Atomistry » Fluorine » PDB 3vrs-3wyk » 3wgv
Atomistry »
  Fluorine »
    PDB 3vrs-3wyk »
      3wgv »

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: Sun Dec 13 11:57:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy