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Sodium in PDB 3v8g: Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)

Protein crystallography data

The structure of Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph), PDB code: 3v8g was solved by G.Verdon, O.Boudker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 4.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 203.692, 119.627, 223.415, 90.00, 113.77, 90.00
R / Rfree (%) 25.5 / 29.4

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) (pdb code 3v8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph), PDB code: 3v8g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 3v8g

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Sodium binding site 1 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:0.4
occ:1.00
 O A:GLY306 2.5 0.6 1.0
O A:ASN310 2.8 0.1 1.0
O A:ASN401 3.1 0.7 1.0
OD2 A:ASP405 3.5 0.4 1.0
O A:ILE309 3.6 0.7 1.0
OD1 A:ASP405 3.7 0.2 1.0
C A:GLY306 3.7 0.9 1.0
C A:ASN401 3.8 0.5 1.0
OG A:SER278 3.8 0.5 1.0
C A:ASN310 3.8 0.6 1.0
CB A:ASN401 3.9 0.3 1.0
CG A:ASP405 4.0 0.9 1.0
CG A:MET311 4.0 0.1 1.0
CE A:MET311 4.2 0.8 1.0
CA A:ASN401 4.2 0.8 1.0
O A:ALA307 4.3 0.0 1.0
CA A:MET311 4.4 0.7 1.0
C A:ALA307 4.4 0.4 1.0
N A:MET311 4.5 0.5 1.0
CA A:ALA307 4.5 0.1 1.0
C A:ILE309 4.6 0.4 1.0
N A:ALA307 4.6 0.5 1.0
CG A:ASN401 4.6 0.6 1.0
CA A:GLY306 4.7 0.7 1.0
CB A:MET311 4.7 0.4 1.0
N A:VAL402 4.8 0.3 1.0
CB A:SER278 4.8 0.1 1.0
CA A:ASN310 4.8 0.1 1.0
SD A:MET311 4.8 0.8 1.0

Sodium binding site 2 out of 12 in 3v8g

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Sodium binding site 2 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:0.9
occ:1.00
 O A:THR308 2.2 0.1 1.0
O A:THR352 2.3 0.7 1.0
O A:ILE350 2.6 0.2 1.0
O A:SER349 2.9 0.9 1.0
C A:ILE350 3.1 0.2 1.0
C A:THR308 3.2 0.5 1.0
C A:THR352 3.4 0.1 1.0
N A:THR352 3.5 0.1 1.0
SD A:MET311 3.5 0.8 1.0
C A:GLY351 3.6 0.8 1.0
CA A:ILE350 3.7 0.5 1.0
N A:GLY351 3.8 0.5 1.0
CA A:THR352 3.9 0.6 1.0
CG A:MET311 3.9 0.1 1.0
C A:SER349 3.9 1.0 1.0
O A:GLY351 3.9 0.2 1.0
CA A:THR308 4.0 0.8 1.0
N A:ILE309 4.0 0.5 1.0
CA A:GLY351 4.1 0.9 1.0
CA A:ILE309 4.2 0.7 1.0
N A:ILE350 4.3 0.9 1.0
CB A:THR352 4.3 0.1 1.0
CB A:THR308 4.4 0.8 1.0
N A:ALA353 4.6 0.1 1.0
C A:ILE309 4.9 0.4 1.0

