Fluorine in PDB 7ddf: Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride
All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride:
7.2.2.13;
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Beryllium Fluoride, PDB code: 7ddf
was solved by
H.Ogawa,
F.Cornelius,
R.Kanai,
K.Motoyama,
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,
90,
90
|
R / Rfree (%)
|
19.4 /
24.2
|
Other elements in 7ddf:
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 7ddf). 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: 7ddf:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:91.1
occ:1.00
|
F1
|
A:BFD369
|
0.0
|
91.1
|
1.0
|
BE
|
A:BFD369
|
1.5
|
92.5
|
1.0
|
F3
|
A:BFD369
|
2.4
|
97.8
|
1.0
|
F2
|
A:BFD369
|
2.5
|
93.9
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
89.8
|
1.0
|
ND2
|
A:ASN713
|
2.8
|
93.4
|
1.0
|
NZ
|
A:LYS691
|
3.0
|
89.5
|
1.0
|
N
|
A:GLY611
|
3.2
|
102.2
|
1.0
|
OG1
|
A:THR610
|
3.3
|
94.7
|
1.0
|
O
|
A:HOH1203
|
3.5
|
87.1
|
1.0
|
CA
|
A:GLY213
|
3.6
|
116.7
|
1.0
|
CA
|
A:THR610
|
3.6
|
98.7
|
1.0
|
CE
|
A:LYS691
|
3.8
|
87.2
|
1.0
|
CG
|
A:BFD369
|
3.9
|
86.5
|
1.0
|
C
|
A:THR610
|
3.9
|
101.0
|
1.0
|
CB
|
A:THR610
|
4.0
|
96.5
|
1.0
|
O
|
A:THR212
|
4.0
|
125.6
|
1.0
|
CG
|
A:ASN713
|
4.1
|
93.8
|
1.0
|
CA
|
A:GLY611
|
4.1
|
103.5
|
1.0
|
OD2
|
A:BFD369
|
4.3
|
85.0
|
1.0
|
MG
|
A:MG1101
|
4.3
|
96.0
|
1.0
|
N
|
A:GLY213
|
4.4
|
120.8
|
1.0
|
O
|
A:GLY213
|
4.5
|
111.6
|
1.0
|
C
|
A:THR212
|
4.5
|
125.4
|
1.0
|
C
|
A:GLY213
|
4.5
|
112.8
|
1.0
|
OD1
|
A:ASN713
|
4.5
|
95.5
|
1.0
|
O
|
A:VAL609
|
4.7
|
98.7
|
1.0
|
OD1
|
A:ASP714
|
4.7
|
102.7
|
1.0
|
C
|
A:GLY611
|
4.8
|
104.8
|
1.0
|
N
|
A:THR610
|
4.9
|
98.3
|
1.0
|
N
|
A:ASP612
|
4.9
|
110.5
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:93.9
occ:1.00
|
F2
|
A:BFD369
|
0.0
|
93.9
|
1.0
|
BE
|
A:BFD369
|
1.5
|
92.5
|
1.0
|
MG
|
A:MG1101
|
2.0
|
96.0
|
1.0
|
O
|
A:HOH1203
|
2.3
|
87.1
|
1.0
|
F1
|
A:BFD369
|
2.5
|
91.1
|
1.0
|
F3
|
A:BFD369
|
2.5
|
97.8
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
89.8
|
1.0
|
OD2
|
A:BFD369
|
2.6
|
85.0
|
1.0
|
O
|
A:THR371
|
2.9
|
91.9
|
1.0
|
CG
|
A:BFD369
|
3.0
|
