Magnesium in PDB 7ddh: Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
Enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
All present enzymatic activity of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin:
7.2.2.13;
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 7ddh
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 /
3.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
114.973,
118.493,
495.137,
90,
90,
90
|
R / Rfree (%)
|
24.1 /
27.2
|
Other elements in 7ddh:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin 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 Digoxin
(pdb code 7ddh). 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 Digoxin, PDB code: 7ddh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7ddh
Go back to
Magnesium Binding Sites List in 7ddh
Magnesium binding site 1 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
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 Digoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:88.0
occ:1.00
|
O
|
A:HOH1201
|
2.0
|
77.8
|
1.0
|
OD2
|
A:PHD369
|
2.0
|
101.1
|
1.0
|
O
|
A:THR371
|
2.1
|
107.8
|
1.0
|
OD1
|
A:ASP710
|
2.1
|
112.0
|
1.0
|
OP3
|
A:PHD369
|
2.1
|
73.6
|
1.0
|
O
|
A:HOH1202
|
2.2
|
87.6
|
1.0
|
OD2
|
A:ASP710
|
2.6
|
84.7
|
1.0
|
CG
|
A:ASP710
|
2.6
|
96.7
|
1.0
|
CG
|
A:PHD369
|
3.1
|
92.0
|
1.0
|
C
|
A:THR371
|
3.3
|
87.3
|
1.0
|
P
|
A:PHD369
|
3.4
|
80.2
|
1.0
|
N
|
A:GLY711
|
3.5
|
83.7
|
1.0
|
OD1
|
A:PHD369
|
3.6
|
97.8
|
1.0
|
OD2
|
A:ASP714
|
3.9
|
76.2
|
1.0
|
CB
|
A:ASP710
|
4.0
|
76.1
|
1.0
|
CA
|
A:GLY372
|
4.0
|
82.4
|
1.0
|
N
|
A:GLY372
|
4.1
|
80.9
|
1.0
|
N
|
A:ASP710
|
4.2
|
76.1
|
1.0
|
CA
|
A:GLY711
|
4.2
|
85.5
|
1.0
|
OP1
|
A:PHD369
|
4.2
|
73.6
|
1.0
|
CA
|
A:THR371
|
4.3
|
85.2
|
1.0
|
CB
|
A:PHD369
|
4.4
|
73.6
|
1.0
|
C
|
A:ASP710
|
4.4
|
76.1
|
1.0
|
CA
|
A:ASP710
|
4.4
|
76.1
|
1.0
|
OP2
|
A:PHD369
|
4.4
|
92.5
|
1.0
|
CB
|
A:THR371
|
4.5
|
103.7
|
1.0
|
OG1
|
A:THR373
|
4.5
|
74.6
|
1.0
|
N
|
A:THR373
|
4.6
|
74.6
|
1.0
|
OD1
|
A:ASN713
|
4.6
|
75.2
|
1.0
|
C
|
A:GLY372
|
4.7
|
85.4
|
1.0
|
N
|
A:THR371
|
4.7
|
89.8
|
1.0
|
O
|
A:SER209
|
4.7
|
93.5
|
1.0
|
CG2
|
A:THR371
|
4.9
|
115.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7ddh
Go back to
Magnesium Binding Sites List in 7ddh
Magnesium binding site 2 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
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 Digoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:67.2
occ:1.00
|
O
|
A:HOH1203
|
2.0
|
75.5
|
1.0
|
OD2
|
A:ASP804
|
2.0
|
93.0
|
1.0
|
OD1
|
A:ASP804
|
2.2
|
74.3
|
1.0
|
OE2
|
A:GLU779
|
2.2
|
70.6
|
1.0
|
CG
|
A:ASP804
|
2.3
|
98.0
|
1.0
|
OE2
|
A:GLU327
|
2.3
|
107.7
|
1.0
|
O
|
A:HOH1204
|
2.4
|
75.2
|
1.0
|
O
|
A:HOH1205
|
2.4
|
68.8
|
1.0
|
CD
|
A:GLU779
|
3.1
|
83.7
|
1.0
|
OE1
|
A:GLU779
|
3.4
|
82.5
|
1.0
|
CD
|
A:GLU327
|
3.4
|
86.7
|
1.0
|
CB
|
A:ASP804
|
3.6
|
108.1
|
1.0
|
OE1
|
A:GLU327
|
3.9
|
83.6
|
1.0
|
ND2
|
A:ASN776
|
4.1
|
67.6
|
1.0
|
OD1
|
A:ASN776
|
4.4
|
108.1
|
1.0
|
CG
|
A:GLU779
|
4.4
|
77.9
|
1.0
|
CG
|
