Calcium in PDB 6oly: Full-Length Mthk Channel at 3.1 Angstrom Resolution
Protein crystallography data
The structure of Full-Length Mthk Channel at 3.1 Angstrom Resolution, PDB code: 6oly
was solved by
B.S.Rothberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.70 /
3.11
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
137.456,
137.456,
373.026,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
23.6 /
27.5
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
(pdb code 6oly). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Full-Length Mthk Channel at 3.1 Angstrom Resolution, PDB code: 6oly:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 1 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca401
b:79.8
occ:1.00
|
O
|
A:ARG241
|
2.4
|
71.2
|
1.0
|
O
|
A:ASP245
|
2.6
|
99.9
|
1.0
|
OE1
|
A:GLU248
|
2.7
|
57.4
|
1.0
|
OE2
|
A:GLU248
|
2.8
|
0.9
|
1.0
|
CD
|
A:GLU248
|
3.1
|
0.3
|
1.0
|
N
|
A:ASP245
|
3.1
|
65.6
|
1.0
|
C
|
A:ARG241
|
3.4
|
87.8
|
1.0
|
C
|
A:ASP245
|
3.5
|
84.4
|
1.0
|
CB
|
A:ASP244
|
3.5
|
0.8
|
1.0
|
CA
|
A:ASP245
|
3.8
|
74.2
|
1.0
|
CA
|
A:ARG241
|
4.0
|
63.3
|
1.0
|
C
|
A:ASP244
|
4.1
|
73.9
|
1.0
|
CA
|
A:ASP244
|
4.2
|
89.0
|
1.0
|
CB
|
A:ASP245
|
4.2
|
91.7
|
1.0
|
CB
|
A:ARG241
|
4.2
|
57.5
|
1.0
|
N
|
A:ASP244
|
4.3
|
95.6
|
1.0
|
N
|
A:SER242
|
4.6
|
91.5
|
1.0
|
CG
|
A:GLU248
|
4.6
|
86.0
|
1.0
|
CG
|
A:ASP244
|
4.6
|
0.3
|
1.0
|
OD2
|
A:ASP244
|
4.7
|
0.9
|
1.0
|
N
|
A:GLY246
|
4.8
|
77.6
|
1.0
|
CA
|
A:SER242
|
4.9
|
79.4
|
1.0
|
CG
|
A:ARG241
|
4.9
|
80.3
|
1.0
|
|
Calcium binding site 2 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 2 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca402
b:0.0
occ:1.00
|
OE2
|
A:GLU210
|
2.3
|
80.8
|
1.0
|
OD1
|
A:ASP184
|
2.5
|
99.6
|
1.0
|
OE1
|
A:GLU212
|
2.9
|
91.8
|
1.0
|
OD2
|
A:ASP184
|
2.9
|
0.7
|
1.0
|
CG
|
A:ASP184
|
3.1
|
96.7
|
1.0
|
OE2
|
A:GLU212
|
3.3
|
98.1
|
1.0
|
CD
|
A:GLU212
|
3.5
|
0.8
|
1.0
|
CD
|
A:GLU210
|
3.5
|
0.1
|
1.0
|
CB
|
A:SER124
|
4.0
|
76.3
|
1.0
|
OG
|
A:SER124
|
4.2
|
77.8
|
1.0
|
OE1
|
A:GLU210
|
4.3
|
96.9
|
1.0
|
CG
|
A:GLU210
|
4.4
|
0.7
|
1.0
|
OG
|
A:SER126
|
4.5
|
78.7
|
1.0
|
O
|
A:HOH502
|
4.6
|
66.0
|
1.0
|
O
|
A:LEU185
|
4.6
|
81.4
|
1.0
|
CB
|
A:ASP184
|
4.6
|
68.2
|
1.0
|
CG
|
A:GLU212
|
5.0
|
97.2
|
1.0
|
|
Calcium binding site 3 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 3 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca403
b:0.2
occ:1.00
|
OD2
|
A:ASP305
|
2.5
|
92.9
|
1.0
|
OD1
|
A:ASP305
|
2.9
|
0.4
|
1.0
|
CG
|
A:ASP305
|
3.1
|
0.3
|
1.0
|
CB
|
A:ASP305
|
4.6
|
0.6
|
1.0
|
O
|
A:PRO306
|
4.8
|
0.8
|
1.0
|
O
|
A:ASP305
|
4.9
|
95.0
|
1.0
|
|
