Magnesium in PDB 7ddk: Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin:
7.2.2.13;
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin, PDB code: 7ddk
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)
|
16.00 /
3.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.357,
118.176,
494.668,
90,
90,
90
|
R / Rfree (%)
|
22 /
26.9
|
Other elements in 7ddk:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin 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 Rostafuroxin
(pdb code 7ddk). 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 Rostafuroxin, PDB code: 7ddk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7ddk
Go back to
Magnesium Binding Sites List in 7ddk
Magnesium binding site 1 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
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 Rostafuroxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:84.5
occ:1.00
|
O
|
A:HOH1201
|
2.0
|
101.1
|
1.0
|
O
|
A:THR371
|
2.0
|
64.2
|
1.0
|
OD2
|
A:PHD369
|
2.0
|
80.0
|
1.0
|
O
|
A:HOH1202
|
2.1
|
67.0
|
1.0
|
OD1
|
A:ASP710
|
2.1
|
82.6
|
1.0
|
OP3
|
A:PHD369
|
2.3
|
68.4
|
1.0
|
OD2
|
A:ASP710
|
2.6
|
78.6
|
1.0
|
CG
|
A:ASP710
|
2.6
|
76.5
|
1.0
|
CG
|
A:PHD369
|
3.2
|
72.8
|
1.0
|
C
|
A:THR371
|
3.2
|
50.3
|
1.0
|
N
|
A:GLY711
|
3.5
|
73.7
|
1.0
|
P
|
A:PHD369
|
3.5
|
55.7
|
1.0
|
OD1
|
A:PHD369
|
3.6
|
76.9
|
1.0
|
OD2
|
A:ASP714
|
3.7
|
59.5
|
1.0
|
CB
|
A:ASP710
|
4.0
|
61.5
|
1.0
|
CA
|
A:GLY372
|
4.0
|
67.8
|
1.0
|
N
|
A:GLY372
|
4.0
|
61.0
|
1.0
|
CA
|
A:GLY711
|
4.1
|
68.2
|
1.0
|
N
|
A:ASP710
|
4.2
|
58.2
|
1.0
|
OP1
|
A:PHD369
|
4.3
|
54.4
|
1.0
|
CA
|
A:THR371
|
4.3
|
65.7
|
1.0
|
C
|
A:ASP710
|
4.4
|
61.9
|
1.0
|
CB
|
A:THR371
|
4.4
|
80.7
|
1.0
|
CA
|
A:ASP710
|
4.4
|
55.5
|
1.0
|
CB
|
A:PHD369
|
4.4
|
64.5
|
1.0
|
N
|
A:THR373
|
4.5
|
68.5
|
1.0
|
CG2
|
A:THR371
|
4.6
|
89.5
|
1.0
|
O
|
A:SER209
|
4.6
|
41.0
|
1.0
|
OP2
|
A:PHD369
|
4.7
|
70.7
|
1.0
|
N
|
A:THR371
|
4.7
|
85.8
|
1.0
|
OG1
|
A:THR373
|
4.7
|
60.1
|
1.0
|
C
|
A:GLY372
|
4.7
|
70.5
|
1.0
|
OD1
|
A:ASN713
|
4.7
|
62.9
|
1.0
|
CG
|
A:ASP714
|
4.9
|
60.5
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7ddk
Go back to
Magnesium Binding Sites List in 7ddk
Magnesium binding site 2 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
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 Rostafuroxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:78.4
occ:1.00
|
OD2
|
A:ASP804
|
2.1
|
74.6
|
1.0
|
O
|
A:HOH1204
|
2.1
|
66.8
|
1.0
|
OD1
|
A:ASP804
|
2.1
|
78.0
|
1.0
|
O
|
A:HOH1205
|
2.2
|
84.1
|
1.0
|
OE2
|
A:GLU779
|
2.3
|
56.9
|
1.0
|
CG
|
A:ASP804
|
2.3
|
74.3
|
1.0
|
OE2
|
A:GLU327
|
2.4
|
92.6
|
1.0
|
O
|
A:HOH1203
|
2.4
|
108.8
|
1.0
|
CD
|
A:GLU779
|
3.0
|
54.4
|
1.0
|
OE1
|
A:GLU779
|
3.2
|
59.3
|
1.0
|
CD
|
A:GLU327
|
3.5
|
80.7
|
1.0
|
CB
|
A:ASP804
|
3.6
|
68.3
|
1.0
|
OE1
|
A:GLU327
|
3.9
|
81.6
|
1.0
|
ND2
|
A:ASN776
|
4.3
|
79.6
|
1.0
|
CG
|
A:GLU779
|
4.3
|
46.0
|
1.0
|
CG2
|
A:ILE800
|
4.5
|
50.5
|
1.0
|
OD1
|
A:ASN776
|
4.5
|
108.4
|
1.0
|
O
|
A:VAL325
|
4.6
|
69.1
|
1.0
|
CG