Sodium binding site 3 out of 12 in 3v8g

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Sodium binding site 3 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:0.9
occ:1.00
 O B:GLY306 2.5 0.1 1.0
O B:ASN310 2.8 0.4 1.0
O B:ASN401 3.1 0.7 1.0
OD2 B:ASP405 3.5 0.6 1.0
O B:ILE309 3.6 0.1 1.0
OD1 B:ASP405 3.7 0.3 1.0
C B:GLY306 3.7 0.4 1.0
OG B:SER278 3.8 0.5 1.0
C B:ASN401 3.8 0.7 1.0
C B:ASN310 3.9 0.6 1.0
CB B:ASN401 3.9 0.6 1.0
CG B:ASP405 4.0 0.7 1.0
CG B:MET311 4.1 0.1 1.0
CE B:MET311 4.1 0.6 1.0
CA B:ASN401 4.2 0.3 1.0
O B:ALA307 4.3 0.3 1.0
C B:ALA307 4.4 0.4 1.0
CA B:MET311 4.5 0.8 1.0
CA B:ALA307 4.5 0.1 1.0
N B:ALA307 4.5 0.6 1.0
N B:MET311 4.6 0.5 1.0
C B:ILE309 4.6 0.5 1.0
CG B:ASN401 4.7 0.2 1.0
CA B:GLY306 4.7 0.4 1.0
CB B:SER278 4.8 0.3 1.0
CB B:MET311 4.8 0.9 1.0
N B:VAL402 4.8 0.1 1.0
SD B:MET311 4.9 0.6 1.0
CA B:ASN310 4.9 0.6 1.0
N B:THR308 5.0 1.0 1.0

Sodium binding site 4 out of 12 in 3v8g

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Sodium binding site 4 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na503

b:0.8
occ:1.00
 O B:THR308 2.1 0.1 1.0
O B:THR352 2.4 0.0 1.0
O B:ILE350 2.6 0.5 1.0
O B:SER349 2.9 0.5 1.0
C B:ILE350 3.1 0.1 1.0
C B:THR308 3.1 0.6 1.0
C B:THR352 3.4 0.7 1.0
N B:THR352 3.5 0.3 1.0
SD B:MET311 3.5 0.6 1.0
C B:GLY351 3.6 0.0 1.0
CA B:ILE350 3.7 0.0 1.0
N B:GLY351 3.8 0.1 1.0
CG B:MET311 3.9 0.1 1.0
CA B:THR352 3.9 0.7 1.0
C B:SER349 3.9 0.3 1.0
CA B:THR308 3.9 0.8 1.0
O B:GLY351 4.0 0.5 1.0
N B:ILE309 4.0 0.8 1.0
CA B:GLY351 4.1 1.0 1.0
CA B:ILE309 4.2 0.2 1.0
N B:ILE350 4.3 0.2 1.0
CB B:THR352 4.3 0.8 1.0
CB B:THR308 4.4 0.6 1.0
N B:ALA353 4.6 0.2 1.0
C B:ILE309 4.9 0.5 1.0

Sodium binding site 5 out of 12 in 3v8g

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Sodium binding site 5 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na502

b:0.8
occ:1.00
 O C:GLY306 2.3 0.1 1.0
OD2 C:ASP405 2.9 0.7 1.0
O C:ASN310 3.1 0.0 1.0
C C:GLY306 3.4 0.9 1.0
CB C:ASN401 3.7 0.3 1.0
O C:ASN401 3.8 0.2 1.0
CA C:ALA307 3.8 0.0 1.0
O C:ILE309 3.9 0.0 1.0
CG C:ASP405 3.9 0.4 1.0
C C:ALA307 3.9 0.7 1.0
C C:ASN310 4.0 0.7 1.0
C C:ASN401 4.0 0.5 1.0
N C:THR308 4.0 0.5 1.0
CG C:MET311 4.0 0.9 1.0
N C:ALA307 4.1 0.6 1.0
OD1 C:ASP405 4.1 0.8 1.0
CE C:MET311 4.2 0.7 1.0
CA C:MET311 4.4 0.3 1.0
CA C:ASN401 4.4 1.0 1.0
OG C:SER278 4.4 0.4 1.0
O C:ALA307 4.4 0.4 1.0
O C:THR308 4.5 0.0 1.0
N C:MET311 4.5 0.8 1.0
C C:THR308 4.6 0.4 1.0
N C:VAL402 4.6 0.2 1.0
CA C:GLY306 4.6 0.0 1.0
CB C:MET311 4.6 0.4 1.0
CA C:THR308 4.7 0.9 1.0
C C:ILE309 4.7 0.3 1.0
SD C:MET311 4.8 0.5 1.0
CA C:VAL402 4.9 0.6 1.0
CG C:ASN401 4.9 0.2 1.0

