Fluorine in PDB 7d91: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (P4(3)2(1)2 Symmetry)
Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (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+ (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+ (P4(3)2(1)2 Symmetry), PDB code: 7d91
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)
|
14.95 /
3.35
|
Space group
|
P 43 21 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
84.325,
84.325,
646.36,
90,
90,
90
|
R / Rfree (%)
|
21.5 /
26
|
Other elements in 7d91:
The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (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+ (P4(3)2(1)2 Symmetry)
(pdb code 7d91). 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+ (P4(3)2(1)2 Symmetry), PDB code: 7d91:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 7d91
Go back to
Fluorine Binding Sites List in 7d91
Fluorine binding site 1 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (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+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:67.1
occ:1.00
|
F1
|
A:BFD369
|
0.0
|
67.1
|
1.0
|
BE
|
A:BFD369
|
1.5
|
76.3
|
1.0
|
F3
|
A:BFD369
|
2.5
|
71.2
|
1.0
|
F2
|
A:BFD369
|
2.5
|
87.9
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
48.3
|
1.0
|
N
|
A:GLY611
|
2.8
|
75.7
|
1.0
|
OG1
|
A:THR610
|
3.1
|
73.6
|
1.0
|
NZ
|
A:LYS691
|
3.2
|
55.3
|
1.0
|
CA
|
A:THR610
|
3.2
|
77.5
|
1.0
|
ND2
|
A:ASN713
|
3.2
|
81.1
|
1.0
|
C
|
A:THR610
|
3.4
|
69.9
|
1.0
|
CB
|
A:THR610
|
3.7
|
71.5
|
1.0
|
CA
|
A:GLY611
|
3.8
|
73.9
|
1.0
|
CA
|
A:GLY213
|
3.8
|
96.1
|
1.0
|
CG
|
A:BFD369
|
3.8
|
46.9
|
1.0
|
CE
|
A:LYS691
|
3.9
|
51.9
|
1.0
|
O
|
A:THR212
|
4.2
|
107.4
|
1.0
|
OD2
|
A:BFD369
|
4.2
|
56.9
|
1.0
|
O
|
A:HOH1201
|
4.4
|
68.5
|
1.0
|
O
|
A:VAL609
|
4.4
|
56.0
|
1.0
|
O
|
A:GLY213
|
4.4
|
103.6
|
1.0
|
N
|
A:THR610
|
4.5
|
80.1
|
1.0
|
CG
|
A:ASN713
|
4.5
|
64.3
|
1.0
|
O
|
A:THR610
|
4.5
|
57.0
|
1.0
|
N
|
A:ASP612
|
4.6
|
66.8
|
1.0
|
C
|
A:GLY213
|
4.6
|
102.0
|
1.0
|
C
|
A:GLY611
|
4.6
|
62.9
|
1.0
|
MG
|
A:MG1101
|
4.6
|
55.0
|
1.0
|
N
|
A:GLY213
|
4.7
|
102.4
|
1.0
|
N
|
A:LYS370
|
4.8
|
55.4
|
1.0
|
N
|
A:THR371
|
4.8
|
57.9
|
1.0
|
C
|
A:THR212
|
4.9
|
106.2
|
1.0
|
C
|
A:VAL609
|
4.9
|
63.0
|
1.0
|
OD1
|
A:ASN713
|
5.0
|
57.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 7d91
Go back to
Fluorine Binding Sites List in 7d91
Fluorine binding site 2 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (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+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:87.9
occ:1.00
|
F2
|
A:BFD369
|
0.0
|
87.9
|
1.0
|
BE
|
A:BFD369
|
1.5
|
76.3
|
1.0
|
MG
|
A:MG1101
|
2.2
|
55.0
|
1.0
|
O
|
A:HOH1201
|
2.4
|
68.5
