Magnesium in PDB 6kpv: Crystal Structures of Na+,K+-Atpase in Complex with Bufalin
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Bufalin, PDB code: 6kpv
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)
|
16.00 /
3.72
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.792,
118.032,
495.452,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
23.8 /
28.6
|
Other elements in 6kpv:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Bufalin 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 Bufalin
(pdb code 6kpv). 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 Bufalin, PDB code: 6kpv:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6kpv
Go back to
Magnesium Binding Sites List in 6kpv
Magnesium binding site 1 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Bufalin
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 Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:0.1
occ:1.00
|
O
|
A:HOH1205
|
2.1
|
97.6
|
1.0
|
OD1
|
A:ASP710
|
2.2
|
0.1
|
1.0
|
O
|
A:THR371
|
2.3
|
0.9
|
1.0
|
OD2
|
A:ASP710
|
2.4
|
0.3
|
1.0
|
OP3
|
A:PHD369
|
2.4
|
0.6
|
1.0
|
O
|
A:HOH1201
|
2.5
|
0.7
|
1.0
|
CG
|
A:ASP710
|
2.6
|
0.8
|
1.0
|
OD2
|
A:PHD369
|
2.6
|
0.9
|
1.0
|
N
|
A:GLY711
|
3.3
|
0.7
|
1.0
|
C
|
A:THR371
|
3.4
|
0.2
|
1.0
|
CG
|
A:PHD369
|
3.7
|
0.1
|
1.0
|
P
|
A:PHD369
|
3.8
|
0.8
|
1.0
|
CA
|
A:GLY711
|
3.9
|
1.0
|
1.0
|
CB
|
A:ASP710
|
4.0
|
0.6
|
1.0
|
OD2
|
A:ASP714
|
4.0
|
0.2
|
1.0
|
OD1
|
A:PHD369
|
4.0
|
0.3
|
1.0
|
CA
|
A:GLY372
|
4.1
|
0.8
|
1.0
|
C
|
A:ASP710
|
4.2
|
0.2
|
1.0
|
N
|
A:GLY372
|
4.2
|
0.8
|
1.0
|
N
|
A:ASP710
|
4.3
|
0.4
|
1.0
|
CA
|
A:ASP710
|
4.4
|
0.5
|
1.0
|
O
|
A:SER209
|
4.4
|
0.6
|
1.0
|
CA
|
A:THR371
|
4.4
|
0.9
|
1.0
|
CB
|
A:THR371
|
4.5
|
0.9
|
1.0
|
OP1
|
A:PHD369
|
4.5
|
0.1
|
1.0
|
OG1
|
A:THR373
|
4.6
|
92.6
|
1.0
|
CG2
|
A:THR371
|
4.7
|
0.3
|
1.0
|
N
|
A:THR373
|
4.7
|
0.5
|
1.0
|
OD1
|
A:ASN713
|
4.8
|
0.3
|
1.0
|
C
|
A:GLY372
|
4.8
|
0.2
|
1.0
|
OP2
|
A:PHD369
|
4.8
|
0.6
|
1.0
|
N
|
A:THR371
|
4.9
|
0.7
|
1.0
|
CB
|
A:PHD369
|
5.0
|
94.0
|
1.0
|
OG
|
A:SER209
|
5.0
|
0.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6kpv
Go back to
Magnesium Binding Sites List in 6kpv
Magnesium binding site 2 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Bufalin
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 Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:89.6
occ:1.00
|
OD2
|
A:ASP804
|
2.1
|
0.7
|
1.0
|
OE2
|
A:GLU779
|
2.1
|
89.0
|
1.0
|
O
|
A:HOH1202
|
2.1
|
96.3
|
1.0
|
O
|
A:HOH1204
|
2.3
|
82.4
|
1.0
|
OD1
|
A:ASP804
|
2.3
|
81.7
|
1.0
|
CG
|
A:ASP804
|
2.4
|
89.5
|
1.0
|
O
|
A:HOH1203
|
2.5
|
0.9
|
1.0
|
CD
|
A:GLU779
|
2.9
|
88.2
|
1.0
|
OE2
|
A:GLU327
|
3.0
|
93.7
|
1.0
|
OE1
|
A:GLU779
|
3.1
|
94.0
|
1.0
|
CB
|
A:ASP804
|
3.8
|
89.0
|
1.0
|
OD1
|
A:ASN776
|
3.9
|
85.5
|
1.0
|
CD
|
A:GLU327
|
3.9
|
95.8
|
1.0
|
CG
|
A:GLU779
|
4.2
|
78.3
|
1.0
|
OE1
|
A:GLU327
|
4.2
|
99.3
|
1.0
|
CG
|
A:ASN776
|
4.4
|
92.6
|
1.0
|
O
|
A:VAL325
|
4.6
|
87.6