Sodium binding site 6 out of 12 in 3v8g

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Sodium binding site 6 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na503

b:0.6
occ:1.00
 O C:THR308 2.2 0.0 1.0
O C:ILE350 2.3 0.0 1.0
O C:THR352 2.3 0.4 1.0
O C:SER349 2.7 0.3 1.0
C C:THR308 3.0 0.4 1.0
C C:ILE350 3.1 0.7 1.0
N C:THR352 3.3 0.5 1.0
C C:THR352 3.4 0.4 1.0
C C:SER349 3.7 0.7 1.0
N C:ILE309 3.7 0.5 1.0
SD C:MET311 3.7 0.5 1.0
CA C:ILE309 3.7 0.2 1.0
CA C:THR352 3.8 0.5 1.0
CG C:MET311 3.8 0.9 1.0
CA C:ILE350 3.8 0.8 1.0
C C:GLY351 3.9 0.6 1.0
N C:GLY351 3.9 0.1 1.0
CA C:THR308 3.9 0.9 1.0
CB C:THR352 4.1 0.4 1.0
N C:ILE350 4.2 0.8 1.0
CA C:GLY351 4.2 0.6 1.0
CB C:THR308 4.3 0.4 1.0
N C:ALA353 4.6 0.4 1.0
C C:ILE309 4.6 0.3 1.0
OG1 C:THR352 4.6 0.5 1.0
O C:GLY351 4.6 0.4 1.0
CA C:SER349 4.8 0.1 1.0
CB C:ILE309 4.8 0.0 1.0
N C:ASN310 4.9 0.8 1.0
CG1 C:ILE309 5.0 0.0 1.0

Sodium binding site 7 out of 12 in 3v8g

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Sodium binding site 7 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na502

b:0.1
occ:1.00
 O D:GLY306 2.5 0.1 1.0
O D:ASN310 2.8 0.2 1.0
O D:ASN401 3.1 0.6 1.0
OD2 D:ASP405 3.6 0.1 1.0
O D:ILE309 3.6 0.6 1.0
OD1 D:ASP405 3.7 0.1 1.0
C D:GLY306 3.8 0.7 1.0
OG D:SER278 3.8 0.8 1.0
C D:ASN401 3.8 0.4 1.0
C D:ASN310 3.8 0.9 1.0
CB D:ASN401 3.9 0.4 1.0
CG D:MET311 4.0 0.1 1.0
CG D:ASP405 4.0 0.1 1.0
CE D:MET311 4.1 0.3 1.0
CA D:ASN401 4.2 0.9 1.0
O D:ALA307 4.3 0.9 1.0
CA D:MET311 4.4 0.8 1.0
C D:ALA307 4.4 0.8 1.0
N D:MET311 4.5 0.9 1.0
CA D:ALA307 4.6 0.4 1.0
C D:ILE309 4.6 0.5 1.0
N D:ALA307 4.6 0.6 1.0
CG D:ASN401 4.6 0.5 1.0
CB D:MET311 4.7 0.6 1.0
CA D:GLY306 4.8 0.5 1.0
N D:VAL402 4.8 0.5 1.0
CB D:SER278 4.8 0.3 1.0
SD D:MET311 4.8 0.2 1.0
CA D:ASN310 4.8 0.5 1.0

Sodium binding site 8 out of 12 in 3v8g

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Sodium binding site 8 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:0.0
occ:1.00
 O D:THR308 2.1 0.8 1.0
O D:THR352 2.4 0.2 1.0
O D:ILE350 2.6 0.1 1.0
O D:SER349 2.9 0.1 1.0
C D:ILE350 3.1 0.1 1.0
C D:THR308 3.1 0.2 1.0
SD D:MET311 3.4 0.2 1.0
C D:THR352 3.4 0.7 1.0
N D:THR352 3.5 0.8 1.0
C D:GLY351 3.6 1.0 1.0
CA D:ILE350 3.7 1.0 1.0
N D:GLY351 3.8 0.3 1.0
CG D:MET311 3.8 0.1 1.0
C D:SER349 3.9 0.0 1.0
CA D:THR352 3.9 1.0 1.0
O D:GLY351 4.0 0.6 1.0
CA D:THR308 4.0 0.1 1.0
N D:ILE309 4.0 0.8 1.0
CA D:GLY351 4.1 0.9 1.0
CA D:ILE309 4.2 0.4 1.0
N D:ILE350 4.3 0.5 1.0
CB D:THR352 4.3 0.3 1.0
CB D:THR308 4.4 0.7 1.0
N D:ALA353 4.6 0.6 1.0
C D:ILE309 4.9 0.5 1.0

