Magnesium in PDB 7d94: Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
Enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
All present enzymatic activity of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin:
7.2.2.13;
Protein crystallography data
The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin, PDB code: 7d94
was solved by
R.Kanai,
F.Cornelius,
H.Ogawa,
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)
|
15.00 /
3.50
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
115.57,
117.31,
490.705,
90,
90,
90
|
R / Rfree (%)
|
22.4 /
26.3
|
Other elements in 7d94:
The structure of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
(pdb code 7d94). 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 Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin, PDB code: 7d94:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 7d94
Go back to
Magnesium Binding Sites List in 7d94
Magnesium binding site 1 out
of 4 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:70.9
occ:1.00
|
OD1
|
A:ASP710
|
2.1
|
64.3
|
1.0
|
O
|
A:HOH1201
|
2.1
|
101.7
|
1.0
|
OP3
|
A:PHD369
|
2.1
|
65.7
|
1.0
|
O
|
A:THR371
|
2.2
|
97.3
|
1.0
|
OD2
|
A:PHD369
|
2.3
|
64.8
|
1.0
|
O
|
A:HOH1204
|
2.4
|
68.4
|
1.0
|
CG
|
A:ASP710
|
2.9
|
68.0
|
1.0
|
OD2
|
A:ASP710
|
3.1
|
69.1
|
1.0
|
CG
|
A:PHD369
|
3.3
|
67.8
|
1.0
|
P
|
A:PHD369
|
3.3
|
69.4
|
1.0
|
C
|
A:THR371
|
3.4
|
70.4
|
1.0
|
OD1
|
A:PHD369
|
3.5
|
83.8
|
1.0
|
N
|
A:GLY711
|
3.6
|
84.0
|
1.0
|
OD2
|
A:ASP714
|
3.8
|
79.8
|
1.0
|
OP1
|
A:PHD369
|
4.0
|
70.8
|
1.0
|
CB
|
A:THR371
|
4.1
|
72.0
|
1.0
|
CA
|
A:GLY711
|
4.1
|
80.8
|
1.0
|
CA
|
A:THR371
|
4.2
|
65.1
|
1.0
|
O
|
A:SER209
|
4.2
|
72.8
|
1.0
|
CB
|
A:ASP710
|
4.3
|
81.8
|
1.0
|
CG2
|
A:THR371
|
4.3
|
83.4
|
1.0
|
OD1
|
A:ASN713
|
4.3
|
91.2
|
1.0
|
N
|
A:GLY372
|
4.4
|
75.5
|
1.0
|
N
|
A:ASP710
|
4.4
|
52.6
|
1.0
|
OP2
|
A:PHD369
|
4.5
|
78.6
|
1.0
|
N
|
A:THR371
|
4.5
|
73.5
|
1.0
|
C
|
A:ASP710
|
4.5
|
69.8
|
1.0
|
CA
|
A:GLY372
|
4.5
|
111.9
|
1.0
|
CB
|
A:PHD369
|
4.6
|
60.4
|
1.0
|
OG1
|
A:THR373
|
4.6
|
102.8
|
1.0
|
CA
|
A:ASP710
|
4.6
|
57.5
|
1.0
|
ND2
|
A:ASN713
|
4.7
|
100.8
|
1.0
|
CG
|
A:ASP714
|
4.9
|
83.4
|
1.0
|
CG
|
A:ASN713
|
5.0
|
75.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 7d94
Go back to
Magnesium Binding Sites List in 7d94
Magnesium binding site 2 out
of 4 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1103
b:50.8
occ:1.00
|
O
|
A:HOH1202
|
2.0
|
45.3
|
1.0
|
OE1
|
A:GLU327
|
2.1
|
63.6
|
1.0
|
O
|
A:ALA323
|
2.9
|
57.3
|
1.0
|
OD1
|
A:ASN776
|
3.0
|
125.0
|
1.0
|
O
|
A:VAL325
|
3.1
|
63.3
|
1.0
|
OD1
|
A:ASP804
|
3.1
|
100.2
|
1.0
|
CD
|
A:GLU327
|
3.3
|
63.2
|
1.0
|
OE2
|
A:GLU779
|
3.8
|
107.1
|
1.0
|
CG
|
A:ASP804
|
3.8
|
77.4
|
1.0
|
RB
|
A:RB1104
|
3.9
|
101.8
|
1.0
|
CG
|
A:ASN776
|
4.0
|
92.7
|
1.0
|
C
|
A:VAL325
|
4.0
|
43.2
|
1.0
|
C
|
A:ALA323
|
4.0
|
87.2
|
1.0
|
CG
|
A:GLU327
|
4.0
|
52.0
|
1.0
|
OD2
|
A:ASP804
|
4.2
|
67.0
|
1.0
|
OE2
|
A:GLU327
|
4.2
|
78.9
|
1.0
|
ND2
|
A:ASN776
|
4.3
|
92.1
|
1.0
|
O24
|
A:BUF1121
|
4.3
|
69.6
|
1.0
|
N
|
A:VAL325
|
4.3
|
66.0
|
1.0
|
N
|
A:GLU327
|
4.5
|
74.5
|
1.0
|
CA
|
A:PRO326