A:ASN776
|
4.4
|
79.0
|
1.0
|
O
|
A:VAL325
|
4.6
|
88.3
|
1.0
|
O
|
A:ALA323
|
4.6
|
89.2
|
1.0
|
CG2
|
A:ILE800
|
4.6
|
74.0
|
1.0
|
CG
|
A:GLU327
|
4.7
|
72.0
|
1.0
|
CA
|
A:ASP804
|
4.8
|
88.4
|
1.0
|
N
|
A:GLU327
|
4.8
|
91.5
|
1.0
|
CB
|
A:GLU779
|
4.8
|
85.2
|
1.0
|
CA
|
A:PRO326
|
4.9
|
76.4
|
1.0
|
OG
|
A:SER775
|
4.9
|
65.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7ddh
Go back to
Magnesium Binding Sites List in 7ddh
Magnesium binding site 3 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
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 Digoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:87.4
occ:1.00
|
O
|
C:HOH1205
|
2.0
|
86.0
|
1.0
|
O
|
C:THR371
|
2.1
|
92.5
|
1.0
|
OD1
|
C:ASP710
|
2.2
|
98.3
|
1.0
|
OD2
|
C:PHD369
|
2.2
|
118.2
|
1.0
|
O
|
C:HOH1201
|
2.3
|
86.3
|
1.0
|
OP3
|
C:PHD369
|
2.3
|
86.4
|
1.0
|
OD2
|
C:ASP710
|
2.5
|
89.0
|
1.0
|
CG
|
C:ASP710
|
2.6
|
97.1
|
1.0
|
C
|
C:THR371
|
3.3
|
92.5
|
1.0
|
CG
|
C:PHD369
|
3.4
|
104.7
|
1.0
|
N
|
C:GLY711
|
3.4
|
83.4
|
1.0
|
P
|
C:PHD369
|
3.6
|
92.1
|
1.0
|
OD1
|
C:PHD369
|
3.9
|
97.5
|
1.0
|
OD2
|
C:ASP714
|
3.9
|
113.7
|
1.0
|
CB
|
C:ASP710
|
3.9
|
96.4
|
1.0
|
CA
|
C:GLY372
|
4.0
|
114.2
|
1.0
|
CA
|
C:GLY711
|
4.0
|
83.4
|
1.0
|
N
|
C:GLY372
|
4.1
|
101.7
|
1.0
|
N
|
C:ASP710
|
4.1
|
83.3
|
1.0
|
C
|
C:ASP710
|
4.3
|
83.3
|
1.0
|
CA
|
C:ASP710
|
4.3
|
83.3
|
1.0
|
CA
|
C:THR371
|
4.3
|
97.1
|
1.0
|
OG1
|
C:THR373
|
4.4
|
82.7
|
1.0
|
OP1
|
C:PHD369
|
4.4
|
86.4
|
1.0
|
CB
|
C:THR371
|
4.5
|
122.2
|
1.0
|
N
|
C:THR373
|
4.5
|
87.2
|
1.0
|
OD1
|
C:ASN713
|
4.6
|
134.1
|
1.0
|
C
|
C:GLY372
|
4.6
|
104.4
|
1.0
|
CB
|
C:PHD369
|
4.6
|
89.1
|
1.0
|
O
|
C:SER209
|
4.6
|
95.3
|
1.0
|
OP2
|
C:PHD369
|
4.7
|
125.8
|
1.0
|
N
|
C:THR371
|
4.7
|
92.5
|
1.0
|
CG2
|
C:THR371
|
4.9
|
134.8
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7ddh
Go back to
Magnesium Binding Sites List in 7ddh
Magnesium binding site 4 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
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 Digoxin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:55.6
occ:1.00
|
O
|
C:HOH1203
|
2.1
|
56.5
|
1.0
|
OD2
|
C:ASP804
|
2.1
|
78.1
|
1.0
|
OD1
|
C:ASP804
|
2.2
|
86.0
|
1.0
|
OE2
|
C:GLU779
|
2.3
|
92.2
|
1.0
|
OE2
|
C:GLU327
|
2.3
|
114.9
|
1.0
|
O
|
C:HOH1202
|
2.4
|
92.0
|
1.0
|
CG
|
C:ASP804
|
2.4
|
82.2
|
1.0
|
O
|
C:HOH1204
|
2.5
|
58.0
|
1.0
|
CD
|
C:GLU779
|
3.1
|
73.9
|
1.0
|
CD
|
C:GLU327
|
3.4
|
116.4
|
1.0
|
OE1
|
C:GLU779
|
3.4
|
85.4
|
1.0
|
CB
|
C:ASP804
|
3.8
|
81.6
|
1.0
|
OE1
|
C:GLU327
|
3.8
|
101.7
|
1.0
|
ND2
|
C:ASN776
|
4.2
|
60.6
|
1.0
|
CG2
|
C:ILE800
|
4.4
|
63.6
|
1.0
|
CG
|
C:GLU779
|
4.5
|
59.5
|
1.0
|
CG
|
C:ASN776
|
4.6
|
83.8
|
1.0
|
OD1
|
C:ASN776
|
4.6
|
95.0
|
1.0
|
CG
|
C:GLU327
|
4.6
|
121.3
|
1.0
|
O
|
C:VAL325
|
4.7
|
86.2
|
1.0
|
N
|
C:GLU327
|
4.8
|
101.7
|
1.0
|
O
|
C:ALA323
|
4.8
|
114.2
|
1.0
|
CB
|
C:GLU779
|
4.9
|
59.5
|
1.0
|
CA
|
C:PRO326
|
4.9
|
65.8
|
1.0
|
CA
|
C:ASP804
|
4.9
|
77.2
|
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 15:47:37 2024
|