Magnesium in PDB 6kpw: Crystal Structures of Na+,K+-Atpase in Complex with Digoxin
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Digoxin, PDB code: 6kpw
was solved by
H.Ogawa,
K.Motoyama,
F.Cornelius,
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,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.8 /
27
|
Other elements in 6kpw:
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 6kpw). 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: 6kpw:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6kpw
Go back to
Magnesium Binding Sites List in 6kpw
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:0.8
occ:1.00
|
O
|
A:HOH1202
|
2.1
|
87.0
|
1.0
|
O
|
A:THR371
|
2.1
|
89.7
|
1.0
|
O
|
A:HOH1201
|
2.1
|
88.7
|
1.0
|
OD1
|
A:ASP710
|
2.1
|
0.2
|
1.0
|
OD2
|
A:PHD369
|
2.2
|
0.2
|
1.0
|
OP3
|
A:PHD369
|
2.3
|
70.7
|
1.0
|
OD2
|
A:ASP710
|
2.4
|
89.5
|
1.0
|
CG
|
A:ASP710
|
2.5
|
1.0
|
1.0
|
C
|
A:THR371
|
3.3
|
86.2
|
1.0
|
CG
|
A:PHD369
|
3.3
|
95.5
|
1.0
|
N
|
A:GLY711
|
3.4
|
90.8
|
1.0
|
P
|
A:PHD369
|
3.6
|
90.0
|
1.0
|
OD1
|
A:PHD369
|
3.8
|
99.0
|
1.0
|
CB
|
A:ASP710
|
3.9
|
91.6
|
1.0
|
OD2
|
A:ASP714
|
4.0
|
90.8
|
1.0
|
CA
|
A:GLY372
|
4.0
|
95.1
|
1.0
|
N
|
A:GLY372
|
4.1
|
89.2
|
1.0
|
CA
|
A:GLY711
|
4.1
|
89.0
|
1.0
|
N
|
A:ASP710
|
4.2
|
87.4
|
1.0
|
OP1
|
A:PHD369
|
4.3
|
86.5
|
1.0
|
C
|
A:ASP710
|
4.3
|
86.8
|
1.0
|
CA
|
A:ASP710
|
4.4
|
86.1
|
1.0
|
CA
|
A:THR371
|
4.4
|
86.6
|
1.0
|
OG1
|
A:THR373
|
4.5
|
88.2
|
1.0
|
CB
|
A:PHD369
|
4.5
|
80.5
|
1.0
|
CB
|
A:THR371
|
4.6
|
97.5
|
1.0
|
N
|
A:THR373
|
4.6
|
81.6
|
1.0
|
OD1
|
A:ASN713
|
4.6
|
88.0
|
1.0
|
C
|
A:GLY372
|
4.6
|
88.2
|
1.0
|
OP2
|
A:PHD369
|
4.7
|
0.1
|
1.0
|
N
|
A:THR371
|
4.7
|
92.5
|
1.0
|
O
|
A:SER209
|
4.7
|
0.3
|
1.0
|
CG2
|
A:THR371
|
4.9
|
0.6
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6kpw
Go back to
Magnesium Binding Sites List in 6kpw
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:67.8
occ:1.00
|
O
|
A:HOH1203
|
2.1
|
85.7
|
1.0
|
OD2
|
A:ASP804
|
2.1
|
0.3
|
1.0
|
OE2
|
A:GLU779
|
2.1
|
93.1
|
1.0
|
O
|
A:HOH1204
|
2.2
|
80.0
|
1.0
|
OD1
|
A:ASP804
|
2.3
|
88.6
|
1.0
|
CG
|
A:ASP804
|
2.4
|
96.2
|
1.0
|
O
|
A:HOH1205
|
2.5
|
77.5
|
1.0
|
CD
|
A:GLU779
|
2.9
|
94.0
|
1.0
|
OE2
|
A:GLU327
|
3.0
|
0.5
|
1.0
|
OE1
|
A:GLU779
|
3.2
|
92.5
|
1.0
|
CB
|
A:ASP804
|
3.8
|
95.0
|
1.0
|
OD1
|
A:ASN776
|
3.9
|
66.9
|
1.0
|
CD
|
A:GLU327
|
3.9
|
91.8
|
1.0
|
OE1
|
A:GLU327
|
4.1
|
87.3
|
1.0
|
CG
|
A:GLU779
|
4.3
|
75.5
|
1.0
|
CG
|
A:ASN776
|
4.3
|
91.0
|
1.0
|
ND2
|
A:ASN776
|
4.5
|
94.2
|
1.0
|
OG
|
A:SER775
|
4.7
|
67.2
|
1.0
|
O
|
A:ALA323
|
4.7
|
0.3
|
1.0
|
CG2
|
A:ILE800
|
4.7
|
84.4
|
1.0
|
CB