|
1.0
|
O
|
A:ALA323
|
4.6
|
81.1
|
1.0
|
CG2
|
A:ILE800
|
4.6
|
80.3
|
1.0
|
ND2
|
A:ASN776
|
4.7
|
0.2
|
1.0
|
OG
|
A:SER775
|
4.7
|
62.8
|
1.0
|
CB
|
A:GLU779
|
4.7
|
79.6
|
1.0
|
CA
|
A:PRO326
|
4.8
|
84.2
|
1.0
|
CA
|
A:ASP804
|
4.9
|
84.6
|
1.0
|
CA
|
A:ASN776
|
4.9
|
78.8
|
1.0
|
N
|
A:GLU327
|
4.9
|
89.2
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6kpv
Go back to
Magnesium Binding Sites List in 6kpv
Magnesium binding site 3 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Bufalin
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 Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:76.4
occ:1.00
|
O
|
C:HOH1204
|
2.1
|
96.4
|
1.0
|
O
|
C:THR371
|
2.1
|
96.0
|
1.0
|
OD1
|
C:ASP710
|
2.3
|
0.4
|
1.0
|
OD2
|
C:ASP710
|
2.3
|
0.8
|
1.0
|
CG
|
C:ASP710
|
2.6
|
0.5
|
1.0
|
OP3
|
C:PHD369
|
2.6
|
97.2
|
1.0
|
O
|
C:HOH1201
|
2.6
|
89.9
|
1.0
|
OD2
|
C:PHD369
|
2.8
|
0.8
|
1.0
|
C
|
C:THR371
|
3.2
|
0.3
|
1.0
|
N
|
C:GLY711
|
3.5
|
99.8
|
1.0
|
CG
|
C:PHD369
|
3.8
|
97.6
|
1.0
|
CA
|
C:GLY372
|
3.9
|
92.5
|
1.0
|
P
|
C:PHD369
|
3.9
|
0.8
|
1.0
|
N
|
C:GLY372
|
4.0
|
97.6
|
1.0
|
CB
|
C:ASP710
|
4.0
|
86.5
|
1.0
|
CA
|
C:GLY711
|
4.0
|
88.2
|
1.0
|
OD2
|
C:ASP714
|
4.2
|
0.3
|
1.0
|
OD1
|
C:PHD369
|
4.2
|
0.7
|
1.0
|
CA
|
C:THR371
|
4.3
|
98.6
|
1.0
|
C
|
C:ASP710
|
4.3
|
97.5
|
1.0
|
CB
|
C:THR371
|
4.4
|
1.0
|
1.0
|
O
|
C:SER209
|
4.4
|
0.5
|
1.0
|
OP1
|
C:PHD369
|
4.4
|
94.3
|
1.0
|
N
|
C:ASP710
|
4.5
|
88.2
|
1.0
|
CA
|
C:ASP710
|
4.5
|
88.9
|
1.0
|
N
|
C:THR373
|
4.6
|
93.9
|
1.0
|
CG2
|
C:THR371
|
4.6
|
0.3
|
1.0
|
C
|
C:GLY372
|
4.6
|
94.5
|
1.0
|
OG1
|
C:THR373
|
4.6
|
79.4
|
1.0
|
N
|
C:THR371
|
4.8
|
95.6
|
1.0
|
OD1
|
C:ASN713
|
4.9
|
95.5
|
1.0
|
OG
|
C:SER209
|
4.9
|
0.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6kpv
Go back to
Magnesium Binding Sites List in 6kpv
Magnesium binding site 4 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Bufalin
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 Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:97.7
occ:1.00
|
OE2
|
C:GLU779
|
2.1
|
76.6
|
1.0
|
O
|
C:HOH1202
|
2.1
|
91.1
|
1.0
|
OD2
|
C:ASP804
|
2.2
|
0.7
|
1.0
|
O
|
C:HOH1205
|
2.4
|
63.6
|
1.0
|
O
|
C:HOH1203
|
2.4
|
90.2
|
1.0
|
OD1
|
C:ASP804
|
2.5
|
72.9
|
1.0
|
CG
|
C:ASP804
|
2.6
|
82.9
|
1.0
|
OE2
|
C:GLU327
|
2.7
|
80.9
|
1.0
|
CD
|
C:GLU779
|
2.9
|
79.3
|
1.0
|
OE1
|
C:GLU779
|
3.1
|
85.8
|
1.0
|
CD
|
C:GLU327
|
3.8
|
71.1
|
1.0
|
OD1
|
C:ASN776
|
4.0
|
65.8
|
1.0
|
CB
|
C:ASP804
|
4.0
|
66.2
|
1.0
|
OE1
|
C:GLU327
|
4.2
|
59.6
|
1.0
|
CG
|
C:GLU779
|
4.2
|
68.9
|
1.0
|
CG
|
C:ASN776
|
4.4
|
69.4
|
1.0
|
O
|
C:VAL325
|
4.5
|
84.5
|
1.0
|
CG2
|
C:ILE800
|
4.6
|
69.1
|
1.0
|
O
|
C:ALA323
|
4.7
|
74.1
|
1.0
|
CB
|
C:GLU779
|
4.7
|
73.9
|
1.0
|
OG
|
C:SER775
|
4.7
|
68.0
|
1.0
|
ND2
|
C:ASN776
|
4.7
|
80.2
|
1.0
|
CA
|
C:PRO326
|
4.8
|
65.5
|
1.0
|
N
|
C:GLU327
|
4.9
|
82.9
|
1.0
|
CA
|
C:ASN776
|
5.0
|
68.2
|
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 08:48:46 2021
|