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Fluorine in PDB 3wgu: Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

Enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin

All present enzymatic activity of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin:
3.6.3.9;

Protein crystallography data

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without Oligomycin, PDB code: 3wgu 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 (°) 106.383, 211.600, 257.124, 90.00, 90.00, 90.00
R / Rfree (%) 26.5 / 29.9

Other elements in 3wgu:

The structure of Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin (pdb code 3wgu). 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 Without Oligomycin, PDB code: 3wgu:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 1 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:16.4
occ:1.00
 F1 A:ALF2002 0.0 16.4 1.0
AL A:ALF2002 1.8 9.4 1.0
F4 A:ALF2002 2.5 0.9 1.0
O3B A:ADP2004 2.5 36.0 1.0
F3 A:ALF2002 2.6 22.8 1.0
N A:LYS370 2.8 29.4 1.0
N A:THR371 2.9 52.4 1.0
OG1 A:THR610 3.0 42.0 1.0
OD1 A:ASP369 3.0 22.8 1.0
CB A:LYS370 3.1 38.2 1.0
OD2 A:ASP369 3.1 38.9 1.0
OG1 A:THR371 3.2 62.6 1.0
CA A:LYS370 3.2 37.8 1.0
CG A:ASP369 3.2 44.7 1.0
CB A:THR610 3.3 46.0 1.0
C A:LYS370 3.5 52.1 1.0
F2 A:ALF2002 3.6 42.8 1.0
CA A:THR610 3.7 29.3 1.0
C A:ASP369 3.9 27.2 1.0
PB A:ADP2004 3.9 41.0 1.0
CA A:THR371 4.0 48.8 1.0
CB A:THR371 4.1 51.8 1.0
N A:GLY611 4.1 52.7 1.0
CA A:ASP369 4.3 24.4 1.0
O A:VAL609 4.3 28.3 1.0
CB A:ASP369 4.4 42.1 1.0
CG A:LYS370 4.4 38.5 1.0
NZ A:LYS691 4.4 27.4 1.0
O1B A:ADP2004 4.5 51.8 1.0
O3A A:ADP2004 4.5 6.8 1.0
C A:THR610 4.5 37.4 1.0
O A:THR371 4.5 35.1 1.0
MG A:MG2003 4.6 24.6 1.0
CD A:LYS370 4.7 41.4 1.0
O A:HOH2109 4.8 36.5 1.0
O A:LYS370 4.8 59.4 1.0
C A:THR371 4.8 37.5 1.0
CG2 A:THR610 4.8 45.4 1.0
N A:THR610 4.8 39.7 1.0
CE A:LYS370 4.9 50.2 1.0
O A:ASP369 5.0 27.6 1.0
C A:VAL609 5.0 38.5 1.0

Fluorine binding site 2 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 2 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:42.8
occ:1.00
 F2 A:ALF2002 0.0 42.8 1.0
AL A:ALF2002 1.8 9.4 1.0
MG A:MG2003 2.3 24.6 1.0
F3 A:ALF2002 2.5 22.8 1.0
F4 A:ALF2002 2.6 0.9 1.0
OD1 A:ASP369 2.8 22.8 1.0
ND2 A:ASN713 2.8 52.7 1.0
O1B A:ADP2004 3.2 51.8 1.0
OD2 A:ASP369 3.2 38.9 1.0
OD1 A:ASN713 3.3 57.4 1.0
O A:HOH2109 3.3 36.5 1.0
CG A:ASP369 3.4 44.7 1.0
CG A:ASN713 3.4 53.4 1.0
F1 A:ALF2002 3.6 16.4 1.0
O3B A:ADP2004 3.6 36.0 1.0
PB A:ADP2004 3.7 41.0 1.0
O3A A:ADP2004 3.8 6.8 1.0
O1A A:ADP2004 3.9 50.1 1.0
NZ A:LYS691 3.9 27.4 1.0
MG A:MG2001 4.1 67.6 1.0
OD1 A:ASP714 4.1 49.7 1.0
OD1 A:ASP710 4.4 42.9 1.0
O A:THR371 4.4 35.1 1.0
PA A:ADP2004 4.4 38.2 1.0
OD2 A:ASP714 4.6 33.3 1.0
OG1 A:THR371 4.7 62.6 1.0
CG A:ASP714 4.7 38.2 1.0
CE A:LYS691 4.8 22.2 1.0
CB A:ASP369 4.8 42.1 1.0
CB A:ASN713 4.9 46.8 1.0

