Sodium in PDB 6wzb: Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury

Protein crystallography data

The structure of Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury, PDB code: 6wzb 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) 49.31 / 3.45
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 112.111, 204.573, 207.372, 90, 90, 90
R / Rfree (%) 23.3 / 26.8

Other elements in 6wzb:

The structure of Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury also contains other interesting chemical elements:

Mercury (Hg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury (pdb code 6wzb). 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-G388C Mutant Cross-Linked with Divalent Mercury, PDB code: 6wzb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 6wzb

Go back to Sodium Binding Sites List in 6wzb
Sodium binding site 1 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:101.2
occ:1.00
O A:SER349 2.2 104.3 1.0
O A:THR352 2.2 96.2 1.0
O A:THR308 2.2 115.8 1.0
O A:ILE350 2.7 76.2 1.0
SD A:MET311 2.8 99.8 1.0
C A:THR352 3.1 89.8 1.0
CE A:MET311 3.2 95.7 1.0
C A:ILE350 3.2 83.5 1.0
N A:THR352 3.3 90.9 1.0
C A:SER349 3.3 97.9 1.0
C A:THR308 3.4 116.0 1.0
CA A:THR352 3.4 89.0 1.0
CB A:THR352 3.5 92.4 1.0
CG A:MET311 3.6 99.2 1.0
CA A:ILE350 3.6 82.4 1.0
N A:ILE350 3.9 92.0 1.0
C A:GLY351 4.0 90.1 1.0
N A:GLY351 4.1 94.9 1.0
N A:ALA353 4.2 83.4 1.0
N A:ILE309 4.3 116.9 1.0
CA A:THR308 4.3 107.8 1.0
CA A:ILE309 4.4 110.7 1.0
CG2 A:THR352 4.4 97.9 1.0
CB A:MET311 4.4 105.9 1.0
CA A:SER349 4.5 97.5 1.0
OG1 A:THR352 4.6 92.0 1.0
CA A:GLY351 4.6 88.9 1.0
O A:GLY351 4.6 88.9 1.0
C A:ILE309 4.7 113.1 1.0
CA A:ALA353 4.8 85.3 1.0
O A:ALA348 4.8 96.2 1.0
C A:ALA353 4.9 98.2 1.0

Sodium binding site 2 out of 6 in 6wzb

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Sodium binding site 2 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:126.2
occ:1.00
O A:GLY306 2.6 96.8 1.0
OD2 A:ASP405 2.9 127.2 1.0
O A:ASN401 2.9 110.4 1.0
C A:ASN401 3.3 108.5 1.0
O A:ASN310 3.3 115.7 1.0
OD1 A:ASP405 3.4 127.5 1.0
CG A:ASP405 3.5 124.9 1.0
CB A:ASN401 3.5 102.9 1.0
C A:GLY306 3.7 99.3 1.0
CB A:SER278 3.8 100.2 1.0
OG A:SER278 3.8 108.8 1.0
O A:ALA307 3.9 96.2 1.0
CA A:ASN401 3.9 106.3 1.0
CA A:ALA307 4.0 99.3 1.0
N A:VAL402 4.0 107.0 1.0
C A:ALA307 4.0 99.1 1.0
CG A:MET311 4.1 99.2 1.0
O A:ILE309 4.1 119.7 1.0
N A:ALA307 4.3 100.1 1.0
CA A:VAL402 4.3 96.8 1.0
C A:ASN310 4.4 117.6 1.0
CE A:MET311 4.6 95.7 1.0
CG A:ASN401 4.6 100.1 1.0
CG2 A:VAL402 4.7 87.0 1.0
CA A:MET311 4.8 114.4 1.0
CA A:GLY306 4.8 104.2 1.0
N A:THR308 4.8 103.2 1.0
O A:ASP501 4.9 104.3 1.0
CB A:ASP405 4.9 117.4 1.0
ND2 A:ASN310 4.9 124.4 1.0
ND2 A:ASN401 5.0 96.4 1.0

Sodium binding site 3 out of 6 in 6wzb

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Sodium binding site 3 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:85.0
occ:1.00
O B:SER349 2.2 86.4 1.0
O B:THR308 2.2 96.0 1.0
O B:THR352 2.2 63.8 1.0
O B:ILE350 2.7 75.4 1.0
SD B:MET311 2.8 92.6 1.0
C B:THR352 3.1 68.1 1.0
C B:ILE350 3.2 81.2 1.0
CE B:MET311 3.2 88.8 1.0
N B:THR352 3.3 83.0 1.0
C B:SER349 3.3 83.0 1.0
CA B:THR352 3.4 79.3 1.0
C B:THR308 3.4 95.3 1.0
CB B:THR352 3.5 76.5 1.0
CG B:MET311 3.6 94.8 1.0
CA B:ILE350 3.6 76.2 1.0
N B:ILE350 3.9 80.5 1.0
C B:GLY351 4.0 82.5 1.0
N B:GLY351 4.1 87.0 1.0
N B:ALA353 4.2 64.5 1.0
N B:ILE309 4.3 94.2 1.0
CA B:ILE309 4.4 94.3 1.0
CA B:THR308 4.4 94.2 1.0
CB B:MET311 4.4 99.9 1.0
CG2 B:THR352 4.4 80.9 1.0
CA B:SER349 4.5 85.6 1.0
CA B:GLY351 4.6 85.7 1.0
OG1 B:THR352 4.6 64.7 1.0
O B:GLY351 4.6 82.0 1.0
C B:ILE309 4.7 104.0 1.0
O B:ALA348 4.8 82.2 1.0
CA B:ALA353 4.8 78.7 1.0
C B:ALA353 4.9 103.9 1.0

