Atomistry » Sodium » PDB 4hfd-4i05 » 4hqj
Atomistry »
  Sodium »
    PDB 4hfd-4i05 »
      4hqj »

Sodium in PDB 4hqj: Crystal Structure of Na+,K+-Atpase in the Na+-Bound State

Enzymatic activity of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State

All present enzymatic activity of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State, PDB code: 4hqj was solved by M.Nyblom, L.Reinhard, P.Gourdon, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.00 / 4.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 109.073, 219.578, 261.958, 90.00, 90.00, 90.00
R / Rfree (%) 26.1 / 28.8

Other elements in 4hqj:

The structure of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State also contains other interesting chemical elements:

Fluorine (F) 8 atoms
Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State (pdb code 4hqj). 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 Na+,K+-Atpase in the Na+-Bound State, PDB code: 4hqj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 1 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1104

b:0.6
occ:1.00
 O A:ALA323 2.4 0.3 1.0
O A:VAL325 2.4 0.2 1.0
OD2 A:ASP804 2.4 0.9 1.0
OE2 A:GLU327 2.4 0.6 1.0
O A:VAL322 2.4 0.9 1.0
OD1 A:ASP804 3.0 0.2 1.0
CG A:ASP804 3.0 0.4 1.0
C A:VAL325 3.2 0.4 1.0
C A:ALA323 3.4 0.8 1.0
C A:VAL322 3.6 0.2 1.0
CD A:GLU327 3.6 0.0 1.0
N A:VAL325 3.9 0.9 1.0
N A:PRO326 3.9 0.4 1.0
CA A:ALA323 3.9 0.2 1.0
CA A:PRO326 4.0 0.6 1.0
CA A:VAL325 4.1 0.3 1.0
N A:ALA323 4.2 0.0 1.0
CG A:GLU327 4.3 0.1 1.0
N A:GLU327 4.3 0.5 1.0
NA A:NA1105 4.4 0.3 1.0
CB A:ASP804 4.5 0.8 1.0
C A:ASN324 4.6 0.3 1.0
N A:ASN324 4.6 0.9 1.0
OE1 A:GLU327 4.6 1.0 1.0
C A:PRO326 4.7 0.6 1.0
O A:ASP804 4.7 0.6 1.0
OD2 A:ASP808 4.7 0.7 1.0
CA A:VAL322 4.8 0.6 1.0
CB A:VAL325 4.9 1.0 1.0
CA A:ASN324 5.0 0.2 1.0
CG1 A:VAL322 5.0 0.5 1.0

Sodium binding site 2 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 2 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1105

b:0.3
occ:1.00
 OG A:SER775 2.4 0.2 1.0
OD1 A:ASN776 2.4 0.9 1.0
OE2 A:GLU779 2.4 0.8 1.0
OD1 A:ASP804 2.4 0.2 1.0
CD A:GLU779 3.2 0.4 1.0
O A:ALA323 3.2 0.3 1.0
OE1 A:GLU779 3.2 0.3 1.0
OD2 A:ASP808 3.6 0.7 1.0
C A:ALA323 3.6 0.8 1.0
CG A:ASN776 3.6 0.6 1.0
CG A:ASP804 3.6 0.4 1.0
CB A:SER775 3.8 0.4 1.0
N A:ASN776 3.9 0.4 1.0
C A:SER775 3.9 0.4 1.0
CA A:ASN776 4.0 0.9 1.0
CA A:ALA323 4.1 0.2 1.0
O A:SER775 4.1 0.6 1.0
N A:ASN324 4.3 0.9 1.0
CB A:ALA323 4.4 0.3 1.0
NA A:NA1104 4.4 0.6 1.0
CB A:ASP804 4.4 0.8 1.0
CB A:ASN776 4.4 0.2 1.0
O A:THR772 4.4 0.7 1.0
CA A:SER775 4.5 0.9 1.0
CA A:ASN324 4.6 0.2 1.0
OD2 A:ASP804 4.6 0.9 1.0
ND2 A:ASN776 4.6 0.7 1.0
CG A:GLU779 4.6 0.8 1.0
CG A:ASP808 4.8 0.8 1.0
CA A:ASP804 4.9 0.9 1.0

