Potassium in PDB 4res: Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Enzymatic activity of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
All present enzymatic activity of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium:
3.6.3.9;
Protein crystallography data
The structure of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium, PDB code: 4res
was solved by
M.Laursen,
L.Yatime,
J.L.Gregersen,
P.Nissen,
N.U.Fedosova,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
49.90 /
3.41
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.910,
240.270,
152.700,
90.00,
102.28,
90.00
|
R / Rfree (%)
|
24.5 /
28.8
|
Other elements in 4res:
The structure of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
(pdb code 4res). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 6 binding sites of Potassium where determined in the
Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium, PDB code: 4res:
Jump to Potassium binding site number:
1;
2;
3;
4;
5;
6;
Potassium binding site 1 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 1 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K2003
b:0.3
occ:1.00
|
OD1
|
A:ASN776
|
2.7
|
64.2
|
1.0
|
O
|
A:THR772
|
2.8
|
78.8
|
1.0
|
OD1
|
A:ASP804
|
2.9
|
85.6
|
1.0
|
OG
|
A:SER775
|
2.9
|
65.2
|
1.0
|
CG
|
A:ASN776
|
3.1
|
64.3
|
1.0
|
ND2
|
A:ASN776
|
3.2
|
64.9
|
1.0
|
OG1
|
A:THR772
|
3.3
|
79.8
|
1.0
|
CG
|
A:ASP804
|
3.7
|
86.3
|
1.0
|
C
|
A:THR772
|
3.7
|
79.0
|
1.0
|
OD2
|
A:ASP804
|
3.8
|
86.8
|
1.0
|
OE1
|
A:GLU779
|
3.9
|
94.3
|
1.0
|
N
|
A:ASN776
|
4.0
|
62.4
|
1.0
|
CB
|
A:PRO326
|
4.0
|
53.4
|
1.0
|
CB
|
A:ASN776
|
4.2
|
64.2
|
1.0
|
CB
|
A:SER775
|
4.3
|
64.6
|
1.0
|
CA
|
A:ASN776
|
4.3
|
63.2
|
1.0
|
C
|
A:SER775
|
4.4
|
65.4
|
1.0
|
CA
|
A:PRO326
|
4.4
|
53.9
|
1.0
|
OE2
|
A:GLU779
|
4.4
|
95.5
|
1.0
|
CB
|
A:THR772
|
4.4
|
79.5
|
1.0
|
CA
|
A:THR772
|
4.5
|
78.8
|
1.0
|
CD
|
A:GLU779
|
4.5
|
94.7
|
1.0
|
N
|
A:LEU773
|
4.6
|
65.0
|
1.0
|
CA
|
A:LEU773
|
4.7
|
65.5
|
1.0
|
CA
|
A:SER775
|
4.7
|
64.8
|
1.0
|
N
|
A:SER775
|
4.9
|
65.1
|
1.0
|
K
|
A:K2004
|
5.0
|
54.9
|
1.0
|
O
|
A:SER775
|
5.0
|
65.4
|
1.0
|
CB
|
A:ASP804
|
5.0
|
86.8
|
1.0
|
CG
|
A:PRO326
|
5.0
|
54.3
|
1.0
|
|
Potassium binding site 2 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 2 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K2004
b:54.9
occ:1.00
|
O
|
A:ALA323
|
2.6
|
75.3
|
1.0
|
O
|
A:VAL325
|
2.9
|
77.3
|
1.0
|
OE2
|
A:GLU327
|
2.9
|
85.5
|
1.0
|
O24
|
A:BUF2001
|
2.9
|
93.8
|
1.0
|
OD2
|
A:ASP804
|
3.2
|
86.8
|
1.0
|
C
|
A:ALA323
|
3.5
|
76.4
|
1.0
|
OD1
|
A:ASN776
|
3.7
|
64.2
|
1.0
|
C
|
A:VAL325
|
3.7
|
77.6
|
1.0
|
CD
|
A:GLU327
|
3.8
|
85.5
|
1.0
|
C24
|
A:BUF2001
|
3.8
|
94.2
|
1.0
|
CA
|
A:ALA323
|
3.9
|
76.8
|
1.0
|
OE2
|
A:GLU779
|
4.0
|
95.5
|
1.0
|
O
|
A:VAL322
|
4.0
|
83.5
|
1.0
|
OE1
|
A:GLU327
