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Fluorine in PDB 3wgv: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv was solved by R.Kanai, H.Ogawa, B.Vilsen, F.Cornelius, C.Toyoshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.99 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 106.285, 210.183, 256.086, 90.00, 90.00, 90.00
R / Rfree (%) 27 / 29.8

Other elements in 3wgv:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Aluminium (Al) 2 atoms
Sodium (Na) 8 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin (pdb code 3wgv). 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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin, PDB code: 3wgv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 1 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:19.1
occ:1.00
 F1 A:ALF2002 0.0 19.1 1.0
AL A:ALF2002 1.8 29.8 1.0
O3B A:ADP2004 2.1 16.2 1.0
OD1 A:ASP369 2.5 21.2 1.0
F3 A:ALF2002 2.5 14.4 1.0
F4 A:ALF2002 2.6 14.1 1.0
OG1 A:THR610 2.7 33.1 1.0
N A:LYS370 3.2 38.1 1.0
CG A:ASP369 3.2 53.4 1.0
OG1 A:THR371 3.2 50.1 1.0
CB A:THR610 3.3 31.9 1.0
N A:THR371 3.3 39.3 1.0
OD2 A:ASP369 3.4 58.3 1.0
CB A:LYS370 3.4 24.0 1.0
PB A:ADP2004 3.5 35.5 1.0
F2 A:ALF2002 3.6 28.4 1.0
CA A:THR610 3.7 29.1 1.0
CA A:LYS370 3.7 34.3 1.0
N A:GLY611 3.8 27.7 1.0
O3A A:ADP2004 3.9 11.4 1.0
C A:LYS370 4.0 37.2 1.0
CB A:THR371 4.2 40.7 1.0
C A:THR610 4.3 32.9 1.0
MG A:MG2003 4.3 15.1 1.0
CA A:THR371 4.3 36.6 1.0
C A:ASP369 4.3 34.1 1.0
O2B A:ADP2004 4.3 47.1 1.0
CB A:ASP369 4.5 22.0 1.0
O1B A:ADP2004 4.5 10.0 1.0
CA A:ASP369 4.6 33.0 1.0
NZ A:LYS691 4.6 41.8 1.0
O A:THR371 4.6 21.6 1.0
CG2 A:THR610 4.7 34.5 1.0
O A:VAL609 4.7 34.1 1.0
N A:ASP612 4.8 19.6 1.0
CG A:LYS370 4.8 25.0 1.0
N A:THR610 4.9 26.7 1.0
CA A:GLY611 4.9 19.7 1.0
CE A:LYS370 5.0 24.2 1.0
C A:THR371 5.0 39.5 1.0
CD A:LYS370 5.0 24.7 1.0

Fluorine binding site 2 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 2 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:28.4
occ:1.00
 F2 A:ALF2002 0.0 28.4 1.0
AL A:ALF2002 1.8 29.8 1.0
MG A:MG2003 2.3 15.1 1.0
F4 A:ALF2002 2.5 14.1 1.0
F3 A:ALF2002 2.5 14.4 1.0
OD2 A:ASP369 2.9 58.3 1.0
OD1 A:ASN713 3.1 50.3 1.0
ND2 A:ASN713 3.1 37.7 1.0
OD1 A:ASP369 3.3 21.2 1.0
CG A:ASP369 3.4 53.4 1.0
O2B A:ADP2004 3.4 47.1 1.0
CG A:ASN713 3.5 39.5 1.0
O3B A:ADP2004 3.6 16.2 1.0
F1 A:ALF2002 3.6 19.1 1.0
O3A A:ADP2004 3.7 11.4 1.0
PB A:ADP2004 3.8 35.5 1.0
MG A:MG2001 4.0 61.4 1.0
O2A A:ADP2004 4.1 21.2 1.0
OD1 A:ASP710 4.1 36.3 1.0
OD2 A:ASP714 4.2 51.9 1.0
OD1 A:ASP714 4.2 26.9 1.0
O A:THR371 4.3 21.6 1.0
NZ A:LYS691 4.3 41.8 1.0
O A:HOH2103 4.5 21.1 1.0
CG A:ASP714 4.5 18.7 1.0
PA A:ADP2004 4.6 22.7 1.0
CA A:GLY711 4.7 26.7 1.0
CB A:ASP369 4.8 22.0 1.0
N A:GLY711 4.9 28.8 1.0
OG1 A:THR371 5.0 50.1 1.0
CB A:ASN713 5.0 29.9 1.0