Sodium binding site 3 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 3 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1106

b:0.1
occ:1.00
 OG1 A:THR774 2.4 0.7 1.0
OD2 A:ASP926 2.4 0.4 1.0
OE1 A:GLN854 2.4 0.3 1.0
OE1 A:GLN923 2.4 0.5 1.0
NE2 A:GLN923 2.6 0.9 1.0
CD A:GLN923 2.9 0.1 1.0
CB A:THR774 2.9 0.4 1.0
N A:SER775 3.1 0.7 1.0
C A:THR774 3.2 0.7 1.0
O A:TYR771 3.2 0.0 1.0
CG A:ASP926 3.5 0.7 1.0
CA A:THR774 3.5 0.2 1.0
CD A:GLN854 3.6 0.3 1.0
O A:THR774 3.6 0.4 1.0
CA A:SER775 3.7 0.9 1.0
CB A:ASP926 4.0 1.0 1.0
NE2 A:GLN854 4.1 0.0 1.0
N A:THR774 4.2 0.3 1.0
CB A:SER775 4.2 0.4 1.0
CG2 A:THR774 4.3 0.2 1.0
C A:TYR771 4.4 0.2 1.0
CG A:GLN923 4.4 0.1 1.0
CE1 A:TYR771 4.4 0.6 1.0
OD1 A:ASP926 4.5 0.1 1.0
CZ A:TYR771 4.5 0.2 1.0
CD1 A:TYR771 4.5 0.6 1.0
CE2 A:TYR771 4.7 0.9 1.0
CG A:TYR771 4.7 0.7 1.0
CD2 A:TYR771 4.8 0.4 1.0
CG A:GLN854 4.8 0.5 1.0
CA A:TYR771 4.9 0.8 1.0
OH A:TYR771 5.0 0.7 1.0

Sodium binding site 4 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 4 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1104

b:0.7
occ:1.00
 O C:ALA323 2.4 0.4 1.0
OD2 C:ASP804 2.4 0.9 1.0
O C:VAL322 2.4 0.3 1.0
O C:VAL325 2.4 0.5 1.0
OE2 C:GLU327 2.4 1.0 1.0
OD1 C:ASP804 2.9 0.2 1.0
CG C:ASP804 3.0 0.9 1.0
C C:VAL325 3.2 0.5 1.0
C C:ALA323 3.4 0.8 1.0
C C:VAL322 3.6 0.7 1.0
CD C:GLU327 3.6 0.4 1.0
N C:VAL325 3.9 0.7 1.0
N C:PRO326 3.9 0.6 1.0
CA C:ALA323 3.9 0.3 1.0
CA C:PRO326 4.0 0.5 1.0
CA C:VAL325 4.1 0.4 1.0
N C:ALA323 4.2 0.9 1.0
CG C:GLU327 4.3 0.3 1.0
NA C:NA1105 4.3 0.9 1.0
N C:GLU327 4.4 0.8 1.0
CB C:ASP804 4.5 0.4 1.0
N C:ASN324 4.6 0.6 1.0
C C:ASN324 4.6 0.5 1.0
OE1 C:GLU327 4.6 0.5 1.0
OD2 C:ASP808 4.7 0.8 1.0
O C:ASP804 4.7 0.8 1.0
C C:PRO326 4.7 0.3 1.0
CA C:VAL322 4.8 0.8 1.0
CB C:VAL325 4.9 0.4 1.0
CA C:ASN324 5.0 0.2 1.0
CG1 C:VAL322 5.0 0.0 1.0

