Fluorine in PDB 7d92: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry):
7.2.2.13;
Protein crystallography data
The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92
was solved by
R.Kanai,
F.Cornelius,
H.Ogawa,
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)
|
14.94 /
3.90
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.234,
84.234,
646.262,
90,
90,
90
|
R / Rfree (%)
|
20.9 /
25.7
|
Other elements in 7d92:
The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry) also contains other interesting chemical elements:
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
(pdb code 7d92). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry), PDB code: 7d92:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7d92
Go back to
Fluorine Binding Sites List in 7d92
Fluorine binding site 1 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
 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 Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:165.0
occ:1.00
|
F1
|
A:BFD369
|
0.0
|
165.0
|
1.0
|
BE
|
A:BFD369
|
1.5
|
168.9
|
1.0
|
F3
|
A:BFD369
|
2.5
|
162.2
|
1.0
|
F2
|
A:BFD369
|
2.5
|
161.5
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
171.7
|
1.0
|
N
|
A:GLY611
|
2.8
|
138.5
|
1.0
|
OG1
|
A:THR610
|
3.0
|
114.0
|
1.0
|
ND2
|
A:ASN713
|
3.1
|
177.1
|
1.0
|
CA
|
A:THR610
|
3.2
|
134.1
|
1.0
|
NZ
|
A:LYS691
|
3.3
|
105.6
|
1.0
|
C
|
A:THR610
|
3.4
|
140.1
|
1.0
|
CA
|
A:GLY213
|
3.6
|
171.2
|
1.0
|
CB
|
A:THR610
|
3.6
|
117.2
|
1.0
|
CG
|
A:BFD369
|
3.8
|
179.4
|
1.0
|
CA
|
A:GLY611
|
3.8
|
134.9
|
1.0
|
O
|
A:THR212
|
3.9
|
155.8
|
1.0
|
CE
|
A:LYS691
|
4.0
|
105.1
|
1.0
|
OD2
|
A:BFD369
|
4.1
|
210.2
|
1.0
|
O
|
A:HOH1201
|
4.2
|
140.2
|
1.0
|
O
|
A:GLY213
|
4.3
|
176.4
|
1.0
|
CG
|
A:ASN713
|
4.4
|
174.5
|
1.0
|
C
|
A:GLY213
|
4.4
|
173.0
|
1.0
|
O
|
A:VAL609
|
4.4
|
137.8
|
1.0
|
N
|
A:GLY213
|
4.5
|
166.2
|
1.0
|
N
|
A:THR610
|
4.5
|
145.2
|
1.0
|
O
|
A:THR610
|
4.5
|
143.8
|
1.0
|
C
|
A:GLY611
|
4.6
|
129.1
|
1.0
|
C
|
A:THR212
|
4.6
|
159.3
|
1.0
|
N
|
A:ASP612
|
4.6
|
146.2
|
1.0
|
MG
|
A:MG1101
|
4.8
|
121.8
|
1.0
|
N
|
A:THR371
|
4.9
|
158.2
|
1.0
|
N
|
A:LYS370
|
4.9
|
115.7
|
1.0
|
OD1
|
A:ASN713
|
4.9
|
177.6
|
1.0
|
C
|
A:VAL609
|
4.9
|
135.4
|
1.0
|
CB
|
A:THR371
|
5.0
|
179.6
|
1.0
|
CG2
|
A:THR610
|
5.0
|
106.6
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7d92
Go back to
Fluorine Binding Sites List in 7d92
Fluorine binding site 2 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
 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 Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:161.5
occ:1.00
|
F2
|
A:BFD369
|
0.0
|
161.5
|
1.0
|
BE
|
A:BFD369
|
1.5
|
168.9
|
1.0
|
MG
|
A:MG1101
|
2.3
|
121.8
|
1.0
|
OD2
|
A:BFD369
|
2.4
|
210.2
|
1.0
|
O
|
A:HOH1201
|
2.4
|
140.2
