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Sodium in PDB 6x01: Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State

Protein crystallography data

The structure of Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State, PDB code: 6x01 was solved by I.Chen, J.Font, R.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.84 / 3.65
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 113.985, 113.985, 321.705, 90, 90, 120
R / Rfree (%) 27.2 / 30.9

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State (pdb code 6x01). 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State, PDB code: 6x01:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6x01

Go back to Sodium Binding Sites List in 6x01
Sodium binding site 1 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:123.8
occ:1.00
 O A:ASN310 2.4 117.7 1.0
O A:GLY306 2.7 111.5 1.0
OD2 A:ASP405 2.7 108.4 1.0
O A:ASN401 3.1 93.7 1.0
OD1 A:ASP405 3.1 125.7 1.0
CG A:ASP405 3.3 119.9 1.0
O A:ALA307 3.3 132.6 1.0
C A:ASN401 3.6 105.1 1.0
CA A:ALA307 3.6 147.9 1.0
C A:GLY306 3.6 127.7 1.0
C A:ASN310 3.6 119.2 1.0
C A:ALA307 3.7 143.4 1.0
SD A:MET311 3.8 121.8 1.0
CB A:ASN401 3.8 126.1 1.0
N A:ALA307 4.0 121.2 1.0
CB A:SER278 4.1 99.3 1.0
OG A:SER278 4.1 134.2 1.0
CA A:ASN401 4.2 121.3 1.0
N A:VAL402 4.2 104.2 1.0
CA A:VAL402 4.5 107.0 1.0
CA A:ASN310 4.5 132.0 1.0
CB A:ASN310 4.5 120.7 1.0
N A:MET311 4.6 93.5 1.0
N A:ASN310 4.6 107.4 1.0
CE A:MET311 4.7 98.3 1.0
CG A:ASN401 4.7 107.5 1.0
CA A:MET311 4.7 106.9 1.0
CG2 A:VAL402 4.7 127.1 1.0
N A:THR308 4.7 149.0 1.0
CB A:ASP405 4.7 118.3 1.0
CG A:MET311 4.8 102.1 1.0
ND2 A:ASN310 4.8 117.6 1.0
CA A:GLY306 4.9 128.6 1.0
CB A:ALA307 4.9 135.9 1.0

Sodium binding site 2 out of 6 in 6x01

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Sodium binding site 2 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:76.7
occ:1.00
 O A:SER349 2.3 106.4 1.0
O A:THR308 2.4 117.4 1.0
O A:THR352 2.4 139.6 1.0
CG A:MET311 2.6 102.1 1.0
CE A:MET311 2.8 98.3 1.0
C A:THR308 3.1 112.9 1.0
O A:ILE350 3.1 122.4 1.0
SD A:MET311 3.4 121.8 1.0
C A:THR352 3.5 107.9 1.0
C A:SER349 3.6 111.8 1.0
C A:ILE350 3.6 128.2 1.0
N A:THR352 3.9 105.5 1.0
CA A:THR308 3.9 129.8 1.0
CB A:MET311 3.9 122.8 1.0
CA A:ILE350 3.9 99.4 1.0
CA A:THR352 3.9 102.9 1.0
CB A:THR352 4.0 138.2 1.0
N A:ILE309 4.0 115.2 1.0
O A:ILE309 4.1 110.7 1.0
C A:ILE309 4.2 114.4 1.0
N A:ILE350 4.2 108.4 1.0
CA A:ILE309 4.2 124.4 1.0
C A:GLY351 4.5 113.4 1.0
N A:GLY351 4.5 128.6 1.0
CG2 A:THR352 4.5 128.6 1.0
N A:ALA353 4.6 111.5 1.0
CA A:SER349 4.7 130.8 1.0
O A:ALA307 4.7 132.6 1.0
N A:MET311 4.7 93.5 1.0
CB A:THR308 4.8 124.3 1.0
N A:ASN310 4.8 107.4 1.0
N A:THR308 4.9 149.0 1.0
CA A:MET311 4.9 106.9 1.0
C A:ASN310 4.9 119.2 1.0

Sodium binding site 3 out of 6 in 6x01

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Sodium binding site 3 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:153.0
occ:1.00
 O B:ASN401 2.5 153.3 1.0
O B:ASN310 2.6 168.6 1.0
OD2 B:ASP405 2.6 169.5 1.0
C B:ASN401 3.0 172.8 1.0
O B:GLY306 3.1 172.4 1.0
CG B:ASP405 3.2 174.0 1.0
OD1 B:ASP405 3.2 186.7 1.0
CB B:ASN401 3.4 167.0 1.0
N B:VAL402 3.6 183.7 1.0
CA B:ASN401 3.7 173.3 1.0
O B:ALA307 3.7 167.9 1.0
C B:ASN310 3.8 176.7 1.0
CA B:ALA307 3.8 175.6 1.0
CA B:VAL402 3.9 172.3 1.0
C B:GLY306 4.0 159.9 1.0
C B:ALA307 4.1 172.4 1.0
CB B:SER278 4.1 148.4 1.0
CG B:MET311 4.1 165.9 1.0
CG2 B:VAL402 4.3 170.4 1.0
N B:ALA307 4.3 157.7 1.0
CB B:ASP405 4.5 175.9 1.0
OG B:SER278 4.5 176.6 1.0
CG B:ASN401 4.5 159.6 1.0
CA B:MET311 4.5 172.4 1.0
N B:MET311 4.6 178.1 1.0
CB B:VAL402 4.8 168.6 1.0
CA B:ASN310 4.8 174.8 1.0
ND2 B:ASN310 4.8 197.8 1.0
CB B:ASN310 4.9 184.0 1.0
CB B:MET311 4.9 161.8 1.0
ND2 B:ASN401 5.0 159.3 1.0

