Calcium in PDB 6os4: Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
Protein crystallography data
The structure of Calmodulin in Complex with Farnesyl Cysteine Methyl Ester, PDB code: 6os4
was solved by
B.M.M.Grant,
M.Enomoto,
K.Y.Lee,
S.I.Back,
T.Gebregiworgis,
N.Ishiyama,
M.Ikura,
C.Marshall,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
34.97 /
2.05
|
Space group
|
P 61 2 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
40.379,
40.379,
338.137,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
19.1 /
22.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
(pdb code 6os4). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
Calmodulin in Complex with Farnesyl Cysteine Methyl Ester, PDB code: 6os4:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6os4
Go back to
Calcium Binding Sites List in 6os4
Calcium binding site 1 out
of 4 in the Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Calmodulin in Complex with Farnesyl Cysteine Methyl Ester within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca201
b:34.2
occ:1.00
|
OD1
|
A:ASP20
|
2.2
|
40.1
|
1.0
|
O
|
A:THR26
|
2.3
|
39.4
|
1.0
|
OD1
|
A:ASP24
|
2.4
|
41.0
|
1.0
|
OD1
|
A:ASP22
|
2.4
|
44.1
|
1.0
|
O
|
A:HOH322
|
2.4
|
39.1
|
1.0
|
OE2
|
A:GLU31
|
2.5
|
37.5
|
1.0
|
OE1
|
A:GLU31
|
2.5
|
33.1
|
1.0
|
CD
|
A:GLU31
|
2.8
|
40.3
|
1.0
|
CG
|
A:ASP22
|
3.4
|
42.7
|
1.0
|
CG
|
A:ASP24
|
3.4
|
45.6
|
1.0
|
CG
|
A:ASP20
|
3.4
|
40.9
|
1.0
|
C
|
A:THR26
|
3.5
|
32.5
|
1.0
|
OD2
|
A:ASP22
|
3.7
|
49.2
|
1.0
|
OD2
|
A:ASP24
|
3.9
|
51.2
|
1.0
|
N
|
A:ASP24
|
4.2
|
48.2
|
1.0
|
OG1
|
A:THR26
|
4.2
|
52.5
|
1.0
|
N
|
A:THR26
|
4.2
|
37.9
|
1.0
|
OD2
|
A:ASP20
|
4.2
|
44.5
|
1.0
|
CA
|
A:ASP20
|
4.2
|
29.7
|
1.0
|
CB
|
A:ASP20
|
4.3
|
36.0
|
1.0
|
CG
|
A:GLU31
|
4.3
|
30.4
|
1.0
|
CA
|
A:THR26
|
4.4
|
35.9
|
1.0
|
N
|
A:ILE27
|
4.4
|
34.1
|
1.0
|
CB
|
A:ASP24
|
4.4
|
51.1
|
1.0
|
N
|
A:ASP22
|
4.4
|
47.8
|
1.0
|
C
|
A:ASP20
|
4.5
|
39.1
|
1.0
|
CA
|
A:ILE27
|
4.5
|
28.3
|
1.0
|
N
|
A:GLY23
|
4.5
|
46.7
|
1.0
|
N
|
A:LYS21
|
4.6
|
41.6
|
1.0
|
CB
|
A:ASP22
|
4.6
|
45.6
|
1.0
|
CA
|
A:ASP24
|
4.7
|
47.1
|
1.0
|
O
|
A:HOH307
|
4.8
|
34.0
|
1.0
|
N
|
A:GLY25
|
4.8
|
41.6
|
1.0
|
N
|
A:THR28
|
4.9
|
30.8
|
1.0
|
CA
|
A:ASP22
|
4.9
|
45.8
|
1.0
|
C
|
A:ASP22
|
4.9
|
52.6
|
1.0
|
CG2
|
A:THR28
|
4.9
|
31.4
|
1.0
|
C
|
A:ASP24
|
4.9
|
47.4
|
1.0
|
CB
|
A:THR26
|
5.0
|
41.0
|
1.0
|
O
|
A:ASP20
|
5.0
|
43.2
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6os4
Go back to
Calcium Binding Sites List in 6os4
Calcium binding site 2 out