Sodium binding site 9 out of 12 in 3v8g

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Sodium binding site 9 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na502

b:0.5
occ:1.00
 O E:GLY306 2.5 0.8 1.0
O E:ASN310 2.8 1.0 1.0
O E:ASN401 3.1 0.5 1.0
OD2 E:ASP405 3.5 1.0 1.0
O E:ILE309 3.6 0.0 1.0
OD1 E:ASP405 3.6 0.9 1.0
C E:GLY306 3.7 0.1 1.0
C E:ASN401 3.8 0.3 1.0
OG E:SER278 3.8 0.7 1.0
C E:ASN310 3.8 0.3 1.0
CB E:ASN401 3.9 0.1 1.0
CG E:ASP405 4.0 0.7 1.0
CG E:MET311 4.1 0.2 1.0
CE E:MET311 4.2 0.2 1.0
CA E:ASN401 4.2 0.9 1.0
O E:ALA307 4.3 0.6 1.0
C E:ALA307 4.4 0.4 1.0
CA E:MET311 4.5 0.4 1.0
CA E:ALA307 4.5 0.9 1.0
N E:MET311 4.5 0.4 1.0
C E:ILE309 4.6 0.6 1.0
N E:ALA307 4.6 0.9 1.0
CG E:ASN401 4.7 0.7 1.0
CA E:GLY306 4.7 1.0 1.0
CB E:MET311 4.8 0.2 1.0
N E:VAL402 4.8 0.2 1.0
CB E:SER278 4.8 0.8 1.0
CA E:ASN310 4.8 0.9 1.0
SD E:MET311 4.9 0.7 1.0

Sodium binding site 10 out of 12 in 3v8g

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Sodium binding site 10 out of 12 in the Crystal Structure of An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph)


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 An Asymmetric Trimer of A Glutamate Transporter Homologue (Gltph) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na503

b:0.5
occ:1.00
 O E:THR308 2.1 0.3 1.0
O E:THR352 2.4 0.4 1.0
O E:ILE350 2.6 0.7 1.0
O E:SER349 2.9 0.0 1.0
C E:ILE350 3.1 0.6 1.0
C E:THR308 3.1 0.1 1.0
C E:THR352 3.4 0.2 1.0
SD E:MET311 3.4 0.7 1.0
N E:THR352 3.5 0.6 1.0
C E:GLY351 3.6 0.2 1.0
CA E:ILE350 3.7 1.0 1.0
N E:GLY351 3.8 0.4 1.0
CG E:MET311 3.9 0.2 1.0
CA E:THR352 3.9 0.2 1.0
C E:SER349 3.9 0.3 1.0
CA E:THR308 3.9 0.2 1.0
O E:GLY351 4.0 0.1 1.0
N E:ILE309 4.0 0.7 1.0
CA E:GLY351 4.2 0.8 1.0
CA E:ILE309 4.2 0.3 1.0
N E:ILE350 4.3 0.3 1.0
CB E:THR352 4.3 0.3 1.0
CB E:THR308 4.4 0.2 1.0
N E:ALA353 4.6 1.0 1.0
C E:ILE309 5.0 0.6 1.0

Reference:

G.Verdon, O.Boudker. Crystal Structure of An Asymmetric Trimer of A Bacterial Glutamate Transporter Homolog. Nat.Struct.Mol.Biol. V. 19 355 2012.
ISSN: ISSN 1545-9993
PubMed: 22343718
DOI: 10.1038/NSMB.2233
Page generated: Mon Oct 7 13:39:53 2024

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