|
4.2
|
84.6
|
1.0
|
N
|
A:VAL325
|
4.2
|
78.4
|
1.0
|
N
|
A:PRO326
|
4.4
|
54.9
|
1.0
|
O21
|
A:BUF2001
|
4.4
|
95.5
|
1.0
|
CG
|
A:ASP804
|
4.4
|
86.3
|
1.0
|
CA
|
A:PRO326
|
4.5
|
53.9
|
1.0
|
N
|
A:ASN324
|
4.5
|
65.4
|
1.0
|
CA
|
A:VAL325
|
4.6
|
78.8
|
1.0
|
C23
|
A:BUF2001
|
4.7
|
93.5
|
1.0
|
C
|
A:ASN324
|
4.8
|
65.4
|
1.0
|
CG
|
A:ASN776
|
4.8
|
64.3
|
1.0
|
C
|
A:VAL322
|
4.9
|
84.1
|
1.0
|
CB
|
A:ALA323
|
4.9
|
76.5
|
1.0
|
N
|
A:ALA323
|
4.9
|
78.4
|
1.0
|
K
|
A:K2003
|
5.0
|
0.3
|
1.0
|
CA
|
A:ASN324
|
5.0
|
65.3
|
1.0
|
N
|
A:GLU327
|
5.0
|
85.9
|
1.0
|
CG
|
A:GLU327
|
5.0
|
87.1
|
1.0
|
|
Potassium binding site 3 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 3 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 3 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K2005
b:0.8
occ:1.00
|
O
|
A:LYS719
|
2.6
|
95.8
|
1.0
|
OD2
|
A:ASP740
|
2.7
|
0.4
|
1.0
|
OD1
|
A:ASP740
|
2.8
|
99.9
|
1.0
|
CG
|
A:ASP740
|
3.1
|
99.9
|
1.0
|
C
|
A:LYS719
|
3.5
|
96.5
|
1.0
|
O
|
A:SER718
|
3.7
|
99.0
|
1.0
|
O
|
A:ALA738
|
3.7
|
76.5
|
1.0
|
CA
|
A:LYS719
|
3.8
|
96.0
|
1.0
|
O
|
A:ALA721
|
3.8
|
56.5
|
1.0
|
CA
|
A:GLY272
|
3.9
|
0.6
|
1.0
|
CD
|
A:LYS719
|
4.0
|
95.4
|
1.0
|
C
|
A:SER718
|
4.6
|
99.8
|
1.0
|
CB
|
A:ASP740
|
4.6
|
99.5
|
1.0
|
CG
|
A:LYS719
|
4.6
|
96.4
|
1.0
|
CE
|
A:LYS719
|
4.7
|
95.7
|
1.0
|
N
|
A:LYS719
|
4.7
|
96.4
|
1.0
|
N
|
A:GLY272
|
4.8
|
1.0
|
1.0
|
N
|
A:LYS720
|
4.8
|
86.8
|
1.0
|
CB
|
A:LYS719
|
4.8
|
96.5
|
1.0
|
N
|
A:GLY724
|
4.8
|
86.5
|
1.0
|
N
|
A:ASP740
|
4.8
|
99.9
|
1.0
|
C
|
A:ALA738
|
4.9
|
76.5
|
1.0
|
O
|
A:GLY272
|
4.9
|
0.1
|
1.0
|
C
|
A:GLY272
|
4.9
|
0.8
|
1.0
|
|
Potassium binding site 4 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 4 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 4 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K1104
b:92.6
occ:1.00
|
OD1
|
C:ASP804
|
2.8
|
70.5
|
1.0
|
OD1
|
C:ASN776
|
2.8
|
52.4
|
1.0
|
OG
|
C:SER775
|
2.8
|
60.6
|
1.0
|
O
|
C:THR772
|
2.8
|
0.2
|
1.0
|
CG
|
C:ASN776
|
3.1
|
52.4
|
1.0
|
ND2
|
C:ASN776
|
3.3
|
52.7
|
1.0
|
OG1
|
C:THR772
|
3.3
|
0.9
|
1.0
|
CG
|
C:ASP804
|
3.5
|
71.4
|
1.0
|
OD2
|
C:ASP804
|
3.7
|
72.2
|
1.0
|
C
|
C:THR772
|
3.8
|
0.1
|
1.0
|
OE1
|
C:GLU779
|
3.9
|
66.5
|
1.0
|
N
|
C:ASN776
|
4.0
|
50.2
|
1.0
|
CB
|
C:PRO326
|
4.1
|
61.2
|
1.0
|
CB
|
C:SER775
|
4.2
|
60.0
|
1.0
|
CB
|
C:ASN776
|
4.2
|
52.3
|
1.0
|
CA
|
C:ASN776
|
4.3
|
51.4
|
1.0
|
C
|
C:SER775
|
4.3
|
61.3
|
1.0
|
OE2
|
C:GLU779
|
4.4
|
68.1
|
1.0
|
CA
|
C:PRO326
|
4.4
|
62.0
|
1.0
|
CD
|
C:GLU779
|
4.5
|
67.2
|
1.0
|
CB
|
C:THR772
|
4.5
|
0.2
|
1.0
|
CA
|
C:THR772
|
4.5
|
0.5
|
1.0
|
N
|
C:LEU773
|
4.6
|
56.0
|
1.0
|
CA
|
C:SER775
|
4.7
|
60.4
|
1.0
|
CA
|
C:LEU773
|
4.7
|
56.9
|
1.0
|
N
|
C:SER775
|
4.9
|
60.4
|
1.0
|
CB
|
C:ASP804
|
4.9
|
71.7
|
1.0
|
K
|
C:K1105
