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Sodium in PDB 6ctf: Crystal Structure of Gltph Fast Mutant - R276S/M395R

Protein crystallography data

The structure of Crystal Structure of Gltph Fast Mutant - R276S/M395R, PDB code: 6ctf was solved by O.Boudker, S.Oh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.90 / 4.05
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 116.475, 196.420, 194.328, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 26.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Gltph Fast Mutant - R276S/M395R (pdb code 6ctf). 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 Fast Mutant - R276S/M395R, PDB code: 6ctf:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6ctf

Go back to Sodium Binding Sites List in 6ctf
Sodium binding site 1 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:0.6
occ:1.00
 O A:ASN401 2.5 0.5 1.0
O A:ASN310 2.5 0.7 1.0
O A:GLY306 2.6 0.1 1.0
OD1 A:ASP405 2.7 0.7 1.0
OD2 A:ASP405 2.8 0.8 1.0
CG A:ASP405 3.1 0.2 1.0
C A:ASN401 3.2 0.2 1.0
C A:ASN310 3.6 0.6 1.0
CB A:ASN401 3.6 0.6 1.0
CA A:ASN401 3.7 0.1 1.0
C A:GLY306 3.8 0.2 1.0
O A:ILE309 3.8 0.5 1.0
CG A:MET311 4.0 0.8 1.0
CA A:MET311 4.0 0.7 1.0
OG A:SER278 4.2 0.6 1.0
N A:VAL402 4.2 0.2 1.0
N A:MET311 4.2 0.4 1.0
O A:ALA307 4.4 0.9 1.0
CB A:MET311 4.4 0.5 1.0
CA A:VAL402 4.5 0.3 1.0
CB A:ASP405 4.5 0.1 1.0
CA A:GLY306 4.6 0.1 1.0
N A:ALA307 4.7 0.2 1.0
CA A:ASN310 4.7 0.2 1.0
C A:ALA307 4.7 0.1 1.0
CG A:ASN401 4.8 0.0 1.0
CA A:ALA307 4.8 0.9 1.0
CB A:ASN310 4.8 0.8 1.0
C A:ILE309 4.8 0.2 1.0
N A:ASP405 4.8 0.2 1.0
ND2 A:ASN310 4.9 0.8 1.0

Sodium binding site 2 out of 6 in 6ctf

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Sodium binding site 2 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:0.5
occ:1.00
 O A:THR352 2.3 0.8 1.0
O A:SER349 2.3 0.3 1.0
O A:THR308 2.3 0.7 1.0
O A:ILE350 2.4 0.4 1.0
SD A:MET311 2.8 0.2 1.0
C A:ILE350 2.9 0.6 1.0
N A:THR352 3.0 0.5 1.0
C A:THR352 3.1 0.6 1.0
C A:SER349 3.4 0.8 1.0
CA A:THR352 3.4 0.6 1.0
CA A:ILE350 3.5 0.7 1.0
C A:THR308 3.5 0.3 1.0
C A:GLY351 3.5 0.9 1.0
N A:GLY351 3.6 0.1 1.0
CB A:THR352 3.7 0.2 1.0
N A:ILE350 3.9 0.9 1.0
CG A:MET311 4.0 0.8 1.0
CA A:GLY351 4.0 0.4 1.0
O A:GLY351 4.3 0.4 1.0
CE A:MET311 4.3 0.5 1.0
CA A:THR308 4.4 0.8 1.0
N A:ALA353 4.4 0.2 1.0
N A:ILE309 4.5 0.7 1.0
OG1 A:THR352 4.5 0.3 1.0
CA A:ILE309 4.6 0.6 1.0
CA A:SER349 4.7 0.0 1.0
CG2 A:THR352 4.8 0.0 1.0
CB A:ILE350 4.9 0.9 1.0
O A:ALA348 4.9 0.8 1.0
CB A:MET311 4.9 0.5 1.0
CB A:THR308 5.0 0.1 1.0

Sodium binding site 3 out of 6 in 6ctf

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Sodium binding site 3 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:0.8
occ:1.00
 O B:ASN310 2.4 0.1 1.0
O B:GLY306 2.5 0.2 1.0
O B:ASN401 2.5 0.2 1.0
OD2 B:ASP405 2.9 0.3 1.0
OD1 B:ASP405 3.0 0.0 1.0
C B:ASN401 3.2 0.5 1.0
CG B:ASP405 3.3 0.2 1.0
CB B:ASN401 3.5 0.5 1.0
C B:ASN310 3.5 0.8 1.0
CA B:ASN401 3.6 0.6 1.0
C B:GLY306 3.7 0.5 1.0
CG B:MET311 3.7 0.2 1.0
O B:ILE309 3.8 0.2 1.0
CA B:MET311 3.9 0.5 1.0
OG B:SER278 4.0 0.9 1.0
N B:MET311 4.1 0.5 1.0
O B:ALA307 4.1 0.0 1.0
N B:VAL402 4.2 0.9 1.0
CB B:MET311 4.2 0.8 1.0
CA B:GLY306 4.5 0.3 1.0
C B:ALA307 4.5 0.6 1.0
N B:ALA307 4.6 0.2 1.0
CA B:VAL402 4.6 0.7 1.0
CA B:ALA307 4.6 0.2 1.0
CG B:ASN401 4.6 0.8 1.0
CA B:ASN310 4.7 0.5 1.0
C B:ILE309 4.8 0.5 1.0
CB B:ASP405 4.8 0.3 1.0
CB B:ASN310 4.9 0.8 1.0
CB B:SER278 5.0 0.9 1.0
ND2 B:ASN310 5.0 0.5 1.0