Fluorine binding site 3 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 3 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:14.4
occ:1.00
 F3 A:ALF2002 0.0 14.4 1.0
AL A:ALF2002 1.8 29.8 1.0
OD1 A:ASP369 2.4 21.2 1.0
F1 A:ALF2002 2.5 19.1 1.0
F2 A:ALF2002 2.5 28.4 1.0
O3A A:ADP2004 3.0 11.4 1.0
NZ A:LYS691 3.0 41.8 1.0
O3B A:ADP2004 3.1 16.2 1.0
N A:GLY611 3.2 27.7 1.0
ND2 A:ASN713 3.2 37.7 1.0
CG A:ASP369 3.4 53.4 1.0
F4 A:ALF2002 3.6 14.1 1.0
PB A:ADP2004 3.6 35.5 1.0
CE A:LYS691 3.7 18.4 1.0
OD2 A:ASP369 3.8 58.3 1.0
CA A:THR610 3.8 29.1 1.0
C A:THR610 3.9 32.9 1.0
OG1 A:THR610 3.9 33.1 1.0
CA A:GLY611 4.1 19.7 1.0
CG A:ASN713 4.1 39.5 1.0
OD1 A:ASN713 4.1 50.3 1.0
PA A:ADP2004 4.2 22.7 1.0
O2B A:ADP2004 4.2 47.1 1.0
OD1 A:ASP714 4.3 26.9 1.0
CB A:THR610 4.4 31.9 1.0
MG A:MG2003 4.4 15.1 1.0
O A:VAL609 4.4 34.1 1.0
O2A A:ADP2004 4.5 21.2 1.0
O1A A:ADP2004 4.7 15.8 1.0
CB A:ASP369 4.7 22.0 1.0
N A:LYS370 4.9 38.1 1.0
O1B A:ADP2004 4.9 10.0 1.0
N A:THR610 5.0 26.7 1.0
CD A:LYS691 5.0 32.9 1.0

Fluorine binding site 4 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 4 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:14.1
occ:1.00
 F4 A:ALF2002 0.0 14.1 1.0
AL A:ALF2002 1.8 29.8 1.0
MG A:MG2003 2.1 15.1 1.0
O A:THR371 2.4 21.6 1.0
OD2 A:ASP369 2.4 58.3 1.0
F2 A:ALF2002 2.5 28.4 1.0
F1 A:ALF2002 2.6 19.1 1.0
O3B A:ADP2004 2.7 16.2 1.0
OG1 A:THR371 2.8 50.1 1.0
N A:THR371 2.9 39.3 1.0
CB A:THR371 3.0 40.7 1.0
C A:THR371 3.1 39.5 1.0
CA A:THR371 3.1 36.6 1.0
CG A:ASP369 3.2 53.4 1.0
OD1 A:ASP369 3.4 21.2 1.0
O2B A:ADP2004 3.4 47.1 1.0
F3 A:ALF2002 3.6 14.4 1.0
PB A:ADP2004 3.6 35.5 1.0
O A:HOH2103 3.8 21.1 1.0
C A:LYS370 4.0 37.2 1.0
OD1 A:ASP710 4.2 36.3 1.0
N A:LYS370 4.2 38.1 1.0
O3A A:ADP2004 4.4 11.4 1.0
N A:GLY372 4.4 23.1 1.0
CG2 A:THR371 4.5 39.8 1.0
MG A:MG2001 4.5 61.4 1.0
CA A:LYS370 4.6 34.3 1.0
CB A:ASP369 4.6 22.0 1.0
O A:LYS370 4.8 38.2 1.0
CB A:LYS370 4.9 24.0 1.0
O1B A:ADP2004 4.9 10.0 1.0
OD2 A:ASP710 4.9 20.9 1.0
CG A:ASP710 5.0 33.9 1.0