86.5
|
1.0
|
O
|
A:HOH1205
|
3.3
|
87.4
|
1.0
|
CA
|
A:GLY213
|
3.6
|
116.7
|
1.0
|
CB
|
A:THR371
|
3.8
|
118.3
|
1.0
|
ND2
|
A:ASN713
|
3.8
|
93.4
|
1.0
|
C
|
A:THR371
|
3.9
|
100.0
|
1.0
|
OD1
|
A:ASP710
|
3.9
|
86.7
|
1.0
|
N
|
A:THR371
|
4.0
|
110.4
|
1.0
|
CA
|
A:THR371
|
4.1
|
110.1
|
1.0
|
OD1
|
A:ASN713
|
4.4
|
95.5
|
1.0
|
O
|
A:GLY213
|
4.4
|
111.6
|
1.0
|
NZ
|
A:LYS691
|
4.4
|
89.5
|
1.0
|
CB
|
A:BFD369
|
4.5
|
87.1
|
1.0
|
OD2
|
A:ASP714
|
4.5
|
102.8
|
1.0
|
O
|
A:SER209
|
4.6
|
128.2
|
1.0
|
C
|
A:GLY213
|
4.6
|
112.8
|
1.0
|
CG
|
A:ASN713
|
4.6
|
93.8
|
1.0
|
OG1
|
A:THR371
|
4.6
|
119.8
|
1.0
|
N
|
A:GLY213
|
4.6
|
120.8
|
1.0
|
OG1
|
A:THR610
|
4.6
|
94.7
|
1.0
|
CG2
|
A:THR371
|
4.7
|
122.1
|
1.0
|
N
|
A:LYS370
|
4.9
|
99.9
|
1.0
|
CG
|
A:ASP710
|
4.9
|
88.0
|
1.0
|
C
|
A:LYS370
|
5.0
|
109.0
|
1.0
|
OD1
|
A:ASP714
|
5.0
|
102.7
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:97.8
occ:1.00
|
F3
|
A:BFD369
|
0.0
|
97.8
|
1.0
|
BE
|
A:BFD369
|
1.5
|
92.5
|
1.0
|
OG1
|
A:THR610
|
2.4
|
94.7
|
1.0
|
F1
|
A:BFD369
|
2.4
|
91.1
|
1.0
|
F2
|
A:BFD369
|
2.5
|
93.9
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
89.8
|
1.0
|
N
|
A:THR371
|
3.0
|
110.4
|
1.0
|
CB
|
A:THR610
|
3.2
|
96.5
|
1.0
|
CG
|
A:BFD369
|
3.3
|
86.5
|
1.0
|
N
|
A:LYS370
|
3.4
|
99.9
|
1.0
|
OD2
|
A:BFD369
|
3.4
|
85.0
|
1.0
|
CB
|
A:THR371
|
3.6
|
118.3
|
1.0
|
OG1
|
A:THR371
|
3.7
|
119.8
|
1.0
|
CB
|
A:LYS370
|
3.7
|
111.4
|
1.0
|
CA
|
A:THR371
|
3.8
|
110.1
|
1.0
|
CA
|
A:THR610
|
3.8
|
98.7
|
1.0
|
CA
|
A:LYS370
|
3.8
|
107.0
|
1.0
|
C
|
A:LYS370
|
3.8
|
109.0
|
1.0
|
O
|
A:THR371
|
4.0
|
91.9
|
1.0
|
MG
|
A:MG1101
|
4.1
|
96.0
|
1.0
|
N
|
A:GLY611
|
4.1
|
102.2
|
1.0
|
O
|
A:GLY213
|
4.2
|
111.6
|
1.0
|
C
|
A:THR371
|
4.4
|
100.0
|
1.0
|
C
|
A:BFD369
|
4.4
|
92.5
|
1.0
|
O
|
A:HOH1203
|
4.4
|
87.1
|
1.0
|
CA
|
A:GLY213
|
4.5
|
116.7
|
1.0
|
CG2
|
A:THR610
|
4.5
|
96.2
|
1.0
|
CB
|
A:BFD369
|
4.5
|
87.1
|
1.0
|
C
|
A:THR610
|
4.5
|
101.0
|
1.0
|
NZ
|
A:LYS691
|
4.6
|
89.5
|
1.0
|
CA
|
A:BFD369
|
4.7
|
89.1
|
1.0
|
NZ
|
A:LYS370
|
4.7
|
112.2
|
1.0
|
O
|
A:VAL609
|
4.8
|
98.7
|
1.0
|
CE
|
A:LYS370
|
4.8
|
113.8
