Fluorine in PDB 3a3y: Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
Protein crystallography data
The structure of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y
was solved by
H.Ogawa,
T.Shinoda,
F.Cornelius,
C.Toyoshima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.00 /
2.80
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
222.884,
50.720,
163.342,
90.00,
104.63,
90.00
|
R / Rfree (%)
|
24.7 /
29.3
|
Other elements in 3a3y:
The structure of Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
(pdb code 3a3y). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the
Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain, PDB code: 3a3y:
Jump to Fluorine binding site number:
1;
2;
3;
4;
Fluorine binding site 1 out
of 4 in 3a3y
Go back to
Fluorine Binding Sites List in 3a3y
Fluorine binding site 1 out
of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
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 the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:24.4
occ:1.00
|
F1
|
A:MF42001
|
0.0
|
24.4
|
1.0
|
MG
|
A:MF42001
|
2.0
|
23.3
|
1.0
|
OD2
|
A:ASP376
|
2.6
|
26.1
|
1.0
|
NZ
|
A:LYS698
|
2.7
|
27.9
|
1.0
|
ND2
|
A:ASN720
|
2.9
|
29.8
|
1.0
|
F2
|
A:MF42001
|
3.1
|
23.5
|
1.0
|
F4
|
A:MF42001
|
3.2
|
23.9
|
1.0
|
F3
|
A:MF42001
|
3.4
|
27.1
|
1.0
|
CE
|
A:LYS698
|
3.4
|
28.0
|
1.0
|
N
|
A:GLY618
|
3.4
|
25.6
|
1.0
|
CG
|
A:ASP376
|
3.5
|
27.0
|
1.0
|
O
|
A:HOH5024
|
3.8
|
26.1
|
1.0
|
O
|
A:THR219
|
3.8
|
30.0
|
1.0
|
OD1
|
A:ASP721
|
3.9
|
30.6
|
1.0
|
CG
|
A:ASN720
|
3.9
|
30.2
|
1.0
|
CA
|
A:THR617
|
4.0
|
24.9
|
1.0
|
O
|
A:VAL616
|
4.1
|
25.9
|
1.0
|
OD1
|
A:ASN720
|
4.1
|
30.6
|
1.0
|
C
|
A:THR617
|
4.2
|
25.2
|
1.0
|
CB
|
A:ASP376
|
4.2
|
26.6
|
1.0
|
OG1
|
A:THR617
|
4.3
|
23.1
|
1.0
|
OD1
|
A:ASP376
|
4.3
|
28.4
|
1.0
|
CA
|
A:GLY618
|
4.3
|
26.2
|
1.0
|
MG
|
A:MG2002
|
4.4
|
25.5
|
1.0
|
CA
|
A:GLY220
|
4.6
|
28.9
|
1.0
|
CD
|
A:LYS698
|
4.7
|
28.1
|
1.0
|
CB
|
A:THR617
|
4.7
|
24.4
|
1.0
|
C
|
A:THR219
|
4.7
|
30.1
|
1.0
|
CG
|
A:ASP721
|
4.8
|
30.2
|
1.0
|
CA
|
A:ASP376
|
4.8
|
26.9
|
1.0
|
N
|
A:LYS377
|
4.9
|
26.6
|
1.0
|
OD2
|
A:ASP721
|
4.9
|
30.1
|
1.0
|
C
|
A:VAL616
|
5.0
|
25.9
|
1.0
|
N
|
A:THR617
|
5.0
|
25.3
|
1.0
|
|
Fluorine binding site 2 out
of 4 in 3a3y
Go back to
Fluorine Binding Sites List in 3a3y
Fluorine binding site 2 out
of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
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 the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:23.5
occ:1.00
|
F2
|
A:MF42001
|
0.0
|
23.5
|
1.0
|
MG
|
A:MG2002
|
1.9
|
25.5
|
1.0
|
MG
|
A:MF42001
|
2.0
|
23.3
|
1.0
|
O
|
A:HOH5026
|
2.5
|
24.7
|
1.0
|
OD2
|
A:ASP376
|
2.6
|
26.1
|
1.0
|
O
|
A:HOH5024
|
2.9
|
26.1
|
1.0
|
F4
|
A:MF42001
|
3.1
|
23.9
|
1.0
|
O
|
A:THR378
|
3.1
|
26.1
|
1.0
|
F1
|
A:MF42001
|
3.1
|
24.4
|
1.0
|
OD1
|
A:ASP376
|
3.2
|
28.4
|
1.0
|
CG
|
A:ASP376
|
3.3
|
27.0
|
1.0
|
F3
|
A:MF42001
|
3.3
|
27.1
|
1.0
|
O
|
A:GLY220
|
3.4
|
28.3
|
1.0
|
CB
|
A:THR378
|
3.5
|
26.4
|
1.0
|
N
|
A:THR378
|
3.6
|
26.3
|
1.0
|
CA
|
A:GLY220
|
3.7
|
28.9
|
1.0
|
CA
|
A:THR378
|
3.8
|
26.3
|
1.0
|
C
|
A:THR378
|
3.8
|
26.4
|
1.0
|
C
|
A:GLY220
|
3.9
|
28.8
|
1.0
|
OD2
|
A:ASP717
|
4.0
|
31.2
|
1.0
|
OG1
|
A:THR378
|
4.2
|
26.3
|
1.0
|
CG2
|
A:THR378
|
4.6
|
26.2
|
1.0
|
O
|
A:THR219
|
4.6
|
30.0
|
1.0
|
OE1
|
A:GLU221
|
4.7
|
30.5
|
1.0
|
C
|
A:LYS377
|
4.7
|
26.4
|
1.0
|
CB
|
A:ASP376
|
4.7
|
26.6
|
1.0
|
OD1
|
A:ASN720
|
4.7
|
30.6
|
1.0
|
ND2
|
A:ASN720
|
4.8
|
29.8
|
1.0
|
N
|
A:LYS377
|
4.8
|
26.6
|
1.0
|
N
|
A:GLY220
|
4.9
|
29.6
|
1.0
|
|
Fluorine binding site 3 out
of 4 in 3a3y
Go back to
Fluorine Binding Sites List in 3a3y
Fluorine binding site 3 out
of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
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 the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:27.1
occ:1.00
|
F3
|
A:MF42001
|
0.0
|
27.1
|
1.0
|
MG
|
A:MF42001
|
2.0
|
23.3
|
1.0
|
O
|
A:THR219
|
2.5
|
30.0
|
1.0
|
OE1
|
A:GLU221
|
2.7
|
30.5
|
1.0
|
F2
|
A:MF42001
|
3.3
|
23.5
|
1.0
|
F4
|
A:MF42001
|
3.4
|
23.9
|
1.0
|
F1
|
A:MF42001
|
3.4
|
24.4
|
1.0
|
CD
|
A:GLU221
|
3.4
|
30.3
|
1.0
|
N
|
A:ASP619
|
3.4
|
27.0
|
1.0
|
C
|
A:GLY220
|
3.5
|
28.8
|
1.0
|
OG1
|
A:THR617
|
3.5
|
23.1
|
1.0
|
C
|
A:THR219
|
3.6
|
30.1
|
1.0
|
N
|
A:GLY618
|
3.6
|
25.6
|
1.0
|
CG
|
A:GLU221
|
3.6
|
29.1
|
1.0
|
CA
|
A:GLY220
|
3.6
|
28.9
|
1.0
|
O
|
A:GLY220
|
3.8
|
28.3
|
1.0
|
C
|
A:GLY618
|
3.8
|
26.9
|
1.0
|
CA
|
A:GLY618
|
3.8
|
26.2
|
1.0
|
N
|
A:GLU221
|
3.9
|
28.9
|
1.0
|
OG1
|
A:THR378
|
3.9
|
26.3
|
1.0
|
CB
|
A:ASP619
|
4.0
|
27.6
|
1.0
|
N
|
A:GLY220
|
4.1
|
29.6
|
1.0
|
CA
|
A:ASP619
|
4.1
|
27.6
|
1.0
|
CB
|
A:THR378
|
4.3
|
26.4
|
1.0
|
OE2
|
A:GLU221
|
4.5
|
31.3
|
1.0
|
OD2