|
4.6
|
54.8
|
1.0
|
N
|
A:PRO326
|
4.7
|
36.5
|
1.0
|
CA
|
A:ALA323
|
4.7
|
86.5
|
1.0
|
CD
|
A:GLU779
|
4.8
|
94.0
|
1.0
|
CA
|
A:VAL325
|
4.8
|
56.0
|
1.0
|
CB
|
A:ASP804
|
4.9
|
66.6
|
1.0
|
O
|
A:VAL322
|
4.9
|
72.2
|
1.0
|
N
|
A:ASN324
|
5.0
|
80.0
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 7d94
Go back to
Magnesium Binding Sites List in 7d94
Magnesium binding site 3 out
of 4 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:63.1
occ:1.00
|
O
|
C:HOH1201
|
2.0
|
63.3
|
1.0
|
O
|
C:THR371
|
2.1
|
70.2
|
1.0
|
OD1
|
C:ASP710
|
2.1
|
56.0
|
1.0
|
OP3
|
C:PHD369
|
2.1
|
87.7
|
1.0
|
O
|
C:HOH1203
|
2.2
|
68.5
|
1.0
|
OD2
|
C:PHD369
|
2.4
|
70.1
|
1.0
|
CG
|
C:ASP710
|
2.9
|
60.1
|
1.0
|
OD2
|
C:ASP710
|
3.0
|
59.6
|
1.0
|
C
|
C:THR371
|
3.3
|
65.8
|
1.0
|
CG
|
C:PHD369
|
3.3
|
70.1
|
1.0
|
P
|
C:PHD369
|
3.4
|
81.1
|
1.0
|
N
|
C:GLY711
|
3.5
|
62.6
|
1.0
|
OD1
|
C:PHD369
|
3.6
|
62.3
|
1.0
|
OD2
|
C:ASP714
|
3.9
|
61.7
|
1.0
|
OP1
|
C:PHD369
|
4.0
|
61.1
|
1.0
|
CB
|
C:THR371
|
4.0
|
95.2
|
1.0
|
CA
|
C:GLY711
|
4.1
|
58.1
|
1.0
|
CA
|
C:THR371
|
4.1
|
63.1
|
1.0
|
O
|
C:SER209
|
4.2
|
80.3
|
1.0
|
N
|
C:GLY372
|
4.3
|
84.4
|
1.0
|
CB
|
C:ASP710
|
4.3
|
52.1
|
1.0
|
CG2
|
C:THR371
|
4.4
|
57.9
|
1.0
|
N
|
C:THR371
|
4.4
|
72.6
|
1.0
|
OD1
|
C:ASN713
|
4.4
|
97.8
|
1.0
|
CA
|
C:GLY372
|
4.4
|
73.8
|
1.0
|
OG1
|
C:THR373
|
4.5
|
64.6
|
1.0
|
C
|
C:ASP710
|
4.5
|
63.2
|
1.0
|
N
|
C:ASP710
|
4.5
|
56.9
|
1.0
|
CB
|
C:PHD369
|
4.5
|
53.5
|
1.0
|
OP2
|
C:PHD369
|
4.5
|
109.1
|
1.0
|
CA
|
C:ASP710
|
4.6
|
51.5
|
1.0
|
ND2
|
C:ASN713
|
4.9
|
113.4
|
1.0
|
N
|
C:THR373
|
4.9
|
87.9
|
1.0
|
CG
|
C:ASP714
|
5.0
|
53.3
|
1.0
|
C
|
C:GLY372
|
5.0
|
60.3
|
1.0
|
CA
|
C:GLY213
|
5.0
|
79.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 7d94
Go back to
Magnesium Binding Sites List in 7d94
Magnesium binding site 4 out
of 4 in the Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of the Na+,K+-Atpase in the E2P State with Bound One MG2+ and One Rb+ in the Presence of Bufalin within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1103
b:28.3
occ:1.00
|
OE2
|
C:GLU327
|
2.0
|
43.5
|
1.0
|
O
|
C:HOH1202
|
2.2
|
44.2
|
1.0
|
OD2
|
C:ASP804
|
2.8
|
52.9
|
1.0
|
O
|
C:ALA323
|
3.1
|
57.1
|
1.0
|
OD1
|
C:ASN776
|
3.1
|
98.4
|
1.0
|
CD
|
C:GLU327
|
3.2
|
52.9
|
1.0
|
O
|
C:VAL325
|
3.2
|
63.1
|
1.0
|
OE1
|
C:GLU779
|
3.4
|
112.6
|
1.0
|
CG
|
C:ASP804
|
3.7
|
55.4
|
1.0
|
RB
|
C:RB1104
|
3.7
|
99.7
|
1.0
|
OE1
|
C:GLU327
|
4.1
|
58.0
|
1.0
|
C
|
C:VAL325
|
4.1
|
50.7
|
1.0
|
CG
|
C:GLU327
|
4.1
|
49.8
|
1.0
|
CG
|
C:ASN776
|
4.1
|
53.8
|
1.0
|
C
|
C:ALA323
|
4.2
|
62.9
|
1.0
|
OD1
|
C:ASP804
|
4.2
|
50.7
|
1.0
|
CD
|
C:GLU779
|
4.4
|
84.9
|
1.0
|
O24
|
C:BUF1121
|
4.5
|
49.2
|
1.0
|
N
|
C:GLU327
|
4.5
|
42.1
|
1.0
|
N
|
C:VAL325
|
4.5
|
42.6
|
1.0
|
CA
|
C:PRO326
|
4.6
|
76.7
|
1.0
|
ND2
|
C:ASN776
|
4.6
|
47.4
|
1.0
|
CB
|
C:ASP804
|
4.7
|
104.2
|
1.0
|
N
|
C:PRO326
|
4.7
|
56.7
|
1.0
|
OE2
|
C:GLU779
|
4.9
|
105.6
|
1.0
|
CA
|
C:ALA323
|
4.9
|
71.3
|
1.0
|
CG2
|
C:ILE800
|
4.9
|
51.8
|
1.0
|
CA
|
C:VAL325
|
5.0
|
45.3
|
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 15:42:27 2024
|