Magnesium in PDB 6kpz: Crystal Structures of Na+,K+-Atpase in Complex with Ouabain
Protein crystallography data
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain, PDB code: 6kpz
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 /
3.00
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.621,
117.810,
493.203,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
26.4 /
30.8
|
Other elements in 6kpz:
The structure of Crystal Structures of Na+,K+-Atpase in Complex with Ouabain 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 Ouabain
(pdb code 6kpz). 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 Ouabain, PDB code: 6kpz:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6kpz
Go back to
Magnesium Binding Sites List in 6kpz
Magnesium binding site 1 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain
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 Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:43.9
occ:1.00
|
O
|
A:HOH1202
|
2.1
|
43.2
|
1.0
|
O
|
A:HOH1201
|
2.1
|
63.0
|
1.0
|
OD1
|
A:ASP710
|
2.2
|
45.9
|
1.0
|
OP3
|
A:PHD369
|
2.2
|
55.9
|
1.0
|
O
|
A:THR371
|
2.2
|
46.0
|
1.0
|
OD2
|
A:PHD369
|
2.6
|
57.7
|
1.0
|
CG
|
A:ASP710
|
2.9
|
49.0
|
1.0
|
OD2
|
A:ASP710
|
3.0
|
52.9
|
1.0
|
C
|
A:THR371
|
3.4
|
49.6
|
1.0
|
P
|
A:PHD369
|
3.5
|
47.4
|
1.0
|
CG
|
A:PHD369
|
3.5
|
51.9
|
1.0
|
N
|
A:GLY711
|
3.5
|
48.3
|
1.0
|
OD1
|
A:PHD369
|
3.8
|
42.1
|
1.0
|
OD2
|
A:ASP714
|
4.0
|
48.3
|
1.0
|
CB
|
A:THR371
|
4.0
|
55.5
|
1.0
|
CA
|
A:GLY711
|
4.0
|
46.8
|
1.0
|
O
|
A:SER209
|
4.0
|
57.2
|
1.0
|
CA
|
A:THR371
|
4.2
|
46.2
|
1.0
|
OP1
|
A:PHD369
|
4.2
|
42.7
|
1.0
|
CG2
|
A:THR371
|
4.3
|
67.5
|
1.0
|
CB
|
A:ASP710
|
4.3
|
46.1
|
1.0
|
N
|
A:GLY372
|
4.4
|
52.0
|
1.0
|
OD1
|
A:ASN713
|
4.4
|
56.9
|
1.0
|
N
|
A:ASP710
|
4.5
|
39.5
|
1.0
|
C
|
A:ASP710
|
4.5
|
52.7
|
1.0
|
CA
|
A:GLY372
|
4.5
|
51.3
|
1.0
|
N
|
A:THR371
|
4.5
|
54.1
|
1.0
|
OG1
|
A:THR373
|
4.6
|
43.0
|
1.0
|
OP2
|
A:PHD369
|
4.6
|
56.8
|
1.0
|
CA
|
A:ASP710
|
4.7
|
44.1
|
1.0
|
ND2
|
A:ASN713
|
4.8
|
51.6
|
1.0
|
CB
|
A:PHD369
|
4.8
|
52.7
|
1.0
|
CA
|
A:GLY213
|
4.9
|
62.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6kpz
Go back to
Magnesium Binding Sites List in 6kpz
Magnesium binding site 2 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain
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 Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:51.2
occ:1.00
|
OE2
|
A:GLU779
|
2.1
|
47.2
|
1.0
|
OD2
|
A:ASP804
|
2.1
|
43.1
|
1.0
|
O
|
A:HOH1203
|
2.2
|
36.8
|
1.0
|
O
|
A:HOH1204
|
2.2
|
46.8
|
1.0
|
OD1
|
A:ASP804
|
2.2
|
32.5
|
1.0
|
CG
|
A:ASP804
|
2.4
|
40.2
|
1.0
|
O
|
A:HOH1205
|
2.5
|
55.3
|
1.0
|
CD
|
A:GLU779
|
2.8
|
51.9
|
1.0
|
OE2
|
A:GLU327
|
2.9
|
67.8
|
1.0
|
OE1
|
A:GLU779
|
3.0
|
54.3
|
1.0
|
CD
|
A:GLU327
|
3.9
|
54.5
|
1.0
|
CB
|
A:ASP804
|
3.9
|
41.5
|
1.0
|
OD1
|
A:ASN776
|
4.0
|
36.2
|
1.0
|
OE1
|
A:GLU327
|
4.1
|
52.4
|
1.0
|
CG
|
A:GLU779
|
4.2
|
39.8
|
1.0
|
CG
|
A:ASN776
|
4.5
|
38.4
|
1.0
|
OG
|
A:SER775
|
4.6
|
31.8
|
1.0
|
O
|
A:VAL325
|
4.6
|
50.0
|
1.0
|
O
|
A:ALA323
|
4.7
|
46.1
|
1.0
|
CB
|
A:GLU779
|
4.7
|
36.9
|
1.0
|
O
|
A:HOH1206
|
4.7
|
45.1
|