Sodium binding site 4 out of 6 in 6wzb

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Sodium binding site 4 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:76.5
occ:1.00
O B:GLY306 2.6 90.1 1.0
OD2 B:ASP405 3.0 113.3 1.0
O B:ASN401 3.1 95.3 1.0
O B:ASN310 3.4 105.0 1.0
CB B:ASN401 3.5 102.9 1.0
C B:ASN401 3.5 98.8 1.0
OG B:SER278 3.6 87.0 1.0
OD1 B:ASP405 3.6 116.4 1.0
CB B:SER278 3.7 76.6 1.0
CG B:ASP405 3.7 115.0 1.0
O B:ALA307 3.7 104.6 1.0
C B:GLY306 3.7 89.2 1.0
C B:ALA307 3.9 101.8 1.0
CA B:ALA307 3.9 103.0 1.0
CA B:ASN401 4.0 103.4 1.0
CG B:MET311 4.0 94.8 1.0
O B:ILE309 4.1 109.0 1.0
N B:VAL402 4.2 97.2 1.0
N B:ALA307 4.3 97.0 1.0
CE B:MET311 4.4 88.8 1.0
C B:ASN310 4.4 107.1 1.0
CG B:ASN401 4.5 100.5 1.0
CA B:VAL402 4.5 92.0 1.0
OXT B:ASP501 4.7 103.3 1.0
N B:THR308 4.7 98.8 1.0
CA B:MET311 4.8 106.7 1.0
CG2 B:VAL402 4.8 83.6 1.0
ND2 B:ASN401 4.9 94.5 1.0
CA B:GLY306 4.9 80.9 1.0
CB B:MET311 5.0 99.9 1.0

Sodium binding site 5 out of 6 in 6wzb

Go back to Sodium Binding Sites List in 6wzb
Sodium binding site 5 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:101.0
occ:1.00
O C:SER349 2.2 100.6 1.0
O C:THR352 2.2 103.5 1.0
O C:THR308 2.2 103.6 1.0
O C:ILE350 2.6 111.5 1.0
SD C:MET311 2.9 102.4 1.0
C C:THR352 3.1 103.8 1.0
C C:ILE350 3.1 103.2 1.0
N C:THR352 3.2 97.7 1.0
C C:SER349 3.3 94.4 1.0
CE C:MET311 3.4 90.9 1.0
CA C:THR352 3.4 101.0 1.0
C C:THR308 3.4 107.3 1.0
CB C:THR352 3.5 102.2 1.0
CA C:ILE350 3.6 91.5 1.0
CG C:MET311 3.7 102.0 1.0
N C:ILE350 3.9 92.8 1.0
C C:GLY351 3.9 100.6 1.0
N C:GLY351 4.0 96.0 1.0
N C:ALA353 4.2 104.1 1.0
N C:ILE309 4.3 108.0 1.0
CA C:ILE309 4.3 102.2 1.0
CA C:THR308 4.4 108.7 1.0
CG2 C:THR352 4.4 107.9 1.0
CA C:GLY351 4.5 96.9 1.0
CB C:MET311 4.5 101.8 1.0
CA C:SER349 4.5 95.8 1.0
OG1 C:THR352 4.5 98.4 1.0
O C:GLY351 4.6 106.4 1.0
C C:ILE309 4.7 115.7 1.0
O C:ALA348 4.8 112.5 1.0
CA C:ALA353 4.8 110.2 1.0
C C:ALA353 5.0 121.5 1.0

Sodium binding site 6 out of 6 in 6wzb

Go back to Sodium Binding Sites List in 6wzb
Sodium binding site 6 out of 6 in the Crystal Structure of the Gltph V216C-G388C Mutant Cross-Linked with Divalent Mercury


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-G388C Mutant Cross-Linked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:113.1
occ:1.00
O C:GLY306 2.5 92.4 1.0
OD2 C:ASP405 3.0 131.6 1.0
O C:ASN401 3.1 114.7 1.0
O C:ASN310 3.2 121.8 1.0
C C:ASN401 3.5 108.9 1.0
CB C:ASN401 3.5 99.8 1.0
OD1 C:ASP405 3.5 130.6 1.0
C C:GLY306 3.6 90.7 1.0
CG C:ASP405 3.7 127.6 1.0
OG C:SER278 3.7 99.5 1.0
O C:ALA307 3.8 112.0 1.0
CB C:SER278 3.8 97.5 1.0
CG C:MET311 3.9 102.0 1.0
C C:ALA307 3.9 105.1 1.0
CA C:ALA307 3.9 98.4 1.0
O C:ILE309 4.0 126.2 1.0
CA C:ASN401 4.0 103.3 1.0
N C:VAL402 4.2 103.3 1.0
C C:ASN310 4.3 124.4 1.0
N C:ALA307 4.3 88.9 1.0
CE C:MET311 4.3 90.9 1.0
CG C:ASN401 4.6 101.5 1.0
CA C:VAL402 4.6 102.9 1.0
CA C:MET311 4.7 106.9 1.0
N C:THR308 4.7 105.9 1.0
O C:ASP501 4.8 122.8 1.0
CA C:GLY306 4.8 88.9 1.0
CB C:MET311 4.8 101.8 1.0
N C:MET311 4.8 116.2 1.0
ND2 C:ASN310 4.9 129.3 1.0
CG2 C:VAL402 4.9 102.7 1.0
ND2 C:ASN401 4.9 104.2 1.0
SD C:MET311 5.0 102.4 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: Wed Mar 3 15:28:46 2021

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