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Sodium in PDB 3v8f: Crystal Structure of Crosslinked Gltph V216C-M385C Mutant

Protein crystallography data

The structure of Crystal Structure of Crosslinked Gltph V216C-M385C Mutant, PDB code: 3v8f 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) 30.00 / 3.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.300, 199.810, 111.251, 90.00, 117.08, 90.00
R / Rfree (%) 24.3 / 25.5

Other elements in 3v8f:

The structure of Crystal Structure of Crosslinked Gltph V216C-M385C Mutant also contains other interesting chemical elements:

Mercury (Hg) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant (pdb code 3v8f). 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 Crosslinked Gltph V216C-M385C Mutant, PDB code: 3v8f:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 1 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na902

b:0.6
occ:1.00
 O A:GLY306 2.3 0.9 1.0
O A:ASN401 2.8 0.1 1.0
OG A:SER278 3.0 1.0 1.0
OD2 A:ASP405 3.1 0.2 1.0
O A:ASN310 3.2 0.1 1.0
C A:ASN401 3.4 0.3 1.0
O A:ALA307 3.4 0.3 1.0
C A:GLY306 3.5 0.1 1.0
OD1 A:ASP405 3.6 0.8 1.0
CB A:ASN401 3.7 0.5 1.0
CG A:ASP405 3.7 0.3 1.0
C A:ALA307 3.7 0.2 1.0
CA A:ALA307 3.9 0.9 1.0
CE A:MET311 4.0 0.3 1.0
CG A:MET311 4.0 0.7 1.0
CA A:ASN401 4.0 0.6 1.0
C A:ASN310 4.1 0.0 1.0
CB A:SER278 4.1 0.6 1.0
N A:ALA307 4.1 0.2 1.0
N A:VAL402 4.2 0.7 1.0
O A:ILE309 4.2 0.1 1.0
CA A:VAL402 4.5 0.9 1.0
CA A:MET311 4.5 0.4 1.0
N A:THR308 4.6 0.7 1.0
N A:MET311 4.6 0.6 1.0
CA A:GLY306 4.7 0.7 1.0
CB A:MET311 4.7 0.5 1.0
CG A:ASN401 4.7 0.3 1.0
O A:THR308 4.7 0.9 1.0
SD A:MET311 4.8 0.1 1.0

Sodium binding site 2 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 2 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:0.7
occ:1.00
 O A:SER349 2.3 0.8 1.0
O A:THR308 2.4 0.9 1.0
O A:THR352 2.4 0.9 1.0
N A:THR352 3.1 0.4 1.0
SD A:MET311 3.1 0.1 1.0
C A:THR352 3.3 0.4 1.0
C A:THR308 3.3 0.4 1.0
CG A:MET311 3.3 0.7 1.0
O A:ILE350 3.4 0.5 1.0
C A:SER349 3.4 0.5 1.0
C A:ILE350 3.5 0.5 1.0
CA A:THR352 3.6 0.3 1.0
N A:GLY351 3.8 0.8 1.0
CB A:THR352 3.9 0.4 1.0
C A:GLY351 3.9 0.6 1.0
CA A:ILE350 4.0 0.1 1.0
N A:ILE309 4.1 0.6 1.0
N A:ILE350 4.1 0.8 1.0
CA A:GLY351 4.2 0.8 1.0
CA A:THR308 4.2 0.4 1.0
CA A:ILE309 4.3 0.7 1.0
CB A:MET311 4.5 0.5 1.0
CA A:SER349 4.6 0.3 1.0
N A:ALA353 4.6 0.6 1.0
C A:ILE309 4.6 0.9 1.0
CE A:MET311 4.7 0.3 1.0
CG2 A:THR352 4.7 0.0 1.0
N A:ASN310 4.7 0.8 1.0
CB A:THR308 4.9 0.6 1.0
O A:GLY351 4.9 0.8 1.0
OG1 A:THR352 5.0 0.9 1.0

Sodium binding site 3 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 3 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na902

b:0.5
occ:1.00
 O B:GLY306 2.3 0.1 1.0
OG B:SER278 3.0 0.8 1.0
O B:ASN401 3.0 0.0 1.0
OD2 B:ASP405 3.0 0.8 1.0
O B:ALA307 3.2 0.9 1.0
O B:ASN310 3.3 0.0 1.0
C B:GLY306 3.4 0.1 1.0
C B:ASN401 3.5 0.5 1.0
OD1 B:ASP405 3.5 0.8 1.0
C B:ALA307 3.6 0.2 1.0
CG B:ASP405 3.7 0.9 1.0
CB B:ASN401 3.8 0.4 1.0
CA B:ALA307 3.8 0.4 1.0
CE B:MET311 4.0 0.0 1.0
N B:ALA307 4.0 0.1 1.0
CG B:MET311 4.1 0.2 1.0
CB B:SER278 4.1 0.3 1.0
C B:ASN310 4.1 0.9 1.0
CA B:ASN401 4.1 0.9 1.0
N B:VAL402 4.2 0.2 1.0
O B:ILE309 4.3 0.2 1.0
N B:THR308 4.5 0.8 1.0
CA B:VAL402 4.5 0.7 1.0
CA B:GLY306 4.6 0.3 1.0
CA B:MET311 4.7 0.6 1.0
O B:THR308 4.7 0.3 1.0
N B:MET311 4.7 0.7 1.0
SD B:MET311 4.8 1.0 1.0
CB B:MET311 4.8 0.5 1.0
CG B:ASN401 4.9 0.5 1.0