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
171.7
|
1.0
|
F3
|
A:BFD369
|
2.5
|
162.2
|
1.0
|
F1
|
A:BFD369
|
2.5
|
165.0
|
1.0
|
CG
|
A:BFD369
|
2.8
|
179.4
|
1.0
|
O
|
A:THR371
|
3.0
|
214.0
|
1.0
|
ND2
|
A:ASN713
|
3.5
|
177.1
|
1.0
|
O
|
A:HOH1202
|
3.6
|
149.1
|
1.0
|
CB
|
A:THR371
|
3.7
|
179.6
|
1.0
|
CA
|
A:GLY213
|
3.8
|
171.2
|
1.0
|
N
|
A:THR371
|
3.9
|
158.2
|
1.0
|
C
|
A:THR371
|
3.9
|
185.1
|
1.0
|
CA
|
A:THR371
|
4.0
|
170.0
|
1.0
|
OD1
|
A:ASN713
|
4.2
|
177.6
|
1.0
|
OD1
|
A:ASP710
|
4.3
|
206.1
|
1.0
|
CG
|
A:ASN713
|
4.3
|
174.5
|
1.0
|
CB
|
A:BFD369
|
4.3
|
141.9
|
1.0
|
OD2
|
A:ASP714
|
4.3
|
139.9
|
1.0
|
NZ
|
A:LYS691
|
4.3
|
105.6
|
1.0
|
O
|
A:SER209
|
4.4
|
122.4
|
1.0
|
O
|
A:GLY213
|
4.5
|
176.4
|
1.0
|
OG1
|
A:THR610
|
4.5
|
114.0
|
1.0
|
CG2
|
A:THR371
|
4.6
|
178.9
|
1.0
|
OG1
|
A:THR371
|
4.6
|
177.7
|
1.0
|
N
|
A:LYS370
|
4.6
|
115.7
|
1.0
|
C
|
A:GLY213
|
4.7
|
173.0
|
1.0
|
N
|
A:GLY213
|
4.8
|
166.2
|
1.0
|
C
|
A:LYS370
|
4.9
|
139.9
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7d92
Go back to
Fluorine Binding Sites List in 7d92
Fluorine binding site 3 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry)
 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 Na+,K+-Atpase in the E2P State with Bound MG2+ and Anthroylouabain (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:162.2
occ:1.00
|
F3
|
A:BFD369
|
0.0
|
162.2
|
1.0
|
BE
|
A:BFD369
|
1.5
|
168.9
|
1.0
|
OG1
|
A:THR610
|
2.4
|
114.0
|
1.0
|
N
|
A:THR371
|
2.4
|
158.2
|
1.0
|
F1
|
A:BFD369
|
2.5
|
165.0
|
1.0
|
F2
|
A:BFD369
|
2.5
|
161.5
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
171.7
|
1.0
|
N
|
A:LYS370
|
3.1
|
115.7
|
1.0
|
CB
|
A:THR610
|
3.2
|
117.2
|
1.0
|
CB
|
A:THR371
|
3.2
|
179.6
|
1.0
|
CG
|
A:BFD369
|
3.3
|
179.4
|
1.0
|
CA
|
A:THR371
|
3.3
|
170.0
|
1.0
|
C
|
A:LYS370
|
3.4
|
139.9
|
1.0
|
OG1
|
A:THR371
|
3.4
|
177.7
|
1.0
|
CA
|
A:LYS370
|
3.5
|
127.4
|
1.0
|
OD2
|
A:BFD369
|
3.5
|
210.2
|
1.0
|
CB
|
A:LYS370
|
3.5
|
125.4
|
1.0
|
CA
|
A:THR610
|
3.8
|
134.1
|
1.0
|
O
|
A:THR371
|
3.8
|
214.0
|
1.0
|
O
|
A:GLY213
|
4.0
|
176.4
|
1.0
|
C
|
A:THR371
|
4.0
|
185.1
|
1.0
|
C
|
A:BFD369
|
4.2
|
104.1
|
1.0
|
N
|
A:GLY611
|
4.2
|
138.5
|
1.0
|
MG
|
A:MG1101
|
4.3
|
121.8
|
1.0
|
CG
|
A:LYS370
|
4.3
|
126.9
|
1.0
|
CA
|
A:GLY213
|
4.5
|
171.2
|
1.0
|
O
|
A:LYS370
|
4.5
|
140.0
|
1.0
|
CB
|
A:BFD369
|
4.5
|
141.9
|
1.0
|
CG2
|
A:THR610
|
4.5
|
106.6
|
1.0
|
CA
|
A:BFD369
|
4.6
|
110.6
|
1.0
|
C
|
A:THR610
|
4.6
|
140.1
|
1.0
|
CG2
|
A:THR371
|
4.6
|
178.9
|
1.0
|
C
|
A:GLY213
|
4.7
|
173.0
|
1.0
|
O
|
A:HOH1201
|
4.8
|
140.2
|
1.0
|
O
|
A:VAL609
|
4.8
|
137.8
|
1.0
|
NZ
|
A:LYS691
|
4.9
|
105.6
|
1.0
|
CD
|
A:LYS370
|
5.0
|
127.5
|
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 06:22:47 2024
|