|
A:ASN776
|
4.6
|
89.9
|
1.0
|
O
|
A:ALA323
|
4.6
|
85.3
|
1.0
|
CA
|
A:PRO326
|
4.7
|
62.8
|
1.0
|
CG
|
A:GLU327
|
4.8
|
69.2
|
1.0
|
CA
|
A:ASP804
|
4.8
|
64.3
|
1.0
|
N
|
A:GLU327
|
4.8
|
70.8
|
1.0
|
CB
|
A:GLU779
|
4.8
|
47.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7ddk
Go back to
Magnesium Binding Sites List in 7ddk
Magnesium binding site 3 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
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 Rostafuroxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:61.9
occ:1.00
|
O
|
C:HOH1201
|
2.0
|
61.1
|
1.0
|
O
|
C:THR371
|
2.1
|
67.1
|
1.0
|
OD1
|
C:ASP710
|
2.2
|
76.5
|
1.0
|
O
|
C:HOH1205
|
2.2
|
54.9
|
1.0
|
OD2
|
C:PHD369
|
2.4
|
83.5
|
1.0
|
OP3
|
C:PHD369
|
2.5
|
60.0
|
1.0
|
OD2
|
C:ASP710
|
2.6
|
80.5
|
1.0
|
CG
|
C:ASP710
|
2.6
|
76.8
|
1.0
|
N
|
C:GLY711
|
3.2
|
60.8
|
1.0
|
C
|
C:THR371
|
3.3
|
67.0
|
1.0
|
CG
|
C:PHD369
|
3.5
|
77.0
|
1.0
|
CA
|
C:GLY711
|
3.8
|
49.7
|
1.0
|
P
|
C:PHD369
|
3.8
|
65.5
|
1.0
|
OD2
|
C:ASP714
|
3.9
|
58.5
|
1.0
|
CB
|
C:ASP710
|
4.0
|
67.8
|
1.0
|
OD1
|
C:PHD369
|
4.0
|
75.2
|
1.0
|
CA
|
C:GLY372
|
4.0
|
80.4
|
1.0
|
N
|
C:GLY372
|
4.1
|
66.3
|
1.0
|
C
|
C:ASP710
|
4.1
|
65.6
|
1.0
|
N
|
C:ASP710
|
4.2
|
47.6
|
1.0
|
CA
|
C:ASP710
|
4.3
|
59.5
|
1.0
|
CA
|
C:THR371
|
4.4
|
78.0
|
1.0
|
O
|
C:SER209
|
4.4
|
53.4
|
1.0
|
CB
|
C:THR371
|
4.4
|
88.3
|
1.0
|
OD1
|
C:ASN713
|
4.5
|
82.4
|
1.0
|
OP1
|
C:PHD369
|
4.5
|
40.4
|
1.0
|
N
|
C:THR373
|
4.6
|
77.3
|
1.0
|
OG1
|
C:THR373
|
4.7
|
79.0
|
1.0
|
CG2
|
C:THR371
|
4.7
|
108.8
|
1.0
|
C
|
C:GLY372
|
4.7
|
85.3
|
1.0
|
CB
|
C:PHD369
|
4.8
|
65.9
|
1.0
|
N
|
C:THR371
|
4.8
|
66.2
|
1.0
|
OP2
|
C:PHD369
|
4.9
|
80.4
|
1.0
|
CG
|
C:ASP714
|
5.0
|
56.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7ddk
Go back to
Magnesium Binding Sites List in 7ddk
Magnesium binding site 4 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Rostafuroxin
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 Rostafuroxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:26.9
occ:1.00
|
O
|
C:HOH1204
|
2.1
|
35.1
|
1.0
|
OD2
|
C:ASP804
|
2.1
|
52.8
|
1.0
|
OD1
|
C:ASP804
|
2.2
|
57.1
|
1.0
|
OE2
|
C:GLU779
|
2.2
|
43.6
|
1.0
|
CG
|
C:ASP804
|
2.3
|
62.6
|
1.0
|
OE2
|
C:GLU327
|
2.4
|
104.2
|
1.0
|
O
|
C:HOH1203
|
2.4
|
34.7
|
1.0
|
O
|
C:HOH1202
|
2.6
|
27.5
|
1.0
|
CD
|
C:GLU779
|
3.0
|
35.2
|
1.0
|
OE1
|
C:GLU779
|
3.2
|
39.4
|
1.0
|
CD
|
C:GLU327
|
3.5
|
89.4
|
1.0
|
CB
|
C:ASP804
|
3.7
|
77.2
|
1.0
|
OE1
|
C:GLU327
|
4.0
|
86.5
|
1.0
|
ND2
|
C:ASN776
|
4.3
|
81.0
|
1.0
|
CG
|
C:GLU779
|
4.3
|
25.0
|
1.0
|
CG2
|
C:ILE800
|
4.4
|
38.6
|
1.0
|
CG
|
C:ASN776
|
4.6
|
78.4
|
1.0
|
O
|
C:VAL325
|
4.6
|
42.6
|
1.0
|
OD1
|
C:ASN776
|
4.6
|
103.6
|
1.0
|
O
|
C:ALA323
|
4.6
|
100.2
|
1.0
|
CG
|
C:GLU327
|
4.7
|
72.3
|
1.0
|
CA
|
C:PRO326
|
4.8
|
37.7
|
1.0
|
CB
|
C:GLU779
|
4.8
|
35.8
|
1.0
|
N
|
C:GLU327
|
4.8
|
51.1
|
1.0
|
CA
|
C:ASP804
|
4.8
|
71.0
|
1.0
|
OG
|
C:SER775
|
5.0
|
34.9
|
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: Wed Oct 2 15:47:48 2024
|