Fluorine in PDB 6kpu: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 6kpu
was solved by
H.Ogawa,
K.Motoyama,
F.Cornelius,
B.Vilsen,
C.Toyoshima,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
15.99 /
4.62
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.481,
118.371,
495.388,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.6 /
24.4
|
Other elements in 6kpu:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
(pdb code 6kpu). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 6kpu:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 1 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1104
b:0.7
occ:1.00
|
F1
|
A:BEF1104
|
0.0
|
0.7
|
1.0
|
BE
|
A:BEF1104
|
1.3
|
0.3
|
1.0
|
F2
|
A:BEF1104
|
2.2
|
0.8
|
1.0
|
F3
|
A:BEF1104
|
2.3
|
0.6
|
1.0
|
OD1
|
A:ASP369
|
2.9
|
0.2
|
1.0
|
ND2
|
A:ASN713
|
2.9
|
1.0
|
1.0
|
N
|
A:GLY611
|
3.2
|
0.9
|
1.0
|
NZ
|
A:LYS691
|
3.2
|
0.7
|
1.0
|
OG1
|
A:THR610
|
3.2
|
0.2
|
1.0
|
O
|
A:HOH1202
|
3.5
|
99.3
|
1.0
|
CA
|
A:GLY213
|
3.6
|
0.1
|
1.0
|
CA
|
A:THR610
|
3.6
|
0.5
|
1.0
|
CG
|
A:ASP369
|
3.8
|
96.9
|
1.0
|
C
|
A:THR610
|
3.9
|
0.2
|
1.0
|
CB
|
A:THR610
|
3.9
|
0.8
|
1.0
|
CE
|
A:LYS691
|
4.0
|
0.5
|
1.0
|
OD2
|
A:ASP369
|
4.0
|
93.7
|
1.0
|
O
|
A:THR212
|
4.1
|
0.1
|
1.0
|
CG
|
A:ASN713
|
4.1
|
0.4
|
1.0
|
CA
|
A:GLY611
|
4.1
|
0.7
|
1.0
|
MG
|
A:MG1101
|
4.3
|
89.5
|
1.0
|
O
|
A:GLY213
|
4.4
|
0.1
|
1.0
|
N
|
A:GLY213
|
4.5
|
0.1
|
1.0
|
C
|
A:GLY213
|
4.5
|
0.6
|
1.0
|
OD1
|
A:ASN713
|
4.6
|
0.6
|
1.0
|
C
|
A:THR212
|
4.7
|
0.4
|
1.0
|
O
|
A:VAL609
|
4.7
|
0.8
|
1.0
|
C
|
A:GLY611
|
4.8
|
0.8
|
1.0
|
OD1
|
A:ASP714
|
4.8
|
0.1
|
1.0
|
N
|
A:THR610
|
4.9
|
0.8
|
1.0
|
N
|
A:ASP612
|
4.9
|
0.9
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 2 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1104
b:0.8
occ:1.00
|
F2
|
A:BEF1104
|
0.0
|
0.8
|
1.0
|
BE
|
A:BEF1104
|
1.3
|
0.3
|
1.0
|
F1
|
A:BEF1104
|
2.2
|
0.7
|
1.0
|
F3
|
A:BEF1104
|
2.3
|
0.6
|
1.0
|
MG
|
A:MG1101
|
2.3
|
89.5
|
1.0
|
O
|
A:HOH1202
|
2.6
|
99.3
|
1.0
|
OD2
|
A:ASP369
|
2.9
|
93.7
|
1.0
|
O
|
A:THR371
|
3.2
|
97.1
|
1.0
|
OD1
|
A:ASP369
|
3.3
|
0.2
|
1.0
|
CA
|
A:GLY213
|
3.3
|
0.1
|
1.0
|
O
|
A:HOH1205
|
3.3
|
0.9
|
1.0
|
CG
|
A:ASP369
|
3.5
|
96.9
|
1.0
|
CB
|
A:THR371
|
3.6
|
0.2
|
1.0
|
ND2
|
A:ASN713
|
3.8
|
1.0
|
1.0
|
N
|
A:THR371
|
3.9
|
0.6
|
1.0
|
C
|
A:THR371
|
4.0
|
0.3
|
1.0
|
O
|
A:GLY213
|
4.0
|
0.1
|
1.0
|
CA
|
A:THR371
|
4.0
|
1.0
|
1.0
|
C
|
A:GLY213
|
4.2
|
0.6
|
1.0
|
OD1
|
A:ASP710
|
4.3
|
98.4
|
1.0
|
OG1
|
A:THR371
|
4.4
|
0.9
|
1.0
|
N
|
A:GLY213
|
4.4
|
0.1
|
1.0
|
O
|
A:SER209
|
4.4
|
0.8
|
1.0
|
OG1
|
A:THR610
|
4.4
|
0.2
|
1.0
|
CG2
|
A:THR371
|
4.5
|
0.8
|
1.0
|
OD1
|
A:ASN713
|
4.5
|
0.6
|
1.0
|
NZ
|
A:LYS691
|
4.6
|
0.7
|
1.0
|
CG
|
A:ASN713
|
4.6
|
0.4
|
1.0
|
OD2
|
A:ASP714
|
4.9
|
0.2
|
1.0
|
C
|
A:LYS370
|
5.0
|
0.7
|
1.0
|
CB
|
A:ASP369
|
5.0
|
98.3
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 3 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F1104
b:0.6
occ:1.00
|
F3
|
A:BEF1104
|
0.0
|
0.6
|
1.0
|
BE
|
A:BEF1104
|
1.5
|
0.3
|
1.0
|
F1
|
A:BEF1104
|
2.3
|
0.7
|
1.0
|
F2
|
A:BEF1104
|
2.3
|
0.8
|
1.0
|
OG1
|
A:THR610
|
2.4
|
0.2
|
1.0
|
N
|
A:THR371
|
2.9
|
0.6
|
1.0
|
OD1
|
A:ASP369
|
3.2
|
0.2
|
1.0
|
CB
|
A:THR610
|
3.3
|
0.8
|
1.0
|
OD2
|
A:ASP369
|
3.4
|
93.7
|
1.0
|
CB
|
A:THR371
|
3.5
|
0.2
|
1.0
|
CG
|
A:ASP369
|
3.6
|
96.9
|
1.0
|
OG1
|
A:THR371
|
3.6
|
0.9
|
1.0
|
N
|
A:LYS370
|
3.6
|
98.7
|
1.0
|
CA
|
A:THR371
|
3.7
|
1.0
|
1.0
|
CB
|
A:LYS370
|
3.8
|
0.8
|
1.0
|
C
|
A:LYS370
|
3.9
|
0.7
|
1.0
|
CA
|
A:THR610
|
3.9
|
0.5
|
1.0
|
CA
|
A:LYS370
|
3.9
|
0.7
|
1.0
|
O
|
A:GLY213
|
4.0
|
0.1
|
1.0
|
O
|
A:THR371
|
4.0
|
97.1
|
1.0
|
N
|
A:GLY611
|
4.1
|
0.9
|
1.0
|
MG
|
A:MG1101
|
4.1
|
89.5
|
1.0
|
CA
|
A:GLY213
|
4.4
|
0.1
|
1.0
|
C
|
A:THR371
|
4.4
|
0.3
|
1.0
|
O
|
A:HOH1202
|
4.4
|
99.3
|
1.0
|
C
|
A:THR610
|
4.6
|
0.2
|
1.0
|
CG2
|
A:THR610
|
4.6
|
0.9
|
1.0
|
C
|
A:ASP369
|
4.6
|
93.2
|
1.0
|
C
|
A:GLY213
|
4.7
|
0.6
|
1.0
|
NZ
|
A:LYS370
|
4.7
|
0.2
|
1.0
|
CE
|
A:LYS370
|
4.7
|
0.9
|
1.0
|
NZ
|
A:LYS691
|
4.8
|
0.7
|
1.0
|
CB
|
A:ASP369
|
4.9
|
98.3
|
1.0
|
CG2
|
A:THR371
|
4.9
|
0.8
|
1.0
|
CB
|
A:ASP612
|
4.9
|
0.1
|
1.0
|
CG
|
A:LYS370
