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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

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