Fluorine binding site 3 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 3 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:22.8
occ:1.00
 F3 A:ALF2002 0.0 22.8 1.0
AL A:ALF2002 1.8 9.4 1.0
F2 A:ALF2002 2.5 42.8 1.0
F1 A:ALF2002 2.6 16.4 1.0
N A:GLY611 2.8 52.7 1.0
O3B A:ADP2004 2.9 36.0 1.0
OD1 A:ASP369 2.9 22.8 1.0
O3A A:ADP2004 3.1 6.8 1.0
NZ A:LYS691 3.2 27.4 1.0
ND2 A:ASN713 3.4 52.7 1.0
CA A:THR610 3.5 29.3 1.0
PB A:ADP2004 3.5 41.0 1.0
CE A:LYS691 3.5 22.2 1.0
F4 A:ALF2002 3.6 0.9 1.0
C A:THR610 3.6 37.4 1.0
CA A:GLY611 3.7 57.1 1.0
OG1 A:THR610 3.7 42.0 1.0
CG A:ASP369 3.9 44.7 1.0
O1B A:ADP2004 4.0 51.8 1.0
CB A:THR610 4.1 46.0 1.0
OD2 A:ASP369 4.2 38.9 1.0
PA A:ADP2004 4.2 38.2 1.0
O A:VAL609 4.4 28.3 1.0
O1A A:ADP2004 4.5 50.1 1.0
CG A:ASN713 4.6 53.4 1.0
MG A:MG2003 4.6 24.6 1.0
C A:GLY611 4.6 53.1 1.0
O2A A:ADP2004 4.6 14.2 1.0
N A:ASP612 4.7 23.5 1.0
N A:THR610 4.7 39.7 1.0
OG1 A:THR371 4.7 62.6 1.0
O A:THR610 4.8 37.5 1.0
O2B A:ADP2004 4.8 24.7 1.0
N A:LYS370 4.9 29.4 1.0
OD1 A:ASP714 5.0 49.7 1.0
OD1 A:ASN713 5.0 57.4 1.0
C A:VAL609 5.0 38.5 1.0
CD A:LYS691 5.0 28.1 1.0

Fluorine binding site 4 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 4 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2002

b:0.9
occ:1.00
 F4 A:ALF2002 0.0 0.9 1.0
AL A:ALF2002 1.8 9.4 1.0
OD2 A:ASP369 1.9 38.9 1.0
O A:THR371 2.3 35.1 1.0
MG A:MG2003 2.4 24.6 1.0
F1 A:ALF2002 2.5 16.4 1.0
F2 A:ALF2002 2.6 42.8 1.0
N A:THR371 2.6 52.4 1.0
O A:HOH2109 2.6 36.5 1.0
CG A:ASP369 2.8 44.7 1.0
CA A:THR371 3.0 48.8 1.0
OG1 A:THR371 3.0 62.6 1.0
C A:THR371 3.0 37.5 1.0
CB A:THR371 3.1 51.8 1.0
OD1 A:ASP369 3.1 22.8 1.0
O3B A:ADP2004 3.2 36.0 1.0
F3 A:ALF2002 3.6 22.8 1.0
O1B A:ADP2004 3.6 51.8 1.0
C A:LYS370 3.7 52.1 1.0
OD1 A:ASP710 3.8 42.9 1.0
N A:LYS370 3.8 29.4 1.0
PB A:ADP2004 4.0 41.0 1.0
CA A:LYS370 4.2 37.8 1.0
CB A:ASP369 4.2 42.1 1.0
N A:GLY372 4.4 25.4 1.0
OG1 A:THR373 4.6 39.8 1.0
C A:ASP369 4.6 27.2 1.0
O A:LYS370 4.6 59.4 1.0
CG2 A:THR371 4.6 42.3 1.0
CG A:ASP710 4.6 45.3 1.0
OD2 A:ASP710 4.7 46.5 1.0
CB A:LYS370 4.7 38.2 1.0
O3A A:ADP2004 4.9 6.8 1.0
O A:HOH2108 4.9 55.3 1.0
CA A:ASP369 4.9 24.4 1.0