Sodium binding site 5 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 5 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1105

b:0.9
occ:1.00
 OD1 C:ASP804 2.4 0.2 1.0
OE2 C:GLU779 2.4 0.1 1.0
OD1 C:ASN776 2.4 0.1 1.0
OG C:SER775 2.4 0.1 1.0
O C:ALA323 3.2 0.4 1.0
CD C:GLU779 3.2 0.5 1.0
OE1 C:GLU779 3.3 0.6 1.0
C C:ALA323 3.6 0.8 1.0
CG C:ASN776 3.6 0.4 1.0
CG C:ASP804 3.6 0.9 1.0
OD2 C:ASP808 3.6 0.8 1.0
CB C:SER775 3.9 0.7 1.0
N C:ASN776 3.9 0.4 1.0
C C:SER775 4.0 0.0 1.0
CA C:ASN776 4.0 0.4 1.0
CA C:ALA323 4.0 0.3 1.0
O C:SER775 4.2 0.0 1.0
N C:ASN324 4.3 0.6 1.0
CB C:ALA323 4.3 1.0 1.0
NA C:NA1104 4.3 0.7 1.0
CB C:ASP804 4.4 0.4 1.0
CB C:ASN776 4.4 0.7 1.0
O C:THR772 4.5 0.1 1.0
CA C:ASN324 4.5 0.2 1.0
CA C:SER775 4.5 0.9 1.0
OD2 C:ASP804 4.5 0.9 1.0
ND2 C:ASN776 4.6 0.2 1.0
CG C:GLU779 4.6 0.1 1.0
CG C:ASP808 4.8 0.1 1.0
CA C:ASP804 4.9 0.7 1.0

Sodium binding site 6 out of 6 in 4hqj

Go back to Sodium Binding Sites List in 4hqj
Sodium binding site 6 out of 6 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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 Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1106

b:0.8
occ:1.00
 OE1 C:GLN923 2.4 0.9 1.0
OE1 C:GLN854 2.4 0.5 1.0
OD2 C:ASP926 2.4 0.4 1.0
OG1 C:THR774 2.4 0.2 1.0
NE2 C:GLN923 2.5 0.9 1.0
CD C:GLN923 2.8 0.4 1.0
CB C:THR774 3.0 0.6 1.0
N C:SER775 3.2 0.4 1.0
C C:THR774 3.2 0.3 1.0
O C:TYR771 3.3 0.2 1.0
CG C:ASP926 3.5 0.0 1.0
CD C:GLN854 3.5 0.1 1.0
CA C:THR774 3.6 0.5 1.0
O C:THR774 3.7 0.7 1.0
CA C:SER775 3.8 0.9 1.0
CB C:ASP926 4.0 0.3 1.0
NE2 C:GLN854 4.1 0.2 1.0
CB C:SER775 4.2 0.7 1.0
CG C:GLN923 4.3 0.1 1.0
N C:THR774 4.3 0.4 1.0
CG2 C:THR774 4.4 0.7 1.0
CE1 C:TYR771 4.4 0.2 1.0
C C:TYR771 4.4 0.3 1.0
CZ C:TYR771 4.4 0.3 1.0
CD1 C:TYR771 4.5 0.7 1.0
OD1 C:ASP926 4.6 0.8 1.0
CE2 C:TYR771 4.6 0.6 1.0
CG C:TYR771 4.7 0.0 1.0
CD2 C:TYR771 4.7 0.8 1.0
CG C:GLN854 4.8 0.1 1.0
OH C:TYR771 4.9 0.6 1.0
CA C:TYR771 4.9 0.1 1.0

Reference:

M.Nyblom, H.Poulsen, P.Gourdon, L.Reinhard, M.Andersson, E.Lindahl, N.Fedosova, P.Nissen. Crystal Structure of Na+, K(+)-Atpase in the Na(+)-Bound State. Science V. 342 123 2013.
ISSN: ISSN 0036-8075
PubMed: 24051246
DOI: 10.1126/SCIENCE.1243352
Page generated: Mon Oct 7 15:52:02 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