Sodium binding site 4 out of 6 in 6ctf

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Sodium binding site 4 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:0.9
occ:1.00
 O B:SER349 2.2 0.6 1.0
O B:THR352 2.2 0.7 1.0
O B:THR308 2.3 0.8 1.0
O B:ILE350 2.3 0.4 1.0
N B:THR352 2.7 0.1 1.0
C B:ILE350 2.7 0.2 1.0
SD B:MET311 2.8 0.7 1.0
C B:THR352 3.0 1.0 1.0
CA B:THR352 3.2 0.5 1.0
C B:SER349 3.3 0.5 1.0
C B:GLY351 3.3 0.2 1.0
CA B:ILE350 3.4 0.3 1.0
N B:GLY351 3.4 0.9 1.0
C B:THR308 3.5 0.0 1.0
CB B:THR352 3.5 0.3 1.0
N B:ILE350 3.8 0.0 1.0
CA B:GLY351 3.8 0.3 1.0
CG B:MET311 4.0 0.2 1.0
O B:GLY351 4.1 0.8 1.0
CE B:MET311 4.3 0.9 1.0
CA B:THR308 4.3 0.2 1.0
N B:ALA353 4.3 0.8 1.0
OG1 B:THR352 4.3 0.9 1.0
N B:ILE309 4.5 0.7 1.0
CA B:SER349 4.5 1.0 1.0
CA B:ILE309 4.6 0.2 1.0
O B:ALA348 4.7 0.2 1.0
CG2 B:THR352 4.7 0.8 1.0
CB B:THR308 4.8 0.9 1.0
CB B:ILE350 4.9 0.1 1.0
CB B:MET311 4.9 0.8 1.0
CA B:ALA353 5.0 0.1 1.0

Sodium binding site 5 out of 6 in 6ctf

Go back to Sodium Binding Sites List in 6ctf
Sodium binding site 5 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:0.6
occ:1.00
 O C:ASN401 2.5 0.9 1.0
O C:GLY306 2.5 0.4 1.0
O C:ASN310 2.5 0.8 1.0
OD1 C:ASP405 2.9 0.0 1.0
OD2 C:ASP405 2.9 0.2 1.0
C C:ASN401 3.1 0.8 1.0
CG C:ASP405 3.2 0.4 1.0
CB C:ASN401 3.3 0.2 1.0
CA C:ASN401 3.5 0.7 1.0
C C:ASN310 3.6 0.1 1.0
O C:ILE309 3.7 0.5 1.0
C C:GLY306 3.7 0.2 1.0
CG C:MET311 3.7 0.3 1.0
OG C:SER278 3.8 1.0 1.0
CA C:MET311 3.9 0.2 1.0
N C:VAL402 4.1 0.6 1.0
N C:MET311 4.1 0.2 1.0
O C:ALA307 4.2 0.4 1.0
CB C:MET311 4.3 0.2 1.0
CA C:VAL402 4.5 0.5 1.0
CA C:GLY306 4.5 0.5 1.0
CG C:ASN401 4.5 1.0 1.0
C C:ALA307 4.6 0.3 1.0
N C:ALA307 4.6 0.3 1.0
CA C:ALA307 4.7 0.3 1.0
CB C:ASP405 4.7 0.9 1.0
C C:ILE309 4.7 0.8 1.0
CA C:ASN310 4.8 0.1 1.0
CB C:SER278 4.8 0.2 1.0
CB C:ASN310 4.9 0.7 1.0
N C:ASN401 5.0 0.6 1.0

Sodium binding site 6 out of 6 in 6ctf

Go back to Sodium Binding Sites List in 6ctf
Sodium binding site 6 out of 6 in the Crystal Structure of Gltph Fast Mutant - R276S/M395R


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 Fast Mutant - R276S/M395R within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:0.1
occ:1.00
 O C:ILE350 2.3 0.8 1.0
O C:THR308 2.5 0.8 1.0
CA C:ILE309 2.6 0.2 1.0
CG1 C:ILE309 2.7 0.5 1.0
CA C:ILE350 2.8 0.5 1.0
C C:ILE350 2.9 0.1 1.0
C C:THR308 3.0 0.6 1.0
N C:ILE309 3.1 1.0 1.0
CB C:ILE309 3.1 0.7 1.0
CG2 C:ILE350 3.2 1.0 1.0
CB C:ILE350 3.4 0.1 1.0
CG2 C:ILE309 3.6 0.3 1.0
C C:ILE309 3.9 0.8 1.0
O C:SER349 4.0 0.5 1.0
CG1 C:ILE350 4.0 0.5 1.0
N C:ILE350 4.0 0.2 1.0
CD1 C:ILE309 4.0 0.6 1.0
N C:GLY351 4.2 0.5 1.0
N C:ASN310 4.3 0.7 1.0
CA C:THR308 4.4 0.3 1.0
C C:SER349 4.4 0.3 1.0
CB C:THR308 4.5 0.9 1.0
OG1 C:THR308 4.6 0.6 1.0
O C:THR352 4.9 0.6 1.0
O C:ILE309 4.9 0.5 1.0
CA C:GLY351 5.0 0.7 1.0

Reference:

S.Oh, O.Boudker. Kinetic Mechanism of Coupled Binding in Sodium-Aspartate Symporter Gltph. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30255846
DOI: 10.7554/ELIFE.37291
Page generated: Tue Dec 15 12:05:35 2020

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