
CA E:VAL402 4.8 0.1 1.0
CA E:GLY306 4.9 0.2 1.0
CA E:ASN310 4.9 0.7 1.0
CG E:ASN310 4.9 0.3 1.0
CA E:MET311 4.9 0.1 1.0
CB E:ASP405 5.0 0.2 1.0
N E:MET311 5.0 0.5 1.0

Sodium binding site 6 out of 6 in 4oyf

Go back to Sodium Binding Sites List in 4oyf
Sodium binding site 6 out of 6 in the Crystal Structure of Gltph R397A in Sodium-Bound State


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 Gltph R397A in Sodium-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na501

b:92.2
occ:1.00
 OD2 F:ASP405 2.7 0.6 1.0
O F:ASN310 2.9 0.5 1.0
O F:GLY306 3.0 0.2 1.0
OD1 F:ASP405 3.4 0.6 1.0
O F:ASN401 3.4 0.6 1.0
CG F:ASP405 3.4 0.3 1.0
C F:ASN401 3.8 0.7 1.0
C F:GLY306 3.8 0.5 1.0
CB F:ASN401 3.8 0.2 1.0
CA F:ALA307 3.8 0.0 1.0
OG F:SER278 4.0 0.2 1.0
CB F:SER278 4.1 0.7 1.0
ND2 F:ASN310 4.1 1.0 1.0
C F:ASN310 4.1 1.0 1.0
N F:ALA307 4.2 0.2 1.0
C F:ALA307 4.3 0.5 1.0
O F:ALA307 4.3 0.8 1.0
CA F:ASN401 4.3 0.6 1.0
N F:VAL402 4.4 0.8 1.0
CG F:ASN401 4.6 0.9 1.0
ND2 F:ASN401 4.7 0.3 1.0
CA F:VAL402 4.7 0.1 1.0
CG F:MET311 4.8 0.2 1.0
CB F:ASN310 4.8 0.6 1.0
CA F:GLY306 4.9 0.7 1.0
CB F:ASP405 4.9 0.6 1.0
CG F:ASN310 5.0 0.1 1.0
CA F:ASN310 5.0 0.9 1.0
CA F:MET311 5.0 0.1 1.0

Reference:

G.Verdon, S.Oh, R.N.Serio, O.Boudker. Coupled Ion Binding and Structural Transitions Along the Transport Cycle of Glutamate Transporters. Elife V. 3 02283 2014.
ISSN: ESSN 2050-084X
PubMed: 24842876
DOI: 10.7554/ELIFE.02283
Page generated: Mon Oct 7 17:36:12 2024

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