|
A:GLU779
|
4.7
|
79.1
|
1.0
|
O
|
A:VAL325
|
4.8
|
91.8
|
1.0
|
CA
|
A:ASN776
|
4.9
|
76.2
|
1.0
|
CA
|
A:ASP804
|
4.9
|
91.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6kpw
Go back to
Magnesium Binding Sites List in 6kpw
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:97.4
occ:1.00
|
O
|
C:HOH1205
|
2.1
|
94.2
|
1.0
|
O
|
C:THR371
|
2.1
|
95.2
|
1.0
|
OD1
|
C:ASP710
|
2.2
|
97.9
|
1.0
|
OD2
|
C:ASP710
|
2.4
|
88.0
|
1.0
|
O
|
C:HOH1201
|
2.4
|
94.3
|
1.0
|
OP3
|
C:PHD369
|
2.5
|
94.0
|
1.0
|
OD2
|
C:PHD369
|
2.5
|
0.7
|
1.0
|
CG
|
C:ASP710
|
2.5
|
94.2
|
1.0
|
C
|
C:THR371
|
3.3
|
96.8
|
1.0
|
N
|
C:GLY711
|
3.4
|
89.0
|
1.0
|
CG
|
C:PHD369
|
3.6
|
98.1
|
1.0
|
P
|
C:PHD369
|
3.8
|
99.1
|
1.0
|
CA
|
C:GLY372
|
3.9
|
99.0
|
1.0
|
CB
|
C:ASP710
|
3.9
|
92.7
|
1.0
|
CA
|
C:GLY711
|
4.0
|
87.0
|
1.0
|
N
|
C:GLY372
|
4.0
|
94.3
|
1.0
|
OD2
|
C:ASP714
|
4.1
|
98.7
|
1.0
|
OD1
|
C:PHD369
|
4.1
|
96.2
|
1.0
|
N
|
C:ASP710
|
4.2
|
86.1
|
1.0
|
C
|
C:ASP710
|
4.3
|
87.4
|
1.0
|
CA
|
C:THR371
|
4.4
|
0.2
|
1.0
|
CA
|
C:ASP710
|
4.4
|
83.4
|
1.0
|
OG1
|
C:THR373
|
4.4
|
79.1
|
1.0
|
OP1
|
C:PHD369
|
4.4
|
87.6
|
1.0
|
CB
|
C:THR371
|
4.5
|
0.8
|
1.0
|
N
|
C:THR373
|
4.5
|
83.9
|
1.0
|
C
|
C:GLY372
|
4.5
|
92.6
|
1.0
|
O
|
C:SER209
|
4.6
|
0.5
|
1.0
|
OD1
|
C:ASN713
|
4.7
|
0.8
|
1.0
|
N
|
C:THR371
|
4.8
|
0.2
|
1.0
|
CB
|
C:PHD369
|
4.8
|
87.4
|
1.0
|
CG2
|
C:THR371
|
4.8
|
0.9
|
1.0
|
OP2
|
C:PHD369
|
4.9
|
0.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6kpw
Go back to
Magnesium Binding Sites List in 6kpw
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:63.2
occ:1.00
|
OE2
|
C:GLU779
|
2.1
|
87.8
|
1.0
|
O
|
C:HOH1202
|
2.1
|
65.8
|
1.0
|
OD2
|
C:ASP804
|
2.2
|
87.5
|
1.0
|
OD1
|
C:ASP804
|
2.2
|
83.4
|
1.0
|
O
|
C:HOH1203
|
2.4
|
83.9
|
1.0
|
CG
|
C:ASP804
|
2.4
|
82.6
|
1.0
|
O
|
C:HOH1204
|
2.4
|
65.0
|
1.0
|
OE2
|
C:GLU327
|
2.8
|
0.7
|
1.0
|
CD
|
C:GLU779
|
2.9
|
73.4
|
1.0
|
OE1
|
C:GLU779
|
3.2
|
73.1
|
1.0
|
CD
|
C:GLU327
|
3.8
|
0.2
|
1.0
|
CB
|
C:ASP804
|
3.9
|
81.1
|
1.0
|
OD1
|
C:ASN776
|
4.0
|
70.6
|
1.0
|
OE1
|
C:GLU327
|
4.1
|
83.9
|
1.0
|
CG
|
C:GLU779
|
4.3
|
57.1
|
1.0
|
CG
|
C:ASN776
|
4.5
|
90.2
|
1.0
|
CG2
|
C:ILE800
|
4.5
|
63.2
|
1.0
|
CB
|
C:GLU779
|
4.7
|
63.9
|
1.0
|
ND2
|
C:ASN776
|
4.8
|
93.0
|
1.0
|
OG
|
C:SER775
|
4.8
|
68.7
|
1.0
|
O
|
C:VAL325
|
4.9
|
90.9
|
1.0
|
O
|
C:ALA323
|
4.9
|
98.7
|
1.0
|
CA
|
C:ASP804
|
4.9
|
82.2
|
1.0
|
CA
|
C:PRO326
|
5.0
|
78.0
|
1.0
|
|
Reference:
H.Ogawa,
K.Motoyama,
F.Cornelius,
B.Vilsen,
C.Toyoshima.
X-Ray Crystal Structures of Na+,K+-Atpase in Complex with Cardiotonic Steroids To Be Published.
Page generated: Mon Jan 25 08:48:49 2021
|