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
48.3
|
1.0
|
F1
|
A:BFD369
|
2.5
|
67.1
|
1.0
|
F3
|
A:BFD369
|
2.5
|
71.2
|
1.0
|
OD2
|
A:BFD369
|
2.5
|
56.9
|
1.0
|
CG
|
A:BFD369
|
2.9
|
46.9
|
1.0
|
O
|
A:THR371
|
3.1
|
87.1
|
1.0
|
ND2
|
A:ASN713
|
3.4
|
81.1
|
1.0
|
O
|
A:HOH1204
|
3.5
|
111.1
|
1.0
|
CA
|
A:GLY213
|
3.9
|
96.1
|
1.0
|
OD1
|
A:ASN713
|
4.0
|
57.1
|
1.0
|
CB
|
A:THR371
|
4.0
|
63.4
|
1.0
|
C
|
A:THR371
|
4.1
|
65.8
|
1.0
|
N
|
A:THR371
|
4.1
|
57.9
|
1.0
|
NZ
|
A:LYS691
|
4.1
|
55.3
|
1.0
|
OD1
|
A:ASP710
|
4.1
|
70.8
|
1.0
|
OD2
|
A:ASP714
|
4.2
|
71.9
|
1.0
|
CG
|
A:ASN713
|
4.2
|
64.3
|
1.0
|
CA
|
A:THR371
|
4.3
|
56.8
|
1.0
|
CB
|
A:BFD369
|
4.3
|
46.8
|
1.0
|
O
|
A:SER209
|
4.6
|
67.5
|
1.0
|
O
|
A:GLY213
|
4.7
|
103.6
|
1.0
|
N
|
A:LYS370
|
4.8
|
55.4
|
1.0
|
OD1
|
A:ASP714
|
4.8
|
57.1
|
1.0
|
CG2
|
A:THR371
|
4.8
|
53.6
|
1.0
|
C
|
A:GLY213
|
4.9
|
102.0
|
1.0
|
OG1
|
A:THR610
|
4.9
|
73.6
|
1.0
|
N
|
A:GLY213
|
4.9
|
102.4
|
1.0
|
OG1
|
A:THR371
|
4.9
|
82.9
|
1.0
|
CG
|
A:ASP714
|
4.9
|
55.7
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 7d91
Go back to
Fluorine Binding Sites List in 7d91
Fluorine binding site 3 out
of 3 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound MG2+ (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+ (P4(3)2(1)2 Symmetry) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F369
b:71.2
occ:1.00
|
F3
|
A:BFD369
|
0.0
|
71.2
|
1.0
|
BE
|
A:BFD369
|
1.5
|
76.3
|
1.0
|
N
|
A:THR371
|
2.4
|
57.9
|
1.0
|
F1
|
A:BFD369
|
2.5
|
67.1
|
1.0
|
OD1
|
A:BFD369
|
2.5
|
48.3
|
1.0
|
F2
|
A:BFD369
|
2.5
|
87.9
|
1.0
|
OG1
|
A:THR610
|
2.9
|
73.6
|
1.0
|
N
|
A:LYS370
|
3.1
|
55.4
|
1.0
|
CB
|
A:THR371
|
3.2
|
63.4
|
1.0
|
CA
|
A:THR371
|
3.2
|
56.8
|
1.0
|
CG
|
A:BFD369
|
3.2
|
46.9
|
1.0
|
C
|
A:LYS370
|
3.3
|
56.0
|
1.0
|
OD2
|
A:BFD369
|
3.4
|
56.9
|
1.0
|
CA
|
A:LYS370
|
3.4
|
52.0
|
1.0
|
OG1
|
A:THR371
|
3.5
|
82.9
|
1.0
|
O
|
A:THR371
|
3.6
|
87.1
|
1.0
|
CB
|
A:LYS370
|
3.6
|
49.4
|
1.0
|
CB
|
A:THR610
|
3.6
|
71.5
|
1.0
|
C
|
A:THR371
|
3.8
|
65.8
|
1.0
|
MG
|
A:MG1101
|
4.0
|
55.0
|
1.0
|
CA
|
A:THR610
|
4.0
|
77.5
|
1.0
|
C
|
A:BFD369
|
4.1
|
53.2
|
1.0
|
O
|
A:GLY213
|
4.1
|
103.6
|
1.0
|
N
|
A:GLY611
|
4.3
|
75.7
|
1.0
|
CG
|
A:LYS370
|
4.4
|
52.5
|
1.0
|
O
|
A:LYS370
|
4.4
|
58.0
|
1.0
|
CB
|
A:BFD369
|
4.5
|
46.8
|
1.0
|
CA
|
A:BFD369
|
4.5
|
46.9
|
1.0
|
CA
|
A:GLY213
|
4.6
|
96.1
|
1.0
|
CG2
|
A:THR371
|
4.6
|
53.6
|
1.0
|
O
|
A:HOH1201
|
4.7
|
68.5
|
1.0
|
C
|
A:THR610
|
4.8
|
69.9
|
1.0
|
NZ
|
A:LYS691
|
4.8
|
55.3
|
1.0
|
C
|
A:GLY213
|
4.9
|
102.0
|
1.0
|
O
|
A:VAL609
|
4.9
|
56.0
|
1.0
|
CD
|
A:LYS370
|
5.0
|
50.9
|
1.0
|
CG2
|
A:THR610
|
5.0
|
59.4
|
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 06:22:42 2024
|