|
1.0
|
C
|
A:GLY213
|
4.8
|
112.8
|
1.0
|
CG
|
A:LYS370
|
4.9
|
114.2
|
1.0
|
O
|
A:LYS370
|
5.0
|
108.7
|
1.0
|
N
|
A:THR610
|
5.0
|
98.3
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:114.1
occ:1.00
|
F1
|
C:BFD369
|
0.0
|
114.1
|
1.0
|
BE
|
C:BFD369
|
1.5
|
113.2
|
1.0
|
F3
|
C:BFD369
|
2.5
|
115.2
|
1.0
|
F2
|
C:BFD369
|
2.5
|
113.3
|
1.0
|
OD1
|
C:BFD369
|
2.5
|
111.5
|
1.0
|
ND2
|
C:ASN713
|
2.6
|
125.1
|
1.0
|
NZ
|
C:LYS691
|
3.1
|
138.6
|
1.0
|
OG1
|
C:THR610
|
3.2
|
116.4
|
1.0
|
N
|
C:GLY611
|
3.2
|
114.8
|
1.0
|
CA
|
C:GLY213
|
3.3
|
157.2
|
1.0
|
O
|
C:HOH1201
|
3.7
|
111.3
|
1.0
|
CA
|
C:THR610
|
3.7
|
112.6
|
1.0
|
CE
|
C:LYS691
|
3.7
|
137.9
|
1.0
|
CG
|
C:ASN713
|
3.8
|
124.5
|
1.0
|
CG
|
C:BFD369
|
3.9
|
108.4
|
1.0
|
CB
|
C:THR610
|
3.9
|
115.6
|
1.0
|
C
|
C:THR610
|
3.9
|
114.0
|
1.0
|
O
|
C:THR212
|
4.1
|
154.4
|
1.0
|
CA
|
C:GLY611
|
4.1
|
115.7
|
1.0
|
N
|
C:GLY213
|
4.1
|
155.8
|
1.0
|
OD2
|
C:BFD369
|
4.3
|
107.8
|
1.0
|
OD1
|
C:ASN713
|
4.3
|
125.2
|
1.0
|
C
|
C:GLY213
|
4.4
|
158.5
|
1.0
|
O
|
C:GLY213
|
4.4
|
157.9
|
1.0
|
C
|
C:THR212
|
4.4
|
154.4
|
1.0
|
MG
|
C:MG1101
|
4.4
|
113.2
|
1.0
|
C
|
C:GLY611
|
4.8
|
117.0
|
1.0
|
O
|
C:VAL609
|
4.8
|
105.0
|
1.0
|
OD1
|
C:ASP714
|
4.9
|
119.7
|
1.0
|
N
|
C:ASP612
|
4.9
|
123.9
|
1.0
|
CB
|
C:ASN713
|
5.0
|
123.0
|
1.0
|
N
|
C:THR610
|
5.0
|
108.4
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:113.3
occ:1.00
|
F2
|
C:BFD369
|
0.0
|
113.3
|
1.0
|
BE
|
C:BFD369
|
1.5
|
113.2
|
1.0
|
MG
|
C:MG1101
|
2.1
|
113.2
|
1.0
|
O
|
C:HOH1201
|
2.4
|
111.3
|
1.0
|
F3
|
C:BFD369
|
2.5
|
115.2
|
1.0
|
F1
|
C:BFD369
|
2.5
|
114.1
|
1.0
|
OD1
|
C:BFD369
|
2.5
|
111.5
|
1.0
|
OD2
|
C:BFD369
|
2.6
|
107.8
|
1.0
|
CG
|
C:BFD369
|
3.0
|
108.4
|
1.0
|
O
|
C:THR371
|
3.1
|
109.5
|
1.0
|
O
|
C:HOH1204
|
3.3
|
105.9
|
1.0
|
CA
|
C:GLY213
|
3.6
|
157.2
|
1.0
|
ND2
|
C:ASN713
|
3.7
|
125.1
|
1.0
|
CB
|
C:THR371
|
3.8
|
127.3
|
1.0
|
C
|
C:THR371
|
4.0
|
113.7
|
1.0
|
N
|
C:THR371
|
4.1
|
124.0
|
1.0
|
OD1
|
C:ASP710
|
4.1
|
106.9
|
1.0
|
OD1
|
C:ASN713
|
4.2
|
125.2
|
1.0
|
O
|
C:SER209
|
4.2
|
134.6
|
1.0
|
CA
|
C:THR371
|
4.2
|
122.0
|
1.0
|