Fluorine binding site 5 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 5 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:38.8
occ:1.00
 F1 C:ALF2002 0.0 38.8 1.0
AL C:ALF2002 1.8 67.6 1.0
O3B C:ADP2004 2.3 64.4 1.0
OG1 C:THR610 2.4 67.7 1.0
F3 C:ALF2002 2.4 56.9 1.0
F4 C:ALF2002 2.5 48.1 1.0
OD1 C:ASP369 2.5 67.4 1.0
N C:GLY611 2.8 52.6 1.0
CB C:THR610 3.2 72.0 1.0
CA C:THR610 3.2 52.5 1.0
O3A C:ADP2004 3.3 8.3 1.0
PB C:ADP2004 3.4 66.1 1.0
C C:THR610 3.5 52.8 1.0
F2 C:ALF2002 3.6 56.6 1.0
CG C:ASP369 3.6 64.3 1.0
CA C:GLY611 4.0 53.1 1.0
OD2 C:ASP369 4.0 64.3 1.0
N C:LYS370 4.0 63.7 1.0
OG1 C:THR371 4.1 85.4 1.0
NZ C:LYS691 4.1 42.4 1.0
O2B C:ADP2004 4.2 58.7 1.0
N C:THR371 4.2 75.6 1.0
N C:ASP612 4.3 63.2 1.0
CB C:LYS370 4.4 71.0 1.0
C C:GLY611 4.5 55.5 1.0
N C:THR610 4.5 60.4 1.0
O1B C:ADP2004 4.6 66.0 1.0
CG2 C:THR610 4.6 76.8 1.0
O C:VAL609 4.6 77.6 1.0
MG C:MG2003 4.7 48.3 1.0
CA C:LYS370 4.7 70.5 1.0
O C:THR610 4.7 54.8 1.0
CE C:LYS691 4.7 43.9 1.0
PA C:ADP2004 4.8 60.8 1.0
CB C:THR371 4.9 80.1 1.0
CB C:ASP369 4.9 59.9 1.0
C C:LYS370 5.0 75.0 1.0
CB C:ASP612 5.0 80.0 1.0

Fluorine binding site 6 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 6 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:56.6
occ:1.00
 F2 C:ALF2002 0.0 56.6 1.0
AL C:ALF2002 1.8 67.6 1.0
MG C:MG2003 2.4 48.3 1.0
F3 C:ALF2002 2.5 56.9 1.0
F4 C:ALF2002 2.6 48.1 1.0
OD2 C:ASP369 2.7 64.3 1.0
O C:HOH2105 2.9 48.9 1.0
MG C:MG2001 3.2 96.2 1.0
OD1 C:ASN713 3.3 51.2 1.0
CG C:ASP369 3.4 64.3 1.0
OD1 C:ASP369 3.5 67.4 1.0
ND2 C:ASN713 3.5 45.5 1.0
F1 C:ALF2002 3.6 38.8 1.0
O3B C:ADP2004 3.6 64.4 1.0
O3A C:ADP2004 3.7 8.3 1.0
CG C:ASN713 3.8 47.6 1.0
OD1 C:ASP710 3.9 84.7 1.0
NZ C:LYS691 4.1 42.4 1.0
PB C:ADP2004 4.1 66.1 1.0
O1B C:ADP2004 4.1 66.0 1.0
O1A C:ADP2004 4.2 66.6 1.0
OD2 C:ASP714 4.2 80.3 1.0
OD1 C:ASP714 4.2 73.4 1.0
O C:THR371 4.4 81.8 1.0
PA C:ADP2004 4.5 60.8 1.0
CG C:ASP714 4.6 70.8 1.0
CA C:GLY711 4.6 63.5 1.0
N C:GLY711 4.7 71.2 1.0
CB C:ASP369 4.7 59.9 1.0
CG C:ASP710 5.0 85.7 1.0

Fluorine binding site 7 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 7 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:56.9
occ:1.00
 F3 C:ALF2002 0.0 56.9 1.0
AL C:ALF2002 1.8 67.6 1.0
F1 C:ALF2002 2.4 38.8 1.0
F2 C:ALF2002 2.5 56.6 1.0
NZ C:LYS691 2.9 42.4 1.0
ND2 C:ASN713 3.0 45.5 1.0
O3A C:ADP2004 3.0 8.3 1.0
OD1 C:ASP369 3.2 67.4 1.0
CE C:LYS691 3.3 43.9 1.0
N C:GLY611 3.3 52.6 1.0
F4 C:ALF2002 3.6 48.1 1.0
O3B C:ADP2004 3.6 64.4 1.0
CG C:ASP369 3.8 64.3 1.0
CG C:ASN713 3.9 47.6 1.0
PA C:ADP2004 4.0 60.8 1.0
OD2 C:ASP369 4.0 64.3 1.0
CA C:GLY611 4.0 53.1 1.0
C C:THR610 4.0 52.8 1.0
PB C:ADP2004 4.1 66.1 1.0
O2A C:ADP2004 4.1 41.3 1.0
OD1 C:ASN713 4.1 51.2 1.0
CA C:THR610 4.2 52.5 1.0
OD1 C:ASP714 4.4 73.4 1.0
O1A C:ADP2004 4.4 66.6 1.0
OG1 C:THR610 4.5 67.7 1.0
CD C:LYS691 4.6 40.1 1.0
MG C:MG2003 4.7 48.3 1.0
O1B C:ADP2004 4.8 66.0 1.0
O C:VAL609 4.9 77.6 1.0
CB C:THR610 4.9 72.0 1.0
O C:THR610 5.0 54.8 1.0
CB C:ASP369 5.0 59.9 1.0

Fluorine binding site 8 out of 8 in 3wgu

Go back to Fluorine Binding Sites List in 3wgu
Fluorine binding site 8 out of 8 in the Crystal Structure of A Na+-Bound Na+,K+-Atpase Preceding the E1P State Without 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 Without Oligomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F2002

b:48.1
occ:1.00
 F4 C:ALF2002 0.0 48.1 1.0
AL C:ALF2002 1.8 67.6 1.0
O3B C:ADP2004 2.2 64.4 1.0
F1 C:ALF2002 2.5 38.8 1.0
MG C:MG2003 2.5 48.3 1.0
F2 C:ALF2002 2.6 56.6 1.0
OD2 C:ASP369 2.7 64.3 1.0
OD1 C:ASP369 2.8 67.4 1.0
N C:THR371 2.8 75.6 1.0
OG1 C:THR371 2.9 85.4 1.0
CB C:THR371 3.0 80.1 1.0
O C:THR371 3.0 81.8 1.0
CG C:ASP369 3.1 64.3 1.0
CA C:THR371 3.2 77.8 1.0
O C:HOH2105 3.4 48.9 1.0
PB C:ADP2004 3.4 66.1 1.0
C C:THR371 3.5 79.8 1.0
F3 C:ALF2002 3.6 56.9 1.0
O1B C:ADP2004 3.9 66.0 1.0
C C:LYS370 3.9 75.0 1.0
O3A C:ADP2004 4.0 8.3 1.0
N C:LYS370 4.0 63.7 1.0
OD1 C:ASP710 4.4 84.7 1.0
CA C:LYS370 4.4 70.5 1.0
OG1 C:THR610 4.4 67.7 1.0
CG2 C:THR371 4.5 80.4 1.0
MG C:MG2001 4.5 96.2 1.0
CB C:ASP369 4.5 59.9 1.0
O2B C:ADP2004 4.7 58.7 1.0
CB C:LYS370 4.7 71.0 1.0
N C:GLY372 4.8 77.6 1.0
C C:ASP369 4.9 64.1 1.0
O C:LYS370 4.9 78.4 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 23:34:11 2024

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