|
4.9
|
0.4
|
1.0
|
N
|
A:ASP612
|
4.9
|
0.9
|
1.0
|
CA
|
A:ASP369
|
5.0
|
96.6
|
1.0
|
O
|
A:LYS370
|
5.0
|
0.0
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 4 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1104
b:0.7
occ:1.00
|
F1
|
C:BEF1104
|
0.0
|
0.7
|
1.0
|
BE
|
C:BEF1104
|
1.3
|
0.7
|
1.0
|
F2
|
C:BEF1104
|
2.2
|
0.1
|
1.0
|
F3
|
C:BEF1104
|
2.3
|
0.1
|
1.0
|
ND2
|
C:ASN713
|
2.8
|
0.8
|
1.0
|
OD1
|
C:ASP369
|
2.8
|
0.1
|
1.0
|
OG1
|
C:THR610
|
3.1
|
0.2
|
1.0
|
NZ
|
C:LYS691
|
3.1
|
0.7
|
1.0
|
N
|
C:GLY611
|
3.2
|
1.0
|
1.0
|
CA
|
C:GLY213
|
3.3
|
0.1
|
1.0
|
O
|
C:HOH1201
|
3.6
|
0.4
|
1.0
|
CA
|
C:THR610
|
3.7
|
0.6
|
1.0
|
CG
|
C:ASP369
|
3.7
|
0.3
|
1.0
|
OD2
|
C:ASP369
|
3.9
|
0.8
|
1.0
|
CB
|
C:THR610
|
3.9
|
0.3
|
1.0
|
CE
|
C:LYS691
|
3.9
|
0.7
|
1.0
|
C
|
C:THR610
|
4.0
|
0.3
|
1.0
|
CG
|
C:ASN713
|
4.0
|
0.6
|
1.0
|
N
|
C:GLY213
|
4.2
|
0.6
|
1.0
|
O
|
C:GLY213
|
4.2
|
0.3
|
1.0
|
MG
|
C:MG1101
|
4.2
|
0.3
|
1.0
|
CA
|
C:GLY611
|
4.2
|
0.8
|
1.0
|
C
|
C:GLY213
|
4.2
|
0.2
|
1.0
|
O
|
C:THR212
|
4.3
|
0.9
|
1.0
|
OD1
|
C:ASN713
|
4.4
|
0.4
|
1.0
|
C
|
C:THR212
|
4.5
|
0.3
|
1.0
|
N
|
C:ASP612
|
4.8
|
0.9
|
1.0
|
O
|
C:VAL609
|
4.8
|
0.5
|
1.0
|
C
|
C:GLY611
|
4.8
|
0.7
|
1.0
|
N
|
C:THR610
|
5.0
|
0.9
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 5 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1104
b:0.1
occ:1.00
|
F2
|
C:BEF1104
|
0.0
|
0.1
|
1.0
|
BE
|
C:BEF1104
|
1.3
|
0.7
|
1.0
|
MG
|
C:MG1101
|
2.2
|
0.3
|
1.0
|
F1
|
C:BEF1104
|
2.2
|
0.7
|
1.0
|
F3
|
C:BEF1104
|
2.3
|
0.1
|
1.0
|
O
|
C:HOH1201
|
2.7
|
0.4
|
1.0
|
OD2
|
C:ASP369
|
2.8
|
0.8
|
1.0
|
O
|
C:THR371
|
3.2
|
0.8
|
1.0
|
OD1
|
C:ASP369
|
3.2
|
0.1
|
1.0
|
CA
|
C:GLY213
|
3.2
|
0.1
|
1.0
|
O
|
C:HOH1203
|
3.3
|
0.8
|
1.0
|
CG
|
C:ASP369
|
3.4
|
0.3
|
1.0
|
CB
|
C:THR371
|
3.5
|
1.0
|
1.0
|
ND2
|
C:ASN713
|
3.8
|
0.8
|
1.0
|
N
|
C:THR371
|
3.8
|
0.7
|
1.0
|
O
|
C:GLY213
|
3.9
|
0.3
|
1.0
|
CA
|
C:THR371
|
4.0
|
0.9
|
1.0
|
O
|
C:SER209
|
4.0
|
0.2
|
1.0
|
C
|
C:THR371
|
4.0
|
0.9
|
1.0
|
C
|
C:GLY213
|
4.1
|
0.2
|
1.0
|
OG1
|
C:THR371
|
4.2
|
0.4
|
1.0
|
OD1
|