CG
|
C:ASN713
|
4.3
|
124.5
|
1.0
|
O
|
C:GLY213
|
4.4
|
157.9
|
1.0
|
NZ
|
C:LYS691
|
4.4
|
138.6
|
1.0
|
C
|
C:GLY213
|
4.5
|
158.5
|
1.0
|
CB
|
C:BFD369
|
4.5
|
107.2
|
1.0
|
OG1
|
C:THR610
|
4.5
|
116.4
|
1.0
|
N
|
C:GLY213
|
4.5
|
155.8
|
1.0
|
OD2
|
C:ASP714
|
4.6
|
120.4
|
1.0
|
OG1
|
C:THR371
|
4.6
|
129.5
|
1.0
|
CG2
|
C:THR371
|
4.8
|
129.2
|
1.0
|
N
|
C:LYS370
|
4.8
|
118.8
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 7ddf
Go back to
Fluorine Binding Sites List in 7ddf
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:F369
b:115.2
occ:1.00
|
F3
|
C:BFD369
|
0.0
|
115.2
|
1.0
|
BE
|
C:BFD369
|
1.5
|
113.2
|
1.0
|
OG1
|
C:THR610
|
2.3
|
116.4
|
1.0
|
F1
|
C:BFD369
|
2.5
|
114.1
|
1.0
|
F2
|
C:BFD369
|
2.5
|
113.3
|
1.0
|
OD1
|
C:BFD369
|
2.5
|
111.5
|
1.0
|
N
|
C:THR371
|
3.1
|
124.0
|
1.0
|
CB
|
C:THR610
|
3.2
|
115.6
|
1.0
|
CG
|
C:BFD369
|
3.3
|
108.4
|
1.0
|
N
|
C:LYS370
|
3.4
|
118.8
|
1.0
|
OD2
|
C:BFD369
|
3.4
|
107.8
|
1.0
|
CB
|
C:THR371
|
3.8
|
127.3
|
1.0
|
CB
|
C:LYS370
|
3.8
|
123.4
|
1.0
|
OG1
|
C:THR371
|
3.9
|
129.5
|
1.0
|
CA
|
C:LYS370
|
3.9
|
123.0
|
1.0
|
CA
|
C:THR610
|
3.9
|
112.6
|
1.0
|
O
|
C:GLY213
|
3.9
|
157.9
|
1.0
|
C
|
C:LYS370
|
4.0
|
124.8
|
1.0
|
CA
|
C:THR371
|
4.0
|
122.0
|
1.0
|
MG
|
C:MG1101
|
4.1
|
113.2
|
1.0
|
N
|
C:GLY611
|
4.2
|
114.8
|
1.0
|
CA
|
C:GLY213
|
4.2
|
157.2
|
1.0
|
O
|
C:THR371
|
4.2
|
109.5
|
1.0
|
C
|
C:BFD369
|
4.4
|
112.4
|
1.0
|
O
|
C:HOH1201
|
4.4
|
111.3
|
1.0
|
CG2
|
C:THR610
|
4.4
|
116.4
|
1.0
|
CB
|
C:BFD369
|
4.5
|
107.2
|
1.0
|
C
|
C:GLY213
|
4.5
|
158.5
|
1.0
|
NZ
|
C:LYS691
|
4.5
|
138.6
|
1.0
|
C
|
C:THR371
|
4.6
|
113.7
|
1.0
|
C
|
C:THR610
|
4.6
|
114.0
|
1.0
|
CA
|
C:BFD369
|
4.6
|
106.7
|
1.0
|
ND2
|
C:ASN713
|
4.8
|
125.1
|
1.0
|
O
|
C:VAL609
|
4.9
|
105.0
|
1.0
|
N
|
C:ASP612
|
4.9
|
123.9
|
1.0
|
CB
|
C:ASP612
|
5.0
|
134.1
|
1.0
|
|
Reference:
R.Kanai,
F.Cornelius,
H.Ogawa,
K.Motoyama,
B.Vilsen,
C.Toyoshima.
Binding of Cardiotonic Steroids to Na + ,K + -Atpase in the E2P State. Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 33318128
DOI: 10.1073/PNAS.2020438118
Page generated: Fri Aug 2 06:27:01 2024
|