|
A:ASP376
|
4.5
|
26.1
|
1.0
|
CA
|
A:GLU221
|
4.6
|
28.8
|
1.0
|
CB
|
A:GLU221
|
4.6
|
28.8
|
1.0
|
C
|
A:THR617
|
4.6
|
25.2
|
1.0
|
O
|
A:GLY618
|
4.7
|
27.4
|
1.0
|
CB
|
A:THR617
|
4.8
|
24.4
|
1.0
|
CA
|
A:THR219
|
4.8
|
30.5
|
1.0
|
ND2
|
A:ASN720
|
4.8
|
29.8
|
1.0
|
CG
|
A:ASP619
|
4.9
|
28.8
|
1.0
|
CA
|
A:THR617
|
4.9
|
24.9
|
1.0
|
N
|
A:THR378
|
5.0
|
26.3
|
1.0
|
|
Fluorine binding site 4 out
of 4 in 3a3y
Go back to
Fluorine Binding Sites List in 3a3y
Fluorine binding site 4 out
of 4 in the Crystal Structure of the Sodium-Potassium Pump with Bound Potassium and Ouabain
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 the Sodium-Potassium Pump with Bound Potassium and Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F2001
b:23.9
occ:1.00
|
F4
|
A:MF42001
|
0.0
|
23.9
|
1.0
|
MG
|
A:MF42001
|
2.0
|
23.3
|
1.0
|
OD2
|
A:ASP376
|
2.2
|
26.1
|
1.0
|
N
|
A:THR378
|
2.6
|
26.3
|
1.0
|
N
|
A:LYS377
|
2.6
|
26.6
|
1.0
|
OG1
|
A:THR617
|
2.7
|
23.1
|
1.0
|
CB
|
A:LYS377
|
3.0
|
26.0
|
1.0
|
CA
|
A:LYS377
|
3.0
|
26.2
|
1.0
|
F2
|
A:MF42001
|
3.1
|
23.5
|
1.0
|
F1
|
A:MF42001
|
3.2
|
24.4
|
1.0
|
C
|
A:LYS377
|
3.3
|
26.4
|
1.0
|
CG
|
A:ASP376
|
3.3
|
27.0
|
1.0
|
F3
|
A:MF42001
|
3.4
|
27.1
|
1.0
|
CB
|
A:THR617
|
3.4
|
24.4
|
1.0
|
OG1
|
A:THR378
|
3.7
|
26.3
|
1.0
|
CA
|
A:THR378
|
3.7
|
26.3
|
1.0
|
C
|
A:ASP376
|
3.7
|
26.9
|
1.0
|
CB
|
A:THR378
|
3.9
|
26.4
|
1.0
|
CA
|
A:THR617
|
3.9
|
24.9
|
1.0
|
OD1
|
A:ASP376
|
4.1
|
28.4
|
1.0
|
CG
|
A:LYS377
|
4.1
|
26.7
|
1.0
|
CA
|
A:ASP376
|
4.2
|
26.9
|
1.0
|
CB
|
A:ASP376
|
4.3
|
26.6
|
1.0
|
MG
|
A:MG2002
|
4.4
|
25.5
|
1.0
|
N
|
A:GLY618
|
4.4
|
25.6
|
1.0
|
O
|
A:LYS377
|
4.5
|
26.6
|
1.0
|
OE1
|
A:GLU221
|
4.5
|
30.5
|
1.0
|
O
|
A:VAL616
|
4.6
|
25.9
|
1.0
|
O
|
A:THR378
|
4.6
|
26.1
|
1.0
|
CE
|
A:LYS377
|
4.6
|
28.4
|
1.0
|
C
|
A:THR378
|
4.6
|
26.4
|
1.0
|
C
|
A:THR617
|
4.7
|
25.2
|
1.0
|
O
|
A:ASP376
|
4.8
|
27.0
|
1.0
|
CG2
|
A:THR617
|
4.8
|
23.9
|
1.0
|
CD
|
A:LYS377
|
4.8
|
28.3
|
1.0
|
NZ
|
A:LYS698
|
4.9
|
27.9
|
1.0
|
N
|
A:THR617
|
5.0
|
25.3
|
1.0
|
|
Reference:
H.Ogawa,
T.Shinoda,
F.Cornelius,
C.Toyoshima.
Crystal Structure of the Sodium-Potassium Pump (Na+,K+-Atpase) with Bound Potassium and Ouabain. Proc.Natl.Acad.Sci.Usa V. 106 13742 2009.
ISSN: ISSN 0027-8424
PubMed: 19666591
DOI: 10.1073/PNAS.0907054106
Page generated: Wed Jul 31 17:03:57 2024
|