Sodium binding site 4 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 4 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na903

b:0.7
occ:1.00
 O B:SER349 2.2 0.5 1.0
O B:THR352 2.3 0.2 1.0
O B:THR308 2.4 0.3 1.0
N B:THR352 3.0 0.3 1.0
SD B:MET311 3.2 1.0 1.0
C B:THR352 3.3 0.8 1.0
O B:ILE350 3.4 0.8 1.0
C B:THR308 3.4 0.6 1.0
C B:ILE350 3.4 1.0 1.0
CG B:MET311 3.4 0.2 1.0
C B:SER349 3.4 0.0 1.0
CA B:THR352 3.5 0.4 1.0
N B:GLY351 3.7 0.1 1.0
C B:GLY351 3.8 0.4 1.0
CB B:THR352 3.8 0.3 1.0
CA B:ILE350 4.0 0.4 1.0
CA B:GLY351 4.0 0.8 1.0
N B:ILE350 4.1 0.0 1.0
N B:ILE309 4.2 0.5 1.0
CA B:THR308 4.3 0.7 1.0
CA B:ILE309 4.4 0.7 1.0
CB B:MET311 4.5 0.5 1.0
N B:ALA353 4.5 0.5 1.0
CA B:SER349 4.6 0.8 1.0
CG2 B:THR352 4.7 0.6 1.0
C B:ILE309 4.7 0.7 1.0
CE B:MET311 4.8 0.0 1.0
N B:ASN310 4.8 0.7 1.0
O B:GLY351 4.8 0.7 1.0
OG1 B:THR352 5.0 0.6 1.0
CB B:THR308 5.0 0.9 1.0

Sodium binding site 5 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 5 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na902

b:0.8
occ:1.00
 O C:GLY306 2.2 0.2 1.0
O C:ASN401 3.0 0.9 1.0
OG C:SER278 3.0 0.2 1.0
OD2 C:ASP405 3.1 0.5 1.0
O C:ASN310 3.2 0.3 1.0
O C:ALA307 3.3 0.9 1.0
C C:GLY306 3.4 0.4 1.0
C C:ASN401 3.5 0.1 1.0
OD1 C:ASP405 3.5 0.5 1.0
C C:ALA307 3.7 0.9 1.0
CG C:ASP405 3.7 0.7 1.0
CB C:ASN401 3.8 0.2 1.0
CA C:ALA307 3.8 0.3 1.0
CG C:MET311 4.0 1.0 1.0
CE C:MET311 4.0 0.3 1.0
N C:ALA307 4.0 0.0 1.0
C C:ASN310 4.0 0.4 1.0
CA C:ASN401 4.1 0.2 1.0
CB C:SER278 4.1 0.1 1.0
O C:ILE309 4.1 0.8 1.0
N C:VAL402 4.3 0.3 1.0
N C:THR308 4.5 0.5 1.0
CA C:MET311 4.5 0.1 1.0
CA C:GLY306 4.6 0.5 1.0
CA C:VAL402 4.6 0.1 1.0
N C:MET311 4.6 0.1 1.0
O C:THR308 4.7 0.1 1.0
SD C:MET311 4.7 0.2 1.0
CB C:MET311 4.7 0.7 1.0
CG C:ASN401 4.9 0.8 1.0

Sodium binding site 6 out of 6 in 3v8f

Go back to Sodium Binding Sites List in 3v8f
Sodium binding site 6 out of 6 in the Crystal Structure of Crosslinked Gltph V216C-M385C Mutant


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 Crosslinked Gltph V216C-M385C Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na903

b:0.9
occ:1.00
 O C:SER349 2.2 0.7 1.0
O C:THR308 2.3 0.1 1.0
O C:THR352 2.6 0.4 1.0
SD C:MET311 3.0 0.2 1.0
N C:THR352 3.1 0.6 1.0
CG C:MET311 3.3 1.0 1.0
O C:ILE350 3.3 0.8 1.0
C C:THR308 3.3 0.0 1.0
C C:SER349 3.3 0.5 1.0
C C:ILE350 3.4 0.6 1.0
C C:THR352 3.5 0.6 1.0
CA C:THR352 3.7 0.3 1.0
N C:GLY351 3.7 0.6 1.0
CA C:ILE350 3.9 0.8 1.0
CB C:THR352 3.9 0.3 1.0
C C:GLY351 3.9 0.9 1.0
N C:ILE350 4.0 0.1 1.0
N C:ILE309 4.0 0.3 1.0
CA C:GLY351 4.1 0.3 1.0
CA C:ILE309 4.3 0.1 1.0
CA C:THR308 4.3 0.4 1.0
CB C:MET311 4.3 0.7 1.0
CA C:SER349 4.5 1.0 1.0
C C:ILE309 4.5 0.2 1.0
N C:ASN310 4.6 0.3 1.0
CE C:MET311 4.7 0.3 1.0
N C:ALA353 4.7 0.0 1.0
CG2 C:THR352 4.8 0.9 1.0
O C:GLY351 4.9 0.6 1.0
N C:MET311 4.9 0.1 1.0
CB C:THR308 5.0 0.2 1.0
OG1 C:THR352 5.0 0.1 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 13:39:46 2024

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