Magnesium in PDB 7evx: Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime:
7.2.2.13;
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime, PDB code: 7evx
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)
|
15.98 /
3.71
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.109,
117.47,
491.339,
90,
90,
90
|
R / Rfree (%)
|
19.3 /
23.9
|
Other elements in 7evx:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
(pdb code 7evx). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime, PDB code: 7evx:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7evx
Go back to
Magnesium Binding Sites List in 7evx
Magnesium binding site 1 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:136.2
occ:1.00
|
OD1
|
A:ASP710
|
2.1
|
151.0
|
1.0
|
O
|
A:THR371
|
2.1
|
123.5
|
1.0
|
O
|
A:HOH1204
|
2.3
|
96.8
|
1.0
|
OP3
|
A:PHD369
|
2.3
|
125.0
|
1.0
|
OD2
|
A:PHD369
|
2.3
|
110.9
|
1.0
|
O
|
A:HOH1201
|
2.4
|
110.4
|
1.0
|
OD2
|
A:ASP710
|
2.5
|
155.2
|
1.0
|
CG
|
A:ASP710
|
2.5
|
148.6
|
1.0
|
C
|
A:THR371
|
3.3
|
112.0
|
1.0
|
N
|
A:GLY711
|
3.4
|
101.1
|
1.0
|
CG
|
A:PHD369
|
3.4
|
107.4
|
1.0
|
P
|
A:PHD369
|
3.6
|
110.6
|
1.0
|
OD2
|
A:ASP714
|
3.8
|
115.0
|
1.0
|
OD1
|
A:PHD369
|
3.9
|
114.3
|
1.0
|
CB
|
A:ASP710
|
3.9
|
129.7
|
1.0
|
CA
|
A:GLY372
|
4.0
|
100.9
|
1.0
|
CA
|
A:GLY711
|
4.1
|
94.4
|
1.0
|
N
|
A:GLY372
|
4.1
|
100.8
|
1.0
|
N
|
A:ASP710
|
4.2
|
100.0
|
1.0
|
C
|
A:ASP710
|
4.3
|
104.8
|
1.0
|
OP1
|
A:PHD369
|
4.4
|
114.8
|
1.0
|
CA
|
A:ASP710
|
4.4
|
110.5
|
1.0
|
CA
|
A:THR371
|
4.4
|
127.5
|
1.0
|
CB
|
A:THR371
|
4.5
|
155.7
|
1.0
|
OG1
|
A:THR373
|
4.5
|
89.2
|
1.0
|
N
|
A:THR373
|
4.5
|
97.4
|
1.0
|
O
|
A:SER209
|
4.6
|
112.0
|
1.0
|
CG2
|
A:THR371
|
4.6
|
166.3
|
1.0
|
C
|
A:GLY372
|
4.7
|
103.0
|
1.0
|
CB
|
A:PHD369
|
4.7
|
103.5
|
1.0
|
OP2
|
A:PHD369
|
4.7
|
127.2
|
1.0
|
OD1
|
A:ASN713
|
4.8
|
105.7
|
1.0
|
N
|
A:THR371
|
4.8
|
110.2
|
1.0
|
CG
|
A:ASP714
|
4.9
|
110.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7evx
Go back to
Magnesium Binding Sites List in 7evx
Magnesium binding site 2 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:193.9
occ:1.00
|
OD2
|
A:ASP804
|
2.0
|
196.9
|
1.0
|
OD1
|
A:ASP804
|
2.1
|
192.2
|
1.0
|
CG
|
A:ASP804
|
2.2
|
175.0
|
1.0
|
OE1
|
A:GLU779
|
2.3
|
143.5
|
1.0
|
O
|
A:HOH1203
|
2.4
|
203.8
|
1.0
|
OE2
|
A:GLU779
|
2.5
|
141.7
|
1.0
|
O
|
A:HOH1202
|
2.5
|
69.1
|
1.0
|
OE2
|
A:GLU327
|
2.6
|
166.0
|
1.0
|
CD
|
A:GLU779
|
2.7
|
133.9
|
1.0
|
O
|
A:HOH1205
|
2.7
|
112.1
|
1.0
|
CB
|
A:ASP804
|
3.5
|
162.2
|
1.0
|
CD
|
A:GLU327
|
3.7
|
145.6
|
1.0
|
CG
|
A:GLU779
|
4.1
|
114.9
|
1.0
|
OE1
|
A:GLU327
|
4.2
|
136.5
|
1.0
|
ND2
|
A:ASN776
|
4.4
|
109.5
|
1.0
|
CG2
|
A:ILE800
|
4.6
|
100.3
|
1.0
|
OG
|
A:SER775
|
4.6
|
67.8
|
1.0
|
CG
|
A:ASN776
|
4.6
|
102.9
|
1.0
|
OD1
|
A:ASN776
|
4.7
|
106.2
|
1.0
|
CA
|
A:ASP804
|
4.7
|
128.2
|
1.0
|
CB
|
A:GLU779
|
4.7
|
98.2
|
1.0