1.0
|
ND2
|
A:ASN776
|
4.8
|
43.7
|
1.0
|
CG2
|
A:ILE800
|
4.8
|
45.9
|
1.0
|
CA
|
A:PRO326
|
4.9
|
32.9
|
1.0
|
CA
|
A:ASP804
|
4.9
|
43.9
|
1.0
|
CA
|
A:ASN776
|
5.0
|
43.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6kpz
Go back to
Magnesium Binding Sites List in 6kpz
Magnesium binding site 3 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain
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 Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:50.3
occ:1.00
|
O
|
C:HOH1201
|
2.0
|
46.4
|
1.0
|
OP3
|
C:PHD369
|
2.1
|
53.3
|
1.0
|
O
|
C:HOH1202
|
2.2
|
60.3
|
1.0
|
OD1
|
C:ASP710
|
2.2
|
43.2
|
1.0
|
O
|
C:THR371
|
2.3
|
46.7
|
1.0
|
OD2
|
C:PHD369
|
2.5
|
49.4
|
1.0
|
CG
|
C:ASP710
|
3.0
|
44.9
|
1.0
|
OD2
|
C:ASP710
|
3.2
|
41.1
|
1.0
|
P
|
C:PHD369
|
3.4
|
63.6
|
1.0
|
CG
|
C:PHD369
|
3.4
|
45.1
|
1.0
|
C
|
C:THR371
|
3.4
|
43.1
|
1.0
|
N
|
C:GLY711
|
3.5
|
55.7
|
1.0
|
OD1
|
C:PHD369
|
3.6
|
48.2
|
1.0
|
OD2
|
C:ASP714
|
3.9
|
44.6
|
1.0
|
CA
|
C:GLY711
|
4.0
|
49.9
|
1.0
|
CB
|
C:THR371
|
4.0
|
36.4
|
1.0
|
O
|
C:SER209
|
4.0
|
66.8
|
1.0
|
OP1
|
C:PHD369
|
4.1
|
52.9
|
1.0
|
CA
|
C:THR371
|
4.2
|
41.7
|
1.0
|
OD1
|
C:ASN713
|
4.2
|
60.7
|
1.0
|
CG2
|
C:THR371
|
4.3
|
33.0
|
1.0
|
CB
|
C:ASP710
|
4.4
|
36.8
|
1.0
|
N
|
C:GLY372
|
4.4
|
43.3
|
1.0
|
OP2
|
C:PHD369
|
4.5
|
60.6
|
1.0
|
N
|
C:THR371
|
4.5
|
49.5
|
1.0
|
C
|
C:ASP710
|
4.5
|
47.9
|
1.0
|
N
|
C:ASP710
|
4.6
|
38.2
|
1.0
|
CA
|
C:GLY372
|
4.6
|
45.0
|
1.0
|
OG1
|
C:THR373
|
4.7
|
45.4
|
1.0
|
ND2
|
C:ASN713
|
4.7
|
47.0
|
1.0
|
CB
|
C:PHD369
|
4.7
|
44.4
|
1.0
|
CA
|
C:ASP710
|
4.7
|
37.2
|
1.0
|
CA
|
C:GLY213
|
4.8
|
49.3
|
1.0
|
CG
|
C:ASN713
|
4.9
|
57.8
|
1.0
|
CG
|
C:ASP714
|
5.0
|
41.5
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6kpz
Go back to
Magnesium Binding Sites List in 6kpz
Magnesium binding site 4 out
of 4 in the Crystal Structures of Na+,K+-Atpase in Complex with Ouabain
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 Ouabain within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:55.4
occ:1.00
|
OE2
|
C:GLU779
|
2.1
|
34.8
|
1.0
|
OD2
|
C:ASP804
|
2.1
|
42.0
|
1.0
|
O
|
C:HOH1203
|
2.1
|
40.9
|
1.0
|
OD1
|
C:ASP804
|
2.3
|
41.2
|
1.0
|
O
|
C:HOH1204
|
2.3
|
37.9
|
1.0
|
O
|
C:HOH1205
|
2.3
|
33.7
|
1.0
|
CG
|
C:ASP804
|
2.4
|
41.5
|
1.0
|
CD
|
C:GLU779
|
2.8
|
42.0
|
1.0
|
OE2
|
C:GLU327
|
2.8
|
41.7
|
1.0
|
OE1
|
C:GLU779
|
3.1
|
36.9
|
1.0
|
CD
|
C:GLU327
|
3.8
|
52.5
|
1.0
|
CB
|
C:ASP804
|
3.9
|
42.6
|
1.0
|
OE1
|
C:GLU327
|
4.1
|
61.3
|
1.0
|
OD1
|
C:ASN776
|
4.1
|
43.8
|
1.0
|
CG
|
C:GLU779
|
4.2
|
35.7
|
1.0
|
O
|
C:VAL325
|
4.5
|
50.7
|
1.0
|
CG
|
C:ASN776
|
4.5
|
42.2
|
1.0
|
O
|
C:HOH1206
|
4.6
|
25.4
|
1.0
|
O
|
C:ALA323
|
4.6
|
40.9
|
1.0
|
CB
|
C:GLU779
|
4.7
|
36.5
|
1.0
|
OG
|
C:SER775
|
4.7
|
26.1
|
1.0
|
CG2
|
C:ILE800
|
4.8
|
42.0
|
1.0
|
ND2
|
C:ASN776
|
4.9
|
37.3
|
1.0
|
CA
|
C:PRO326
|
4.9
|
35.8
|
1.0
|
CA
|
C:ASP804
|
4.9
|
35.9
|
1.0
|
N
|
C:GLU327
|
5.0
|
41.0
|
1.0
|
|
Reference:
H.Ogawa,
K.Motoyama,
F.Cornelius,
B.Vilsen,
C.Toyoshima.
Crystal Structure of the Na,K-Atpase in Complex with Ouabain To Be Published.
Page generated: Mon Jan 25 08:48:54 2021
|