|
4.9
|
60.9
|
1.0
|
O
|
C:SER775
|
4.9
|
61.5
|
1.0
|
|
Potassium binding site 5 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 5 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 5 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K1105
b:60.9
occ:1.00
|
O
|
C:ALA323
|
2.6
|
65.0
|
1.0
|
O
|
C:VAL325
|
2.8
|
63.8
|
1.0
|
OE2
|
C:GLU327
|
2.9
|
90.0
|
1.0
|
O24
|
C:BUF1102
|
3.1
|
90.2
|
1.0
|
OD2
|
C:ASP804
|
3.3
|
72.2
|
1.0
|
C
|
C:ALA323
|
3.4
|
66.3
|
1.0
|
C
|
C:VAL325
|
3.6
|
63.9
|
1.0
|
OD1
|
C:ASN776
|
3.7
|
52.4
|
1.0
|
CD
|
C:GLU327
|
3.8
|
89.8
|
1.0
|
C24
|
C:BUF1102
|
3.9
|
90.8
|
1.0
|
CA
|
C:ALA323
|
3.9
|
67.0
|
1.0
|
O
|
C:VAL322
|
4.0
|
68.7
|
1.0
|
OE2
|
C:GLU779
|
4.0
|
68.1
|
1.0
|
N
|
C:VAL325
|
4.1
|
65.3
|
1.0
|
OE1
|
C:GLU327
|
4.2
|
88.7
|
1.0
|
N
|
C:PRO326
|
4.3
|
63.3
|
1.0
|
CA
|
C:PRO326
|
4.4
|
62.0
|
1.0
|
CG
|
C:ASP804
|
4.5
|
71.4
|
1.0
|
N
|
C:ASN324
|
4.5
|
78.3
|
1.0
|
CA
|
C:VAL325
|
4.5
|
65.3
|
1.0
|
O21
|
C:BUF1102
|
4.5
|
92.4
|
1.0
|
C
|
C:ASN324
|
4.7
|
77.7
|
1.0
|
CG
|
C:ASN776
|
4.7
|
52.4
|
1.0
|
C23
|
C:BUF1102
|
4.8
|
90.3
|
1.0
|
C
|
C:VAL322
|
4.9
|
69.6
|
1.0
|
CA
|
C:ASN324
|
4.9
|
78.0
|
1.0
|
N
|
C:ALA323
|
4.9
|
68.8
|
1.0
|
N
|
C:GLU327
|
4.9
|
89.7
|
1.0
|
K
|
C:K1104
|
4.9
|
92.6
|
1.0
|
CB
|
C:ALA323
|
4.9
|
66.9
|
1.0
|
|
Potassium binding site 6 out
of 6 in 4res
Go back to
Potassium Binding Sites List in 4res
Potassium binding site 6 out
of 6 in the Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium
Mono view
Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 6 of Crystal Structure of the Na,K-Atpase E2P-Bufalin Complex with Bound Potassium within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:K1106
b:69.5
occ:1.00
|
O
|
C:LYS719
|
2.6
|
0.9
|
1.0
|
OD2
|
C:ASP740
|
2.7
|
99.9
|
1.0
|
OD1
|
C:ASP740
|
2.8
|
99.8
|
1.0
|
CG
|
C:ASP740
|
3.1
|
99.7
|
1.0
|
C
|
C:LYS719
|
3.5
|
0.3
|
1.0
|
O
|
C:SER718
|
3.7
|
0.5
|
1.0
|
O
|
C:ALA738
|
3.7
|
0.0
|
1.0
|
CA
|
C:LYS719
|
3.7
|
0.9
|
1.0
|
O
|
C:ALA721
|
3.9
|
68.2
|
1.0
|
CD
|
C:LYS719
|
3.9
|
0.7
|
1.0
|
CA
|
C:GLY272
|
4.0
|
0.2
|
1.0
|
C
|
C:SER718
|
4.6
|
0.0
|
1.0
|
CB
|
C:ASP740
|
4.6
|
99.5
|
1.0
|
CE
|
C:LYS719
|
4.6
|
0.0
|
1.0
|
CG
|
C:LYS719
|
4.6
|
0.4
|
1.0
|
N
|
C:LYS719
|
4.7
|
0.1
|
1.0
|
N
|
C:LYS720
|
4.7
|
76.6
|
1.0
|
CB
|
C:LYS719
|
4.7
|
0.4
|
1.0
|
N
|
C:GLY724
|
4.8
|
0.4
|
1.0
|
N
|
C:ASP740
|
4.8
|
99.8
|
1.0
|
N
|
C:GLY272
|
4.9
|
0.6
|
1.0
|
C
|
C:ALA738
|
4.9
|
1.0
|
1.0
|
|
Reference:
M.Laursen,
J.L.Gregersen,
L.Yatime,
P.Nissen,
N.U.Fedosova.
Structures and Characterization of Digoxin- and Bufalin-Bound Na+,K+-Atpase Compared with the Ouabain-Bound Complex. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25624492
DOI: 10.1073/PNAS.1422997112
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