Calcium binding site 4 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 4 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca401
b:98.4
occ:1.00
|
OE2
|
B:GLU248
|
2.3
|
89.8
|
1.0
|
O
|
B:ARG241
|
2.4
|
0.8
|
1.0
|
O
|
B:ASP245
|
2.6
|
86.3
|
1.0
|
OE1
|
B:GLU248
|
2.9
|
82.0
|
1.0
|
CD
|
B:GLU248
|
3.0
|
90.1
|
1.0
|
N
|
B:ASP245
|
3.4
|
95.2
|
1.0
|
C
|
B:ARG241
|
3.5
|
91.8
|
1.0
|
C
|
B:ASP245
|
3.6
|
89.4
|
1.0
|
CB
|
B:ASP244
|
4.0
|
0.1
|
1.0
|
CA
|
B:ASP245
|
4.0
|
95.3
|
1.0
|
CA
|
B:ARG241
|
4.2
|
84.7
|
1.0
|
CB
|
B:ASP245
|
4.4
|
0.8
|
1.0
|
C
|
B:ASP244
|
4.4
|
0.2
|
1.0
|
CG
|
B:GLU248
|
4.5
|
76.7
|
1.0
|
N
|
B:ASP244
|
4.5
|
0.8
|
1.0
|
CB
|
B:ARG241
|
4.5
|
91.6
|
1.0
|
CA
|
B:ASP244
|
4.5
|
0.2
|
1.0
|
N
|
B:SER242
|
4.6
|
76.5
|
1.0
|
N
|
B:GLY246
|
4.8
|
88.7
|
1.0
|
CA
|
B:SER242
|
4.8
|
79.0
|
1.0
|
|
Calcium binding site 5 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 5 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca402
b:87.2
occ:1.00
|
OE2
|
B:GLU210
|
2.3
|
0.7
|
1.0
|
OE1
|
B:GLU212
|
2.4
|
67.2
|
1.0
|
OD1
|
B:ASP184
|
2.5
|
68.6
|
1.0
|
OD2
|
B:ASP184
|
2.9
|
74.2
|
1.0
|
CG
|
B:ASP184
|
3.1
|
68.5
|
1.0
|
CD
|
B:GLU210
|
3.5
|
81.4
|
1.0
|
CD
|
B:GLU212
|
3.6
|
0.8
|
1.0
|
OG
|
B:SER124
|
3.8
|
75.4
|
1.0
|
CB
|
B:SER124
|
3.9
|
86.4
|
1.0
|
O
|
B:HOH501
|
3.9
|
43.6
|
1.0
|
OE2
|
B:GLU212
|
4.2
|
0.8
|
1.0
|
OG
|
B:SER126
|
4.2
|
83.2
|
1.0
|
OE1
|
B:GLU210
|
4.3
|
87.4
|
1.0
|
CG
|
B:GLU210
|
4.5
|
62.9
|
1.0
|
CB
|
B:ASP184
|
4.6
|
60.4
|
1.0
|
O
|
B:LEU185
|
4.7
|
86.8
|
1.0
|
CG
|
B:GLU212
|
4.7
|
0.4
|
1.0
|
|
Calcium binding site 6 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 6 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca403
b:84.0
occ:1.00
|
OD2
|
B:ASP305
|
2.5
|
0.5
|
1.0
|
OD1
|
B:ASP305
|
3.0
|
0.5
|
1.0
|
CG
|
B:ASP305
|
3.0
|
0.5
|
1.0
|
O
|
B:ASP305
|
4.1
|
0.4
|
1.0
|
O
|
B:PRO306
|
4.3
|
0.1
|
1.0
|
CB
|
B:ASP305
|
4.5
|
0.1
|
1.0
|
C
|
B:ASP305
|
4.9
|
0.1
|
1.0
|
|
Calcium binding site 7 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 7 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca401
b:84.8
occ:1.00
|
O
|
C:ARG241
|
2.4
|
0.2
|
1.0
|
O
|
C:ASP245
|
2.4
|
0.7
|
1.0
|
OE1
|
C:GLU248
|
2.8
|
0.4
|
1.0
|
O
|
C:HOH505
|
2.8
|
59.1
|
1.0
|
OE2
|
C:GLU248
|
3.1
|
0.9
|
1.0
|
N
|
C:ASP245
|
3.1
|
0.1
|
1.0
|
CD
|
C:GLU248
|
3.3
|
0.7
|
1.0
|
C
|
C:ASP245
|
3.4
|
0.5
|
1.0
|
C
|
C:ARG241
|
3.6
|
99.4
|
1.0
|
CB
|
C:ASP244
|
3.6
|
0.3
|
1.0
|
CA
|
C:ASP245
|
3.8
|
0.3
|
1.0
|
C
|
C:ASP244
|
4.1
|
0.9
|
1.0
|
N
|
C:ASP244
|
4.2
|
0.1
|
1.0
|
CA
|
C:ASP244
|
4.2
|
0.4
|
1.0
|
CB
|
C:ASP245
|
4.4
|
0.2
|
1.0
|
N
|
C:SER242
|
4.5
|
90.3
|
1.0
|
CA
|
C:SER242
|
4.5
|
97.7
|