C:ASP710
|
4.2
|
0.2
|
1.0
|
N
|
C:GLY213
|
4.3
|
0.6
|
1.0
|
OG1
|
C:THR610
|
4.3
|
0.2
|
1.0
|
OD1
|
C:ASN713
|
4.4
|
0.4
|
1.0
|
CG
|
C:ASN713
|
4.5
|
0.6
|
1.0
|
CG2
|
C:THR371
|
4.6
|
0.1
|
1.0
|
NZ
|
C:LYS691
|
4.6
|
0.7
|
1.0
|
CB
|
C:ASP369
|
4.9
|
0.8
|
1.0
|
N
|
C:LYS370
|
4.9
|
0.8
|
1.0
|
C
|
C:LYS370
|
4.9
|
0.2
|
1.0
|
OD2
|
C:ASP714
|
5.0
|
0.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 6kpu
Go back to
Fluorine Binding Sites List in 6kpu
Fluorine binding site 6 out
of 6 in the Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F1104
b:0.1
occ:1.00
|
F3
|
C:BEF1104
|
0.0
|
0.1
|
1.0
|
BE
|
C:BEF1104
|
1.5
|
0.7
|
1.0
|
OG1
|
C:THR610
|
2.3
|
0.2
|
1.0
|
F1
|
C:BEF1104
|
2.3
|
0.7
|
1.0
|
F2
|
C:BEF1104
|
2.3
|
0.1
|
1.0
|
N
|
C:THR371
|
3.0
|
0.7
|
1.0
|
CB
|
C:THR610
|
3.3
|
0.3
|
1.0
|
OD1
|
C:ASP369
|
3.3
|
0.1
|
1.0
|
OD2
|
C:ASP369
|
3.4
|
0.8
|
1.0
|
OG1
|
C:THR371
|
3.5
|
0.4
|
1.0
|
O
|
C:GLY213
|
3.5
|
0.3
|
1.0
|
CB
|
C:THR371
|
3.6
|
1.0
|
1.0
|
N
|
C:LYS370
|
3.6
|
0.8
|
1.0
|
CG
|
C:ASP369
|
3.6
|
0.3
|
1.0
|
CB
|
C:LYS370
|
3.8
|
0.8
|
1.0
|
CA
|
C:THR371
|
3.8
|
0.9
|
1.0
|
C
|
C:LYS370
|
3.9
|
0.2
|
1.0
|
CA
|
C:LYS370
|
3.9
|
1.0
|
1.0
|
CA
|
C:GLY213
|
4.0
|
0.1
|
1.0
|
CA
|
C:THR610
|
4.0
|
0.6
|
1.0
|
MG
|
C:MG1101
|
4.1
|
0.3
|
1.0
|
N
|
C:GLY611
|
4.2
|
1.0
|
1.0
|
C
|
C:GLY213
|
4.2
|
0.2
|
1.0
|
O
|
C:THR371
|
4.2
|
0.8
|
1.0
|
CG2
|
C:THR610
|
4.5
|
0.0
|
1.0
|
C
|
C:THR371
|
4.5
|
0.9
|
1.0
|
O
|
C:HOH1201
|
4.6
|
0.4
|
1.0
|
C
|
C:THR610
|
4.6
|
0.3
|
1.0
|
CB
|
C:ASP612
|
4.7
|
0.9
|
1.0
|
C
|
C:ASP369
|
4.7
|
0.5
|
1.0
|
N
|
C:ASP612
|
4.7
|
0.9
|
1.0
|
NZ
|
C:LYS691
|
4.7
|
0.7
|
1.0
|
NZ
|
C:LYS370
|
4.8
|
0.9
|
1.0
|
CE
|
C:LYS370
|
4.8
|
0.3
|
1.0
|
CB
|
C:ASP369
|
4.9
|
0.8
|
1.0
|
ND2
|
C:ASN713
|
4.9
|
0.8
|
1.0
|
CG
|
C:LYS370
|
4.9
|
0.6
|
1.0
|
CA
|
C:ASP369
|
5.0
|
0.5
|
1.0
|
CG2
|
C:THR371
|
5.0
|
0.1
|
1.0
|
|
Reference:
H.Ogawa,
K.Motoyama,
F.Cornelius,
B.Vilsen,
C.Toyoshima.
X-Ray Crystal Structures of Na+,K+-Atpase in Complex with Cardiotonic Steroids To Be Published.
Page generated: Sun Dec 13 12:55:39 2020
|