of 4 in the Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Calmodulin in Complex with Farnesyl Cysteine Methyl Ester within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:38.7
occ:1.00
|
OD1
|
A:ASP56
|
2.3
|
50.5
|
1.0
|
O
|
A:THR62
|
2.3
|
35.7
|
1.0
|
OD1
|
A:ASN60
|
2.4
|
49.2
|
1.0
|
OD1
|
A:ASP58
|
2.4
|
47.0
|
1.0
|
O
|
A:HOH303
|
2.4
|
52.6
|
1.0
|
OE1
|
A:GLU67
|
2.5
|
48.2
|
1.0
|
OE2
|
A:GLU67
|
2.6
|
48.8
|
1.0
|
CD
|
A:GLU67
|
2.9
|
49.0
|
1.0
|
CG
|
A:ASP58
|
3.3
|
57.2
|
1.0
|
CG
|
A:ASN60
|
3.3
|
56.2
|
1.0
|
CG
|
A:ASP56
|
3.5
|
52.2
|
1.0
|
C
|
A:THR62
|
3.5
|
36.0
|
1.0
|
OD2
|
A:ASP58
|
3.6
|
57.8
|
1.0
|
O
|
A:HOH324
|
3.8
|
46.5
|
1.0
|
ND2
|
A:ASN60
|
3.9
|
50.2
|
1.0
|
N
|
A:ASN60
|
4.2
|
54.8
|
1.0
|
N
|
A:THR62
|
4.2
|
43.4
|
1.0
|
CA
|
A:ASP56
|
4.2
|
53.7
|
1.0
|
OD2
|
A:ASP56
|
4.3
|
51.8
|
1.0
|
CG
|
A:GLU67
|
4.4
|
47.9
|
1.0
|
CB
|
A:ASP56
|
4.4
|
51.2
|
1.0
|
N
|
A:ILE63
|
4.4
|
39.9
|
1.0
|
CA
|
A:ILE63
|
4.5
|
41.2
|
1.0
|
CA
|
A:THR62
|
4.5
|
37.7
|
1.0
|
N
|
A:ASP58
|
4.5
|
51.5
|
1.0
|
CB
|
A:ASN60
|
4.5
|
56.4
|
1.0
|
OG1
|
A:THR62
|
4.5
|
39.9
|
1.0
|
N
|
A:ASP64
|
4.5
|
40.7
|
1.0
|
C
|
A:ASP56
|
4.6
|
53.7
|
1.0
|
N
|
A:GLY59
|
4.6
|
58.6
|
1.0
|
CB
|
A:ASP58
|
4.6
|
58.6
|
1.0
|
N
|
A:ALA57
|
4.7
|
55.4
|
1.0
|
N
|
A:GLY61
|
4.7
|
45.4
|
1.0
|
CA
|
A:ASN60
|
4.7
|
51.4
|
1.0
|
OD2
|
A:ASP64
|
4.8
|
52.0
|
1.0
|
C
|
A:ASN60
|
4.9
|
51.4
|
1.0
|
CG
|
A:ASP64
|
4.9
|
48.0
|
1.0
|
CA
|
A:ASP58
|
4.9
|
60.4
|
1.0
|
C
|
A:ILE63
|
4.9
|
41.0
|
1.0
|
C
|
A:ASP58
|
4.9
|
58.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6os4
Go back to
Calcium Binding Sites List in 6os4
Calcium binding site 3 out
of 4 in the Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Calmodulin in Complex with Farnesyl Cysteine Methyl Ester within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:26.1
occ:1.00
|
OD1
|
A:ASP93
|
2.2
|
31.2
|
1.0
|
O
|
A:TYR99
|
2.3
|
29.5
|
1.0
|
OD1
|
A:ASP95
|
2.4
|
35.8
|
1.0
|
OD1
|
A:ASN97
|
2.4
|
28.2
|
1.0
|
O
|
A:HOH308
|
2.4
|
37.6
|
1.0
|
OE1
|
A:GLU104
|
2.4
|
30.1
|
1.0
|
OE2
|
A:GLU104
|
2.6
|
34.1
|
1.0
|
CD
|
A:GLU104
|
2.8
|
31.4
|
1.0
|
CG
|
A:ASP95
|
3.3
|
36.0
|
1.0
|
CG
|
A:ASN97
|
3.4
|
26.7
|
1.0
|
CG
|
A:ASP93
|
3.4
|
31.5
|
1.0
|
C
|
A:TYR99
|
3.5
|
28.7
|
1.0
|
OD2
|
A:ASP95
|
3.7
|
36.3
|
1.0
|
ND2
|
A:ASN97
|
4.1
|
25.9
|
1.0
|
N
|
A:TYR99
|
4.1
|
25.4
|
1.0
|
CA
|
A:ASP93
|
4.1
|
34.2
|
1.0
|
O
|
A:HOH316
|
4.2
|
31.2
|
1.0
|
N
|
A:ASN97
|
4.2
|
25.2
|
1.0
|
CB
|
A:ASP93
|
4.3
|
32.7
|
1.0
|
OD2
|
A:ASP93
|
4.3
|
31.0
|
1.0
|
CG
|
A:GLU104
|
4.3
|
30.8
|
1.0
|
CA