1.0
|
CA
|
C:ARG241
|
4.5
|
94.8
|
1.0
|
N
|
C:GLY246
|
4.7
|
0.5
|
1.0
|
CG
|
C:ASP244
|
4.7
|
0.7
|
1.0
|
OD2
|
C:ASP244
|
4.7
|
0.3
|
1.0
|
C
|
C:SER242
|
4.7
|
90.3
|
1.0
|
CG
|
C:GLU248
|
4.8
|
0.2
|
1.0
|
CB
|
C:ARG241
|
4.9
|
93.0
|
1.0
|
N
|
C:ILE243
|
5.0
|
88.2
|
1.0
|
|
Calcium binding site 8 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 8 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca402
b:72.2
occ:1.00
|
OE2
|
C:GLU210
|
2.4
|
0.9
|
1.0
|
OE1
|
C:GLU212
|
2.4
|
83.9
|
1.0
|
OD1
|
C:ASP184
|
2.5
|
64.6
|
1.0
|
OD2
|
C:ASP184
|
3.1
|
51.8
|
1.0
|
CG
|
C:ASP184
|
3.1
|
64.1
|
1.0
|
CD
|
C:GLU212
|
3.6
|
85.8
|
1.0
|
CD
|
C:GLU210
|
3.6
|
0.7
|
1.0
|
CB
|
C:SER124
|
3.8
|
79.8
|
1.0
|
OG
|
C:SER124
|
3.9
|
60.2
|
1.0
|
OG
|
C:SER126
|
4.1
|
72.1
|
1.0
|
OE1
|
C:GLU210
|
4.2
|
98.7
|
1.0
|
CG
|
C:GLU212
|
4.4
|
69.5
|
1.0
|
OE2
|
C:GLU212
|
4.4
|
0.4
|
1.0
|
CG
|
C:GLU210
|
4.6
|
67.2
|
1.0
|
CB
|
C:ASP184
|
4.6
|
53.3
|
1.0
|
O
|
C:LEU185
|
5.0
|
91.0
|
1.0
|
|
Calcium binding site 9 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 9 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca403
b:0.8
occ:1.00
|
OD1
|
C:ASP305
|
2.6
|
0.4
|
1.0
|
OD2
|
C:ASP305
|
2.7
|
0.2
|
1.0
|
CG
|
C:ASP305
|
3.0
|
1.0
|
1.0
|
CB
|
C:ASP305
|
4.5
|
0.4
|
1.0
|
O
|
C:PRO306
|
4.6
|
0.2
|
1.0
|
O
|
C:ASP305
|
4.7
|
0.3
|
1.0
|
|
Calcium binding site 10 out
of 12 in 6oly
Go back to
Calcium Binding Sites List in 6oly
Calcium binding site 10 out
of 12 in the Full-Length Mthk Channel at 3.1 Angstrom Resolution
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Full-Length Mthk Channel at 3.1 Angstrom Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca401
b:82.4
occ:1.00
|
OE2
|
D:GLU248
|
2.4
|
0.6
|
1.0
|
O
|
D:ARG241
|
2.5
|
81.0
|
1.0
|
O
|
D:ASP245
|
2.8
|
0.9
|
1.0
|
CD
|
D:GLU248
|
3.1
|
98.9
|
1.0
|
OE1
|
D:GLU248
|
3.1
|
78.0
|
1.0
|
N
|
D:ASP245
|
3.2
|
0.1
|
1.0
|
C
|
D:ARG241
|
3.6
|
86.4
|
1.0
|
C
|
D:ASP245
|
3.7
|
0.6
|
1.0
|
CB
|
D:ASP244
|
3.8
|
0.8
|
1.0
|
CA
|
D:ASP245
|
3.8
|
0.4
|
1.0
|
CB
|
D:ASP245
|
4.0
|
0.9
|
1.0
|
C
|
D:ASP244
|
4.2
|
0.6
|
1.0
|
CA
|
D:ARG241
|
4.3
|
87.3
|
1.0
|
CA
|
D:ASP244
|
4.3
|
0.4
|
1.0
|
N
|
D:ASP244
|
4.4
|
0.7
|
1.0
|
CG
|
D:GLU248
|
4.6
|
89.9
|
1.0
|
CB
|
D:ARG241
|
4.6
|
87.5
|
1.0
|
N
|
D:SER242
|
4.7
|
93.2
|
1.0
|
CA
|
D:SER242
|
4.9
|
96.6
|
1.0
|
N
|
D:GLY246
|
4.9
|
96.0
|
1.0
|
|
Reference:
W.Kopec,
B.S.Rothberg,
B.L.De Groot.
Molecular Mechanism of A Potassium Channel Gating Through Activation Gate-Selectivity Filter Coupling. Nat Commun V. 10 5366 2019.
ISSN: ESSN 2041-1723
PubMed: 31772184
DOI: 10.1038/S41467-019-13227-W
Page generated: Tue Jul 16 12:33:17 2024
|