Atomistry » Sodium » PDB 3v45-3vi2 » 3v8f
Atomistry »
  Sodium »
    PDB 3v45-3vi2 »
      3v8f »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy