Atomistry » Sodium » PDB 3k9g-3la1 » 3kbc
Atomistry »
  Sodium »
    PDB 3k9g-3la1 »
      3kbc »

Sodium in PDB 3kbc: Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury

Protein crystallography data

The structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury, PDB code: 3kbc was solved by N.Reyes, C.Ginter, O.Boudker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 3.51
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 113.142, 206.780, 205.971, 90.00, 90.00, 90.00
R / Rfree (%) 26.7 / 27

Other elements in 3kbc:

The structure of Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury (pdb code 3kbc). 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury, PDB code: 3kbc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 1 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na454

b:86.1
occ:1.00
O A:GLY306 2.1 0.3 1.0
O A:ASN310 2.5 0.8 1.0
OD1 A:ASP405 2.7 0.1 1.0
O A:ASN401 3.0 0.4 1.0
OD2 A:ASP405 3.1 0.7 1.0
O A:ILE309 3.2 1.0 1.0
CG A:ASP405 3.3 1.0 1.0
C A:GLY306 3.3 0.3 1.0
C A:ASN310 3.4 0.7 1.0
C A:ASN401 3.6 0.4 1.0
CB A:ASN401 3.9 0.6 1.0
CG A:MET311 4.0 0.2 1.0
CA A:ASN401 4.0 0.5 1.0
CA A:MET311 4.1 0.0 1.0
N A:MET311 4.1 0.9 1.0
CA A:GLY306 4.2 0.2 1.0
CB A:ASN310 4.3 0.5 1.0
N A:ALA307 4.3 0.4 1.0
C A:ILE309 4.3 0.9 1.0
OG A:SER278 4.3 0.2 1.0
CA A:ASN310 4.4 0.5 1.0
CA A:ALA307 4.5 0.6 1.0
CG A:ASN310 4.5 0.3 1.0
N A:VAL402 4.5 0.3 1.0
C A:ALA307 4.6 0.7 1.0
CB A:MET311 4.6 0.2 1.0
O A:ALA307 4.7 0.8 1.0
CB A:ASP405 4.7 0.6 1.0
OD1 A:ASN310 4.8 0.8 1.0
N A:ASN310 4.8 0.2 1.0
CG A:ASN401 4.9 0.6 1.0
CA A:VAL402 5.0 0.2 1.0

Sodium binding site 2 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 2 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na453

b:97.5
occ:1.00
O A:SER349 2.3 99.1 1.0
C A:ILE350 2.5 99.1 1.0
O A:THR352 2.6 100.0 1.0
O A:ILE350 2.7 99.1 1.0
O A:THR308 2.7 0.3 1.0
N A:GLY351 3.0 99.2 1.0
CA A:ILE350 3.0 99.0 1.0
N A:THR352 3.0 99.9 1.0
C A:SER349 3.2 99.0 1.0
C A:GLY351 3.2 99.7 1.0
C A:THR352 3.4 0.1 1.0
N A:ILE350 3.5 99.0 1.0
CA A:GLY351 3.6 99.5 1.0
CA A:THR352 3.6 0.1 1.0
SD A:MET311 3.6 0.8 1.0
C A:THR308 3.8 0.3 1.0
O A:GLY351 3.9 99.8 1.0
CB A:THR352 4.0 0.1 1.0
CG A:MET311 4.3 0.2 1.0
CB A:ILE350 4.4 99.0 1.0
CA A:ILE309 4.5 0.6 1.0
N A:ILE309 4.5 0.5 1.0
CA A:SER349 4.6 99.0 1.0
CG2 A:ILE350 4.6 99.0 1.0
N A:ALA353 4.7 0.3 1.0
CA A:THR308 4.7 0.2 1.0
OG1 A:THR352 4.8 0.1 1.0

Sodium binding site 3 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 3 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na454

b:85.4
occ:1.00
O B:GLY306 2.1 0.5 1.0
O B:ASN310 2.5 0.6 1.0
OD1 B:ASP405 2.7 0.8 1.0
O B:ASN401 3.1 0.6 1.0
OD2 B:ASP405 3.1 0.0 1.0
O B:ILE309 3.2 0.9 1.0
CG B:ASP405 3.3 0.7 1.0
C B:GLY306 3.3 0.6 1.0
C B:ASN310 3.4 0.5 1.0
C B:ASN401 3.7 0.5 1.0
CB B:ASN401 3.9 0.5 1.0
CG B:MET311 4.0 0.1 1.0
CA B:ASN401 4.1 0.5 1.0
CA B:MET311 4.1 0.8 1.0
N B:MET311 4.1 0.7 1.0
CA B:GLY306 4.1 0.5 1.0
CB B:ASN310 4.2 0.3 1.0
C B:ILE309 4.3 0.9 1.0
N B:ALA307 4.3 0.7 1.0
CA B:ASN310 4.3 0.3 1.0
OG B:SER278 4.4 0.6 1.0
CA B:ALA307 4.5 0.8 1.0
CG B:ASN310 4.5 0.2 1.0
C B:ALA307 4.5 0.9 1.0
N B:VAL402 4.6 0.4 1.0
CB B:MET311 4.6 0.9 1.0
O B:ALA307 4.7 1.0 1.0
OD1 B:ASN310 4.8 0.8 1.0
CB B:ASP405 4.8 0.6 1.0
N B:ASN310 4.8 0.1 1.0
CG B:ASN401 4.9 0.6 1.0
ND2 B:ASN310 5.0 0.5 1.0