|
A:TYR99
|
4.3
|
26.4
|
1.0
|
N
|
A:ILE100
|
4.4
|
28.3
|
1.0
|
CB
|
A:ASN97
|
4.4
|
25.8
|
1.0
|
C
|
A:ASP93
|
4.4
|
29.8
|
1.0
|
N
|
A:ASP95
|
4.5
|
40.0
|
1.0
|
CA
|
A:ILE100
|
4.5
|
25.4
|
1.0
|
CB
|
A:ASP95
|
4.6
|
39.5
|
1.0
|
O
|
A:HOH313
|
4.6
|
35.9
|
1.0
|
N
|
A:GLY96
|
4.6
|
32.4
|
1.0
|
N
|
A:LYS94
|
4.6
|
42.9
|
1.0
|
N
|
A:SER101
|
4.7
|
29.3
|
1.0
|
CA
|
A:ASN97
|
4.7
|
25.1
|
1.0
|
N
|
A:GLY98
|
4.8
|
27.1
|
1.0
|
CB
|
A:TYR99
|
4.8
|
27.8
|
1.0
|
CA
|
A:ASP95
|
4.9
|
38.7
|
1.0
|
C
|
A:ASP95
|
4.9
|
39.9
|
1.0
|
C
|
A:ASN97
|
5.0
|
25.6
|
1.0
|
O
|
A:ASP93
|
5.0
|
33.4
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6os4
Go back to
Calcium Binding Sites List in 6os4
Calcium binding site 4 out
of 4 in the Calmodulin in Complex with Farnesyl Cysteine Methyl Ester
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Calmodulin in Complex with Farnesyl Cysteine Methyl Ester within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca204
b:23.7
occ:1.00
|
OD1
|
A:ASP129
|
2.3
|
26.4
|
1.0
|
O
|
A:GLN135
|
2.3
|
26.4
|
1.0
|
OD2
|
A:ASP131
|
2.4
|
27.7
|
1.0
|
OD1
|
A:ASP133
|
2.4
|
25.0
|
1.0
|
OE1
|
A:GLU140
|
2.4
|
26.6
|
1.0
|
O
|
A:HOH318
|
2.5
|
29.4
|
1.0
|
OE2
|
A:GLU140
|
2.5
|
29.4
|
1.0
|
CD
|
A:GLU140
|
2.8
|
28.9
|
1.0
|
CG
|
A:ASP131
|
3.2
|
26.2
|
1.0
|
CG
|
A:ASP133
|
3.3
|
25.6
|
1.0
|
CG
|
A:ASP129
|
3.4
|
28.6
|
1.0
|
C
|
A:GLN135
|
3.5
|
23.2
|
1.0
|
OD1
|
A:ASP131
|
3.5
|
30.9
|
1.0
|
OD2
|
A:ASP133
|
3.7
|
27.7
|
1.0
|
N
|
A:ASP133
|
4.1
|
27.1
|
1.0
|
N
|
A:GLN135
|
4.1
|
22.3
|
1.0
|
OD2
|
A:ASP129
|
4.1
|
28.5
|
1.0
|
N
|
A:ASP131
|
4.2
|
28.1
|
1.0
|
N
|
A:ILE130
|
4.3
|
27.1
|
1.0
|
CG
|
A:GLU140
|
4.3
|
30.6
|
1.0
|
CA
|
A:ASP129
|
4.3
|
29.2
|
1.0
|
CB
|
A:ASP129
|
4.3
|
29.4
|
1.0
|
N
|
A:VAL136
|
4.4
|
27.4
|
1.0
|
N
|
A:GLY132
|
4.4
|
23.4
|
1.0
|
CB
|
A:ASP133
|
4.4
|
25.5
|
1.0
|
CA
|
A:GLN135
|
4.4
|
21.4
|
1.0
|
CA
|
A:VAL136
|
4.4
|
27.1
|
1.0
|
N
|
A:ASN137
|
4.4
|
27.1
|
1.0
|
CB
|
A:ASP131
|
4.5
|
26.3
|
1.0
|
N
|
A:GLY134
|
4.6
|
26.6
|
1.0
|
CA
|
A:ASP133
|
4.6
|
24.4
|
1.0
|
CA
|
A:ASP131
|
4.7
|
28.2
|
1.0
|
C
|
A:ASP129
|
4.8
|
32.6
|
1.0
|
C
|
A:ASP133
|
4.9
|
23.2
|
1.0
|
C
|
A:ASP131
|
4.9
|
26.3
|
1.0
|
C
|
A:VAL136
|
4.9
|
25.9
|
1.0
|
|
Reference:
B.M.M.Grant,
M.Enomoto,
S.-I.Back,
K.-Y.Lee,
T.Gebregiworgis,
N.Ishiyama,
M.Ikura,
C.Marshall.
Calmodulin Disrupts Plasma Membrane Localization of Farnesylated KRAS4B By Sequestering Its Lipid Moiety Sci.Signal. V. 13 2020.
ISSN: ESSN 1937-9145
DOI: 10.1126/SCISIGNAL.AAZ0344
Page generated: Tue Jul 16 12:36:25 2024
|