|
CA
|
A:PRO326
|
4.8
|
107.3
|
1.0
|
O
|
A:VAL325
|
4.9
|
93.9
|
1.0
|
N
|
A:GLU327
|
4.9
|
90.9
|
1.0
|
O
|
A:ALA323
|
5.0
|
124.5
|
1.0
|
CG
|
A:GLU327
|
5.0
|
129.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7evx
Go back to
Magnesium Binding Sites List in 7evx
Magnesium binding site 3 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:124.8
occ:1.00
|
O
|
C:THR371
|
2.1
|
123.2
|
1.0
|
OD2
|
C:PHD369
|
2.1
|
108.5
|
1.0
|
OD1
|
C:ASP710
|
2.2
|
132.8
|
1.0
|
O
|
C:HOH1201
|
2.2
|
128.2
|
1.0
|
OP3
|
C:PHD369
|
2.2
|
92.4
|
1.0
|
O
|
C:HOH1204
|
2.2
|
97.5
|
1.0
|
CG
|
C:ASP710
|
2.7
|
131.3
|
1.0
|
OD2
|
C:ASP710
|
2.8
|
142.8
|
1.0
|
CG
|
C:PHD369
|
3.3
|
101.0
|
1.0
|
C
|
C:THR371
|
3.3
|
123.9
|
1.0
|
N
|
C:GLY711
|
3.4
|
98.5
|
1.0
|
P
|
C:PHD369
|
3.5
|
92.4
|
1.0
|
OD2
|
C:ASP714
|
3.7
|
93.9
|
1.0
|
OD1
|
C:PHD369
|
3.7
|
103.2
|
1.0
|
CA
|
C:GLY711
|
4.0
|
102.7
|
1.0
|
CB
|
C:ASP710
|
4.1
|
110.4
|
1.0
|
CA
|
C:GLY372
|
4.1
|
122.8
|
1.0
|
OP1
|
C:PHD369
|
4.1
|
92.4
|
1.0
|
N
|
C:GLY372
|
4.2
|
122.5
|
1.0
|
N
|
C:ASP710
|
4.2
|
98.2
|
1.0
|
C
|
C:ASP710
|
4.3
|
95.5
|
1.0
|
CA
|
C:THR371
|
4.4
|
124.5
|
1.0
|
CA
|
C:ASP710
|
4.4
|
96.6
|
1.0
|
O
|
C:SER209
|
4.4
|
101.9
|
1.0
|
OG1
|
C:THR373
|
4.5
|
94.0
|
1.0
|
CB
|
C:PHD369
|
4.5
|
95.8
|
1.0
|
CB
|
C:THR371
|
4.6
|
140.1
|
1.0
|
OD1
|
C:ASN713
|
4.6
|
110.5
|
1.0
|
N
|
C:THR373
|
4.6
|
110.3
|
1.0
|
OP2
|
C:PHD369
|
4.6
|
96.1
|
1.0
|
N
|
C:THR371
|
4.7
|
111.9
|
1.0
|
C
|
C:GLY372
|
4.8
|
119.0
|
1.0
|
CG
|
C:ASP714
|
4.8
|
93.9
|
1.0
|
CG2
|
C:THR371
|
4.9
|
143.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7evx
Go back to
Magnesium Binding Sites List in 7evx
Magnesium binding site 4 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structures of Na+,K+-Atpase in Complex with Istaroxime within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:207.2
occ:1.00
|
OD2
|
C:ASP804
|
2.0
|
191.2
|
1.0
|
OD1
|
C:ASP804
|
2.2
|
157.6
|
1.0
|
CG
|
C:ASP804
|
2.2
|
157.1
|
1.0
|
OE1
|
C:GLU779
|
2.3
|
167.3
|
1.0
|
O
|
C:HOH1202
|
2.5
|
152.4
|
1.0
|
OE2
|
C:GLU779
|
2.6
|
165.6
|
1.0
|
O
|
C:HOH1205
|
2.6
|
63.9
|
1.0
|
OE2
|
C:GLU327
|
2.6
|
123.8
|
1.0
|
CD
|
C:GLU779
|
2.7
|
153.7
|
1.0
|
O
|
C:HOH1203
|
2.8
|
167.9
|
1.0
|
CB
|
C:ASP804
|
3.6
|
124.3
|
1.0
|
CD
|
C:GLU327
|
3.7
|
111.6
|
1.0
|
CG
|
C:GLU779
|
4.1
|
123.9
|
1.0
|
OE1
|
C:GLU327
|
4.2
|
104.7
|
1.0
|
ND2
|
C:ASN776
|
4.3
|
93.6
|
1.0
|
CG2
|
C:ILE800
|
4.4
|
96.8
|
1.0
|
OG
|
C:SER775
|
4.6
|
60.5
|
1.0
|
CG
|
C:ASN776
|
4.7
|
87.6
|
1.0
|
CA
|
C:ASP804
|
4.7
|
96.7
|
1.0
|
CB
|
C:GLU779
|
4.8
|
93.5
|
1.0
|
O
|
C:VAL325
|
4.9
|
84.8
|
1.0
|
OD1
|
C:ASN776
|
4.9
|
88.2
|
1.0
|
O
|
C:ALA323
|
4.9
|
92.3
|
1.0
|
CA
|
C:PRO326
|
4.9
|
68.5
|
1.0
|
CG
|
C:GLU327
|
5.0
|
100.2
|
1.0
|
N
|
C:GLU327
|
5.0
|
88.0
|
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: Sun Jul 11 17:36:31 2021
|