Fluorine binding site 5 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 5 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:24.5
occ:1.00
 F1 C:ALF2002 0.0 24.5 1.0
AL C:ALF2002 1.8 20.9 1.0
OD1 C:ASP369 2.1 51.9 1.0
OG1 C:THR610 2.2 37.2 1.0
O3B C:ADP2004 2.3 46.7 1.0
F4 C:ALF2002 2.5 51.7 1.0
F3 C:ALF2002 2.5 0.8 1.0
CB C:THR610 3.1 37.5 1.0
N C:GLY611 3.1 36.5 1.0
CA C:THR610 3.2 36.7 1.0
CG C:ASP369 3.3 52.9 1.0
F2 C:ALF2002 3.6 71.1 1.0
PB C:ADP2004 3.6 53.1 1.0
N C:LYS370 3.6 55.9 1.0
O3A C:ADP2004 3.6 31.4 1.0
C C:THR610 3.7 70.0 1.0
OD2 C:ASP369 3.7 51.1 1.0
NZ C:LYS691 3.8 34.1 1.0
CB C:LYS370 3.8 59.8 1.0
N C:THR371 3.9 58.6 1.0
OG1 C:THR371 4.0 69.2 1.0
CA C:LYS370 4.2 60.0 1.0
CA C:GLY611 4.3 36.6 1.0
N C:ASP612 4.4 38.0 1.0
O2B C:ADP2004 4.5 47.1 1.0
O C:VAL609 4.5 61.5 1.0
CG2 C:THR610 4.5 90.8 1.0
N C:THR610 4.5 54.3 1.0
CB C:ASP369 4.5 51.1 1.0
C C:LYS370 4.6 61.1 1.0
C C:ASP369 4.6 50.9 1.0
O1B C:ADP2004 4.6 57.5 1.0
MG C:MG2003 4.7 51.8 1.0
CA C:ASP369 4.7 47.6 1.0
C C:GLY611 4.7 49.9 1.0
CB C:THR371 4.8 61.3 1.0
O C:THR610 4.9 46.8 1.0
CE C:LYS691 4.9 34.5 1.0
CA C:THR371 4.9 61.5 1.0
C C:VAL609 4.9 57.9 1.0

Fluorine binding site 6 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 6 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:71.1
occ:1.00
 F2 C:ALF2002 0.0 71.1 1.0
AL C:ALF2002 1.8 20.9 1.0
F3 C:ALF2002 2.5 0.8 1.0
F4 C:ALF2002 2.5 51.7 1.0
MG C:MG2003 2.6 51.8 1.0
MG C:MG2001 3.0 55.0 1.0
OD2 C:ASP369 3.0 51.1 1.0
O C:HOH2102 3.2 15.3 1.0
O3A C:ADP2004 3.3 31.4 1.0
O3B C:ADP2004 3.4 46.7 1.0
OD1 C:ASN713 3.5 46.4 1.0
ND2 C:ASN713 3.5 58.7 1.0
F1 C:ALF2002 3.6 24.5 1.0
OD1 C:ASP369 3.6 51.9 1.0
O1B C:ADP2004 3.6 57.5 1.0
CG C:ASP369 3.6 52.9 1.0
PB C:ADP2004 3.7 53.1 1.0
O1A C:ADP2004 3.8 51.1 1.0
CG C:ASN713 3.9 50.6 1.0
PA C:ADP2004 4.2 53.9 1.0
NZ C:LYS691 4.2 34.1 1.0
OD1 C:ASP710 4.3 58.2 1.0
OD2 C:ASP714 4.6 65.8 1.0
O C:THR371 4.6 73.4 1.0
CA C:GLY711 4.7 56.1 1.0
O2A C:ADP2004 4.9 51.6 1.0
N C:GLY711 4.9 55.5 1.0
OD1 C:ASP714 4.9 65.5 1.0