Sodium binding site 4 out of 6 in 6x01

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Sodium binding site 4 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:151.8
occ:1.00
 O B:SER349 2.3 164.7 1.0
O B:THR308 2.3 169.3 1.0
O B:THR352 2.3 147.9 1.0
O B:ILE350 2.4 161.8 1.0
SD B:MET311 2.7 161.5 1.0
C B:ILE350 2.9 147.7 1.0
C B:THR352 3.3 156.3 1.0
N B:THR352 3.3 166.3 1.0
C B:SER349 3.3 173.7 1.0
C B:THR308 3.3 157.3 1.0
CA B:ILE350 3.5 167.0 1.0
CE B:MET311 3.6 164.2 1.0
CA B:THR352 3.6 166.3 1.0
N B:GLY351 3.8 143.9 1.0
C B:GLY351 3.8 150.9 1.0
N B:ILE350 3.8 175.7 1.0
CB B:THR352 3.8 170.3 1.0
CG B:MET311 4.0 165.9 1.0
O B:ILE309 4.0 165.7 1.0
N B:ILE309 4.1 161.8 1.0
CA B:ILE309 4.2 170.1 1.0
CA B:GLY351 4.3 140.2 1.0
CA B:THR308 4.3 169.1 1.0
C B:ILE309 4.3 168.6 1.0
O B:GLY351 4.5 141.1 1.0
N B:ALA353 4.5 157.6 1.0
CA B:SER349 4.5 172.3 1.0
CB B:MET311 4.6 161.8 1.0
OG1 B:THR352 4.8 166.0 1.0
CG2 B:THR352 4.8 166.4 1.0
O B:ALA348 4.8 177.6 1.0
CB B:ILE350 4.9 156.2 1.0

Sodium binding site 5 out of 6 in 6x01

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Sodium binding site 5 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:174.0
occ:1.00
 O C:ASN310 2.5 170.6 1.0
O C:ASN401 2.5 164.6 1.0
OD2 C:ASP405 2.6 169.7 1.0
C C:ASN401 3.0 165.4 1.0
OD1 C:ASP405 3.1 184.4 1.0
CG C:ASP405 3.1 177.4 1.0
O C:GLY306 3.2 149.7 1.0
CB C:ASN401 3.4 176.7 1.0
O C:ALA307 3.6 178.3 1.0
CA C:ASN401 3.7 172.8 1.0
N C:VAL402 3.7 168.5 1.0
C C:ASN310 3.7 182.7 1.0
CA C:ALA307 3.9 167.8 1.0
CG C:MET311 4.0 151.2 1.0
CA C:VAL402 4.0 167.3 1.0
C C:ALA307 4.0 166.2 1.0
C C:GLY306 4.1 154.2 1.0
CB C:SER278 4.2 150.9 1.0
CA C:MET311 4.4 162.1 1.0
CG2 C:VAL402 4.4 185.4 1.0
N C:ALA307 4.4 161.8 1.0
OG C:SER278 4.5 187.1 1.0
N C:MET311 4.5 174.8 1.0
CG C:ASN401 4.5 159.5 1.0
CB C:ASP405 4.5 177.6 1.0
ND2 C:ASN310 4.6 176.4 1.0
CA C:ASN310 4.7 178.3 1.0
CB C:MET311 4.8 162.2 1.0
CB C:VAL402 4.8 164.5 1.0
CB C:ASN310 4.9 182.6 1.0
N C:ASN310 5.0 170.9 1.0
CE C:MET311 5.0 148.8 1.0

Sodium binding site 6 out of 6 in 6x01

Go back to Sodium Binding Sites List in 6x01
Sodium binding site 6 out of 6 in the Crystal Structure of the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing 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 the Gltph V216C-A391C Mutant Cross-Linked in Outward-Facing State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:162.9
occ:1.00
 O C:THR308 2.3 153.6 1.0
O C:SER349 2.3 164.4 1.0
O C:THR352 2.4 167.0 1.0
O C:ILE350 2.5 168.4 1.0
SD C:MET311 2.8 168.2 1.0
C C:ILE350 3.1 159.6 1.0
C C:THR308 3.3 150.9 1.0
C C:THR352 3.4 159.2 1.0
C C:SER349 3.4 176.4 1.0
N C:THR352 3.5 159.6 1.0
CA C:ILE350 3.6 156.2 1.0
CE C:MET311 3.6 148.8 1.0
CG C:MET311 3.8 151.2 1.0
CA C:THR352 3.8 165.0 1.0
O C:ILE309 3.9 161.1 1.0
N C:GLY351 3.9 162.8 1.0
CB C:THR352 3.9 166.1 1.0
N C:ILE350 4.0 170.7 1.0
C C:GLY351 4.0 161.7 1.0
N C:ILE309 4.0 159.6 1.0
CA C:ILE309 4.1 154.9 1.0
C C:ILE309 4.1 159.6 1.0
CA C:THR308 4.2 164.4 1.0
CB C:MET311 4.4 162.2 1.0
CA C:GLY351 4.4 163.8 1.0
O C:GLY351 4.6 173.1 1.0
N C:ALA353 4.6 149.7 1.0
CA C:SER349 4.6 185.0 1.0
OG1 C:THR352 4.9 166.7 1.0
CG2 C:THR352 4.9 156.2 1.0
N C:ASN310 5.0 170.9 1.0

Reference:

I.Chen, S.Pant, Q.Wu, R.Cater, M.Sobti, R.Vandenberg, A.G.Stewart, E.Tajkhorshid, J.Font, R.M.Ryan. Glutamate Transporters Have A Chloride Channel with Two Hydrophobic Gates Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03240-9
Page generated: Tue Oct 8 14:44:07 2024

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