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Fluorine 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:

Magnesium (Mg) 2 atoms
Aluminium (Al) 2 atoms
Sodium (Na) 6 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State, PDB code: 4hqj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 1 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


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Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1102

b:0.2
occ:1.00
 F1 A:ALF1102 0.0 0.2 1.0
AL A:ALF1102 1.8 0.3 1.0
O3B A:ADP1101 2.5 0.4 1.0
F4 A:ALF1102 2.5 0.7 1.0
F3 A:ALF1102 2.5 0.9 1.0
OD1 A:ASP369 3.1 0.8 1.0
MG A:MG1103 3.4 0.5 1.0
O3A A:ADP1101 3.5 0.6 1.0
OD2 A:ASP369 3.5 0.9 1.0
NZ A:LYS691 3.5 0.0 1.0
O2A A:ADP1101 3.5 0.7 1.0
CG A:ASP369 3.6 0.8 1.0
F2 A:ALF1102 3.6 0.3 1.0
PB A:ADP1101 3.6 0.6 1.0
OD1 A:ASN713 3.8 0.9 1.0
OD1 A:ASP714 4.0 0.3 1.0
PA A:ADP1101 4.1 0.8 1.0
ND2 A:ASN713 4.1 0.1 1.0
CG A:ASN713 4.1 0.2 1.0
O2B A:ADP1101 4.4 0.5 1.0
CE A:LYS691 4.4 0.5 1.0
OG1 A:THR610 4.4 0.8 1.0
N A:GLY611 4.5 1.0 1.0
O1B A:ADP1101 4.7 0.9 1.0
O1A A:ADP1101 4.7 0.0 1.0
CB A:ASP369 4.9 0.1 1.0

Fluorine binding site 2 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 2 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1102

b:0.3
occ:1.00
 F2 A:ALF1102 0.0 0.3 1.0
AL A:ALF1102 1.8 0.3 1.0
OG1 A:THR610 2.2 0.8 1.0
O3B A:ADP1101 2.5 0.4 1.0
F4 A:ALF1102 2.5 0.7 1.0
F3 A:ALF1102 2.5 0.9 1.0
N A:THR371 2.7 0.6 1.0
OG1 A:THR371 3.1 0.1 1.0
OD1 A:ASP369 3.1 0.8 1.0
CB A:THR371 3.2 0.7 1.0
CB A:LYS370 3.4 0.6 1.0
CA A:THR371 3.5 0.3 1.0
CB A:THR610 3.5 0.0 1.0
F1 A:ALF1102 3.6 0.2 1.0
N A:LYS370 3.6 0.1 1.0
C A:LYS370 3.7 0.3 1.0
PB A:ADP1101 3.7 0.6 1.0
CA A:LYS370 3.7 0.9 1.0
CG A:ASP369 3.9 0.8 1.0
OD1 A:ASP612 4.0 0.0 1.0
CE A:LYS370 4.1 0.6 1.0
CB A:ASP612 4.1 0.8 1.0
MG A:MG1103 4.1 0.5 1.0
OD2 A:ASP369 4.2 0.9 1.0
O1B A:ADP1101 4.2 0.9 1.0
O A:THR371 4.2 0.3 1.0
O2B A:ADP1101 4.3 0.5 1.0
CA A:THR610 4.3 0.4 1.0
C A:THR371 4.4 0.8 1.0
CG A:ASP612 4.5 0.0 1.0
CG A:LYS370 4.5 0.5 1.0
N A:GLY611 4.5 1.0 1.0
CG2 A:THR610 4.6 1.0 1.0
N A:ASP612 4.6 0.0 1.0
CG2 A:THR371 4.7 0.7 1.0
CD A:LYS370 4.7 0.3 1.0
C A:ASP369 4.8 0.4 1.0
O A:LYS370 4.8 0.8 1.0
NZ A:LYS370 4.9 0.7 1.0
O3A A:ADP1101 5.0 0.6 1.0
C A:THR610 5.0 0.3 1.0
CA A:ASP612 5.0 0.4 1.0

Fluorine binding site 3 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 3 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1102

b:0.9
occ:1.00
 F3 A:ALF1102 0.0 0.9 1.0
MG A:MG1103 1.7 0.5 1.0
AL A:ALF1102 1.8 0.3 1.0
O3B A:ADP1101 2.5 0.4 1.0
F2 A:ALF1102 2.5 0.3 1.0
F1 A:ALF1102 2.5 0.2 1.0
OD2 A:ASP369 2.7 0.9 1.0
O A:THR371 2.7 0.3 1.0
OD1 A:ASP369 3.1 0.8 1.0
CB A:THR371 3.2 0.7 1.0
CG A:ASP369 3.2 0.8 1.0
N A:THR371 3.4 0.6 1.0
C A:THR371 3.4 0.8 1.0
CA A:THR371 3.5 0.3 1.0
PB A:ADP1101 3.5 0.6 1.0
F4 A:ALF1102 3.6 0.7 1.0
O2B A:ADP1101 3.6 0.5 1.0
OD2 A:ASP710 3.8 1.0 1.0
OG1 A:THR371 3.9 0.1 1.0
O3A A:ADP1101 4.2 0.6 1.0
CG2 A:THR371 4.2 0.7 1.0
C A:LYS370 4.4 0.3 1.0
OG1 A:THR610 4.5 0.8 1.0
N A:LYS370 4.6 0.1 1.0
N A:GLY372 4.7 0.8 1.0
CB A:ASP369 4.7 0.1 1.0
O1B A:ADP1101 4.7 0.9 1.0
CG A:ASP710 4.8 0.5 1.0

Fluorine binding site 4 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 4 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
A:F1102

b:0.7
occ:1.00
 F4 A:ALF1102 0.0 0.7 1.0
AL A:ALF1102 1.8 0.3 1.0
OG1 A:THR610 2.2 0.8 1.0
N A:GLY611 2.4 1.0 1.0
O3B A:ADP1101 2.4 0.4 1.0
F1 A:ALF1102 2.5 0.2 1.0
F2 A:ALF1102 2.5 0.3 1.0
CA A:THR610 3.0 0.4 1.0
OD1 A:ASP369 3.1 0.8 1.0
CB A:THR610 3.1 0.0 1.0
C A:THR610 3.1 0.3 1.0
CA A:GLY611 3.5 0.6 1.0
F3 A:ALF1102 3.6 0.9 1.0
N A:ASP612 3.6 0.0 1.0
PB A:ADP1101 3.7 0.6 1.0
O2A A:ADP1101 3.8 0.7 1.0
C A:GLY611 3.9 0.0 1.0
O1B A:ADP1101 4.1 0.9 1.0
NZ A:LYS691 4.2 0.0 1.0
CG2 A:THR610 4.2 1.0 1.0
CG A:ASP369 4.2 0.8 1.0
N A:THR610 4.3 0.2 1.0
O3A A:ADP1101 4.3 0.6 1.0
O A:THR610 4.4 0.2 1.0
O A:VAL609 4.5 0.9 1.0
CB A:ASP612 4.5 0.8 1.0
CA A:ASP612 4.6 0.4 1.0
CE A:LYS691 4.6 0.5 1.0
PA A:ADP1101 4.7 0.8 1.0
OD2 A:ASP369 4.7 0.9 1.0
N A:LYS370 4.7 0.1 1.0
C A:VAL609 4.9 0.2 1.0
O A:GLY611 4.9 0.0 1.0
O2B A:ADP1101 5.0 0.5 1.0

Fluorine binding site 5 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 5 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1102

b:0.9
occ:1.00
 F1 C:ALF1102 0.0 0.9 1.0
AL C:ALF1102 1.8 0.9 1.0
O3B C:ADP1101 2.5 0.9 1.0
F4 C:ALF1102 2.5 0.8 1.0
F3 C:ALF1102 2.5 0.3 1.0
O2A C:ADP1101 3.0 0.7 1.0
OD1 C:ASP369 3.1 0.1 1.0
O3A C:ADP1101 3.3 0.7 1.0
PB C:ADP1101 3.3 0.8 1.0
MG C:MG1103 3.4 0.3 1.0
OD2 C:ASP369 3.5 0.1 1.0
F2 C:ALF1102 3.6 0.2 1.0
PA C:ADP1101 3.6 0.3 1.0
CG C:ASP369 3.6 0.4 1.0
O2B C:ADP1101 3.7 0.6 1.0
NZ C:LYS691 3.7 0.3 1.0
OD1 C:ASN713 3.9 0.7 1.0
OD1 C:ASP714 4.1 0.4 1.0
ND2 C:ASN713 4.1 0.1 1.0
O1A C:ADP1101 4.2 0.2 1.0
CG C:ASN713 4.2 0.1 1.0
OG1 C:THR610 4.4 0.5 1.0
N C:GLY611 4.5 0.1 1.0
CE C:LYS691 4.6 0.9 1.0
O1B C:ADP1101 4.7 0.7 1.0
CB C:ASP369 5.0 0.2 1.0

Fluorine binding site 6 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 6 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F1102

b:0.2
occ:1.00
 F2 C:ALF1102 0.0 0.2 1.0
AL C:ALF1102 1.8 0.9 1.0
OG1 C:THR610 2.2 0.5 1.0
O3B C:ADP1101 2.5 0.9 1.0
F4 C:ALF1102 2.5 0.8 1.0
F3 C:ALF1102 2.5 0.3 1.0
N C:THR371 2.6 0.8 1.0
OG1 C:THR371 3.0 0.8 1.0
OD1 C:ASP369 3.1 0.1 1.0
CB C:THR371 3.2 0.2 1.0
CB C:LYS370 3.3 0.1 1.0
CA C:THR371 3.4 0.5 1.0
N C:LYS370 3.5 0.8 1.0
C C:LYS370 3.5 0.5 1.0
CB C:THR610 3.6 0.5 1.0
F1 C:ALF1102 3.6 0.9 1.0
CA C:LYS370 3.6 0.9 1.0
PB C:ADP1101 3.8 0.8 1.0
CG C:ASP369 3.9 0.4 1.0
OD1 C:ASP612 4.0 0.3 1.0
CE C:LYS370 4.0 0.1 1.0
CB C:ASP612 4.1 1.0 1.0
MG C:MG1103 4.1 0.3 1.0
OD2 C:ASP369 4.2 0.1 1.0
O C:THR371 4.2 0.6 1.0
O2B C:ADP1101 4.3 0.6 1.0
C C:THR371 4.3 0.9 1.0
CG C:LYS370 4.4 0.5 1.0
CA C:THR610 4.4 0.5 1.0
O1B C:ADP1101 4.4 0.7 1.0
CG C:ASP612 4.5 0.8 1.0
CG2 C:THR610 4.6 0.9 1.0
CD C:LYS370 4.6 0.6 1.0
N C:GLY611 4.6 0.1 1.0
CG2 C:THR371 4.7 0.9 1.0
O2A C:ADP1101 4.7 0.7 1.0
O C:LYS370 4.7 0.8 1.0
N C:ASP612 4.7 0.7 1.0
C C:ASP369 4.7 0.7 1.0
NZ C:LYS370 4.8 0.6 1.0
O3A C:ADP1101 5.0 0.7 1.0

Fluorine binding site 7 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 7 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:0.3
occ:1.00
 F3 C:ALF1102 0.0 0.3 1.0
MG C:MG1103 1.7 0.3 1.0
AL C:ALF1102 1.8 0.9 1.0
O3B C:ADP1101 2.5 0.9 1.0
F1 C:ALF1102 2.5 0.9 1.0
F2 C:ALF1102 2.5 0.2 1.0
OD2 C:ASP369 2.7 0.1 1.0
O C:THR371 2.7 0.6 1.0
O2B C:ADP1101 2.8 0.6 1.0
OD1 C:ASP369 3.1 0.1 1.0
CB C:THR371 3.1 0.2 1.0
PB C:ADP1101 3.1 0.8 1.0
CG C:ASP369 3.2 0.4 1.0
N C:THR371 3.4 0.8 1.0
C C:THR371 3.4 0.9 1.0
CA C:THR371 3.4 0.5 1.0
F4 C:ALF1102 3.6 0.8 1.0
OD2 C:ASP710 3.8 0.8 1.0
OG1 C:THR371 3.9 0.8 1.0
O3A C:ADP1101 4.1 0.7 1.0
CG2 C:THR371 4.1 0.9 1.0
C C:LYS370 4.4 0.5 1.0
O1B C:ADP1101 4.4 0.7 1.0
OG1 C:THR610 4.5 0.5 1.0
N C:LYS370 4.6 0.8 1.0
N C:GLY372 4.6 0.3 1.0
CB C:ASP369 4.7 0.2 1.0
CG C:ASP710 4.8 0.8 1.0
O2A C:ADP1101 4.8 0.7 1.0
CA C:LYS370 5.0 0.9 1.0
OD1 C:ASP710 5.0 0.9 1.0

Fluorine binding site 8 out of 8 in 4hqj

Go back to Fluorine Binding Sites List in 4hqj
Fluorine binding site 8 out of 8 in the Crystal Structure of Na+,K+-Atpase in the Na+-Bound State


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Na+,K+-Atpase in the Na+-Bound State within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1102

b:0.8
occ:1.00
 F4 C:ALF1102 0.0 0.8 1.0
AL C:ALF1102 1.8 0.9 1.0
OG1 C:THR610 2.1 0.5 1.0
O3B C:ADP1101 2.5 0.9 1.0
N C:GLY611 2.5 0.1 1.0
F1 C:ALF1102 2.5 0.9 1.0
F2 C:ALF1102 2.5 0.2 1.0
O2A C:ADP1101 2.8 0.7 1.0
CA C:THR610 3.0 0.5 1.0
CB C:THR610 3.1 0.5 1.0
OD1 C:ASP369 3.1 0.1 1.0
C C:THR610 3.2 0.9 1.0
CA C:GLY611 3.5 0.3 1.0
N C:ASP612 3.6 0.7 1.0
F3 C:ALF1102 3.6 0.3 1.0
C C:GLY611 3.9 0.3 1.0
PB C:ADP1101 3.9 0.8 1.0
PA C:ADP1101 4.1 0.3 1.0
CG2 C:THR610 4.2 0.9 1.0
CG C:ASP369 4.2 0.4 1.0
O3A C:ADP1101 4.3 0.7 1.0
NZ C:LYS691 4.3 0.3 1.0
N C:THR610 4.4 0.1 1.0
CB C:ASP612 4.4 1.0 1.0
O C:THR610 4.4 0.6 1.0
CA C:ASP612 4.5 0.0 1.0
O C:VAL609 4.6 0.3 1.0
OD2 C:ASP369 4.7 0.1 1.0
N C:LYS370 4.7 0.8 1.0
O1B C:ADP1101 4.7 0.7 1.0
CE C:LYS691 4.8 0.9 1.0
O2B C:ADP1101 4.9 0.6 1.0
O C:GLY611 4.9 0.2 1.0
C C:VAL609 4.9 0.8 1.0
C5' C:ADP1101 4.9 0.4 1.0
N C:THR371 5.0 0.8 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: Thu Aug 1 02:06:55 2024

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