Fluorine binding site 7 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 7 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:0.8
occ:1.00
 F3 C:ALF2002 0.0 0.8 1.0
AL C:ALF2002 1.8 20.9 1.0
F2 C:ALF2002 2.5 71.1 1.0
F1 C:ALF2002 2.5 24.5 1.0
NZ C:LYS691 2.7 34.1 1.0
O3A C:ADP2004 2.8 31.4 1.0
OD1 C:ASP369 3.1 51.9 1.0
ND2 C:ASN713 3.1 58.7 1.0
N C:GLY611 3.2 36.5 1.0
O3B C:ADP2004 3.3 46.7 1.0
F4 C:ALF2002 3.6 51.7 1.0
CE C:LYS691 3.6 34.5 1.0
PB C:ADP2004 3.7 53.1 1.0
PA C:ADP2004 3.7 53.9 1.0
CA C:GLY611 3.8 36.6 1.0
O2A C:ADP2004 3.8 51.6 1.0
CG C:ASP369 3.8 52.9 1.0
C C:THR610 3.9 70.0 1.0
OD2 C:ASP369 4.1 51.1 1.0
CA C:THR610 4.1 36.7 1.0
CG C:ASN713 4.1 50.6 1.0
OG1 C:THR610 4.3 37.2 1.0
O1A C:ADP2004 4.3 51.1 1.0
OD1 C:ASN713 4.4 46.4 1.0
O1B C:ADP2004 4.5 57.5 1.0
CD C:LYS691 4.8 50.7 1.0
C C:GLY611 4.8 49.9 1.0
MG C:MG2003 4.8 51.8 1.0
CB C:THR610 4.8 37.5 1.0
OD1 C:ASP714 4.8 65.5 1.0
O2B C:ADP2004 4.9 47.1 1.0
O C:VAL609 4.9 61.5 1.0
O C:THR610 4.9 46.8 1.0

Fluorine binding site 8 out of 8 in 3wgv

Go back to Fluorine Binding Sites List in 3wgv
Fluorine binding site 8 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin


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 A Na+-Bound Na+,K+-Atpase Preceding the E1P State with Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:51.7
occ:1.00
 F4 C:ALF2002 0.0 51.7 1.0
AL C:ALF2002 1.8 20.9 1.0
O3B C:ADP2004 2.3 46.7 1.0
F1 C:ALF2002 2.5 24.5 1.0
MG C:MG2003 2.5 51.8 1.0
F2 C:ALF2002 2.5 71.1 1.0
OD2 C:ASP369 2.6 51.1 1.0
OD1 C:ASP369 2.8 51.9 1.0
OG1 C:THR371 2.9 69.2 1.0
N C:THR371 2.9 58.6 1.0
O C:THR371 3.0 73.4 1.0
CB C:THR371 3.0 61.3 1.0
CG C:ASP369 3.0 52.9 1.0
O C:HOH2102 3.2 15.3 1.0
CA C:THR371 3.2 61.5 1.0
PB C:ADP2004 3.5 53.1 1.0
C C:THR371 3.5 68.8 1.0
F3 C:ALF2002 3.6 0.8 1.0
O1B C:ADP2004 3.7 57.5 1.0
C C:LYS370 3.9 61.1 1.0
N C:LYS370 4.0 55.9 1.0
O3A C:ADP2004 4.1 31.4 1.0
OD1 C:ASP710 4.2 58.2 1.0
CA C:LYS370 4.4 60.0 1.0
OG1 C:THR610 4.4 37.2 1.0
CG2 C:THR371 4.5 60.0 1.0
CB C:ASP369 4.5 51.1 1.0
MG C:MG2001 4.6 55.0 1.0
CB C:LYS370 4.6 59.8 1.0
O2B C:ADP2004 4.8 47.1 1.0
N C:GLY372 4.8 66.2 1.0
O C:LYS370 4.9 62.6 1.0
C C:ASP369 4.9 50.9 1.0

Reference:

R.Kanai, H.Ogawa, B.Vilsen, F.Cornelius, C.Toyoshima. Crystal Structure of A NA1-Bound NA1,K1-Atpase Preceding the E1P State Nature V. 502 201 2013.
ISSN: ISSN 0028-0836
Page generated: Wed Jul 31 23:34:09 2024

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