Sodium binding site 4 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 4 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na453

b:98.1
occ:1.00
O B:SER349 2.2 98.9 1.0
C B:ILE350 2.5 99.4 1.0
O B:THR352 2.6 0.2 1.0
O B:ILE350 2.6 99.4 1.0
O B:THR308 2.7 0.5 1.0
N B:GLY351 2.9 99.5 1.0
CA B:ILE350 2.9 99.2 1.0
N B:THR352 3.0 0.1 1.0
C B:SER349 3.1 99.0 1.0
C B:GLY351 3.2 99.9 1.0
N B:ILE350 3.4 99.1 1.0
C B:THR352 3.5 0.2 1.0
CA B:GLY351 3.5 99.8 1.0
CA B:THR352 3.6 0.2 1.0
SD B:MET311 3.6 0.4 1.0
C B:THR308 3.8 0.5 1.0
O B:GLY351 3.9 0.0 1.0
CB B:THR352 3.9 0.1 1.0
CG B:MET311 4.3 0.1 1.0
CB B:ILE350 4.3 99.2 1.0
CA B:ILE309 4.5 0.7 1.0
CA B:SER349 4.5 98.9 1.0
N B:ILE309 4.6 0.6 1.0
CG2 B:ILE350 4.6 98.9 1.0
N B:ALA353 4.7 0.3 1.0
CA B:THR308 4.8 0.4 1.0
OG1 B:THR352 4.8 0.3 1.0

Sodium binding site 5 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 5 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na454

b:86.8
occ:1.00
O C:GLY306 2.1 0.3 1.0
O C:ASN310 2.5 0.8 1.0
OD1 C:ASP405 2.6 0.2 1.0
O C:ASN401 3.0 0.5 1.0
OD2 C:ASP405 3.1 0.3 1.0
O C:ILE309 3.2 0.2 1.0
CG C:ASP405 3.2 0.0 1.0
C C:GLY306 3.3 0.4 1.0
C C:ASN310 3.5 0.8 1.0
C C:ASN401 3.7 0.5 1.0
CB C:ASN401 3.9 0.5 1.0
CG C:MET311 4.0 0.2 1.0
CA C:ASN401 4.1 0.5 1.0
CA C:GLY306 4.1 0.3 1.0
CA C:MET311 4.2 0.0 1.0
N C:MET311 4.2 0.9 1.0
CB C:ASN310 4.3 0.7 1.0
N C:ALA307 4.3 0.5 1.0
C C:ILE309 4.3 0.1 1.0
OG C:SER278 4.3 0.8 1.0
CA C:ASN310 4.4 0.6 1.0
CA C:ALA307 4.4 0.7 1.0
CG C:ASN310 4.5 0.7 1.0
C C:ALA307 4.5 0.9 1.0
N C:VAL402 4.5 0.5 1.0
O C:ALA307 4.7 0.9 1.0
CB C:MET311 4.7 0.1 1.0
CB C:ASP405 4.7 0.8 1.0
OD1 C:ASN310 4.8 0.6 1.0
N C:ASN310 4.8 0.3 1.0
CG C:ASN401 4.9 0.5 1.0
CA C:VAL402 5.0 0.5 1.0
ND2 C:ASN310 5.0 0.6 1.0

Sodium binding site 6 out of 6 in 3kbc

Go back to Sodium Binding Sites List in 3kbc
Sodium binding site 6 out of 6 in the Crystal Structure of Gltph K55C-A364C Mutant Crosslinked 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 Gltph K55C-A364C Mutant Crosslinked with Divalent Mercury within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na453

b:98.6
occ:1.00
O C:SER349 2.2 99.1 1.0
C C:ILE350 2.5 99.2 1.0
O C:ILE350 2.6 99.2 1.0
O C:THR352 2.6 0.2 1.0
O C:THR308 2.7 0.5 1.0
CA C:ILE350 2.9 99.1 1.0
N C:GLY351 2.9 99.3 1.0
N C:THR352 3.0 99.8 1.0
C C:SER349 3.1 99.1 1.0
C C:GLY351 3.2 99.7 1.0
N C:ILE350 3.4 99.1 1.0
C C:THR352 3.5 0.2 1.0
CA C:GLY351 3.5 99.5 1.0
CA C:THR352 3.6 0.1 1.0
SD C:MET311 3.6 0.3 1.0
C C:THR308 3.8 0.5 1.0
O C:GLY351 3.9 99.7 1.0
CB C:THR352 4.0 0.1 1.0
CB C:ILE350 4.3 99.1 1.0
CG C:MET311 4.3 0.2 1.0
CA C:ILE309 4.5 0.9 1.0
CA C:SER349 4.5 99.0 1.0
N C:ILE309 4.6 0.7 1.0
CG2 C:ILE350 4.6 99.0 1.0
CA C:THR308 4.8 0.4 1.0
N C:ALA353 4.8 0.3 1.0
OG1 C:THR352 4.8 0.1 1.0

Reference:

N.Reyes, C.Ginter, O.Boudker. Transport Mechanism of A Bacterial Homologue of Glutamate Transporters. Nature V. 462 880 2009.
ISSN: ISSN 0028-0836
PubMed: 19924125
DOI: 10.1038/NATURE08616
Page generated: Tue Dec 15 06:16:11 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy