Calcium in PDB 6eeb: Calmodulin in Complex with Malbrancheamide
Protein crystallography data
The structure of Calmodulin in Complex with Malbrancheamide, PDB code: 6eeb
was solved by
T.S.Beyett,
A.E.Fraley,
J.J.G.Tesmer,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
37.17 /
1.96
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.113,
56.880,
116.781,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
21.5 /
26.3
|
Other elements in 6eeb:
The structure of Calmodulin in Complex with Malbrancheamide also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Calmodulin in Complex with Malbrancheamide
(pdb code 6eeb). 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 Malbrancheamide, PDB code: 6eeb:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 6eeb
Go back to
Calcium Binding Sites List in 6eeb
Calcium binding site 1 out
of 4 in the Calmodulin in Complex with Malbrancheamide
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 Malbrancheamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:34.5
occ:1.00
|
OE1
|
A:GLU68
|
2.3
|
34.5
|
1.0
|
OD1
|
A:ASP59
|
2.3
|
45.6
|
1.0
|
OD1
|
A:ASP57
|
2.4
|
39.2
|
1.0
|
O
|
A:THR63
|
2.4
|
35.1
|
1.0
|
O
|
A:HOH320
|
2.4
|
42.1
|
1.0
|
OD1
|
A:ASN61
|
2.5
|
42.9
|
1.0
|
OE2
|
A:GLU68
|
2.6
|
27.5
|
1.0
|
CD
|
A:GLU68
|
2.8
|
34.1
|
1.0
|
CG
|
A:ASP59
|
3.2
|
51.2
|
1.0
|
CG
|
A:ASN61
|
3.5
|
41.7
|
1.0
|
C
|
A:THR63
|
3.6
|
32.3
|
1.0
|
CG
|
A:ASP57
|
3.6
|
46.7
|
1.0
|
OD2
|
A:ASP59
|
3.6
|
53.8
|
1.0
|
O
|
A:HOH319
|
3.8
|
44.8
|
1.0
|
ND2
|
A:ASN61
|
4.0
|
47.6
|
1.0
|
N
|
A:THR63
|
4.3
|
33.0
|
1.0
|
CG
|
A:GLU68
|
4.3
|
28.4
|
1.0
|
N
|
A:ASN61
|
4.3
|
38.8
|
1.0
|
OD2
|
A:ASP57
|
4.4
|
44.9
|
1.0
|
CA
|
A:ASP57
|
4.4
|
40.0
|
1.0
|
N
|
A:ASP59
|
4.5
|
37.7
|
1.0
|
N
|
A:ASP65
|
4.5
|
36.4
|
1.0
|
N
|
A:ILE64
|
4.5
|
29.8
|
1.0
|
CA
|
A:ILE64
|
4.5
|
31.6
|
1.0
|
OG1
|
A:THR63
|
4.5
|
42.4
|
1.0
|
CB
|
A:ASP59
|
4.5
|
45.9
|
1.0
|
CA
|
A:THR63
|
4.5
|
32.3
|
1.0
|
CB
|
A:ASP57
|
4.5
|
42.1
|
1.0
|
OD2
|
A:ASP65
|
4.5
|
49.0
|
1.0
|
CB
|
A:ASN61
|
4.6
|
35.0
|
1.0
|
C
|
A:ASP57
|
4.7
|
33.5
|
1.0
|
N
|
A:GLY60
|
4.7
|
41.2
|
1.0
|
CG
|
A:ASP65
|
4.7
|
45.1
|
1.0
|
O
|
A:HOH315
|
4.7
|
37.7
|
1.0
|
N
|
A:ALA58
|
4.8
|
33.4
|
1.0
|
N
|
A:GLY62
|
4.8
|
40.1
|
1.0
|
C
|
A:ILE64
|
4.8
|
32.9
|
1.0
|
CA
|
A:ASN61
|
4.9
|
41.1
|
1.0
|
CA
|
A:ASP59
|
4.9
|
38.3
|
1.0
|
OD1
|
A:ASP65
|
4.9
|
43.9
|
1.0
|
CB
|
A:GLU68
|
5.0
|
29.4
|
1.0
|
|
Calcium binding site 2 out
of 4 in 6eeb
Go back to
Calcium Binding Sites List in 6eeb
Calcium binding site 2 out
of 4 in the Calmodulin in Complex with Malbrancheamide
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 Malbrancheamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:35.9
occ:1.00
|
O
|
A:THR27
|
2.3
|
36.8
|
1.0
|
OD1
|
A:ASP21
|
2.3
|
37.4
|
1.0
|
O
|
A:HOH342
|
2.3
|
37.7
|
1.0
|
OD1
|
A:ASP25
|
2.3
|
40.9
|
1.0
|
OD1
|
A:ASP23
|
2.4
|
56.4
|
1.0
|
OE2
|
A:GLU32
|
2.5
|
38.7
|
1.0
|
OE1
|
A:GLU32
|
2.6
|
35.9
|
1.0
|
CD
|
A:GLU32
|
2.9
|
46.0
|
1.0
|
CG
|
A:ASP25
|
3.4
|
45.5
|
1.0
|
CG
|
A:ASP23
|
3.4
|
56.6
|
1.0
|
CG
|
A:ASP21
|
3.4
|
42.6
|
1.0
|
C
|
A:THR27
|
3.5
|
38.7
|
1.0
|
OD2
|
A:ASP23
|
3.8
|
52.8
|
1.0
|
OG1
|
A:THR27
|
3.8
|
50.4
|
1.0
|
OD2
|
A:ASP25
|
3.9
|
51.2
|
1.0
|
N
|
A:THR27
|
4.2
|
38.3
|
1.0
|
CA
|
A:ASP21
|
4.2
|
36.9
|
1.0
|
CB
|
A:ASP21
|
4.2
|
38.4
|
1.0
|
OD2
|
A:ASP21
|
4.2
|
39.9
|
1.0
|
N
|
A:ASP25
|
4.2
|
42.5
|
1.0
|
CA
|
A:THR27
|
4.3
|
38.2
|
1.0
|
CG
|
A:GLU32
|
4.4
|
40.6
|
1.0
|
N
|
A:ILE28
|
4.4
|
30.1
|
1.0
|
N
|
A:ASP23
|
4.4
|
47.9
|
1.0
|
CA
|
A:ILE28
|
4.5
|
25.9
|
1.0
|
C
|
A:ASP21
|
4.5
|
44.8
|
1.0
|
CB
|
A:ASP25
|
4.5
|
41.0
|
1.0
|
N
|
A:LYS22
|
4.6
|
43.7
|
1.0
|
N
|
A:GLY24
|
4.6
|
37.2
|
1.0
|
CB
|
A:ASP23
|
4.7
|
51.8
|
1.0
|
CB
|
A:THR27
|
4.7
|
41.5
|
1.0
|
O
|
A:HOH307
|
4.7
|
40.6
|
1.0
|
O
|
A:HOH322
|
4.8
|
49.5
|
1.0
|
CA
|
A:ASP25
|
4.8
|
38.3
|
1.0
|
N
|
A:THR29
|
4.9
|
33.6
|
1.0
|
CA
|
A:ASP23
|
4.9
|
49.2
|
1.0
|
CG2
|
A:THR29
|
4.9
|
47.2
|
1.0
|
C
|
A:ASP23
|
4.9
|
44.0
|
1.0
|
N
|
A:GLY26
|
4.9
|
33.5
|
1.0
|
|
Calcium binding site 3 out
of 4 in 6eeb
Go back to
Calcium Binding Sites List in 6eeb
Calcium binding site 3 out
of 4 in the Calmodulin in Complex with Malbrancheamide
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 Malbrancheamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca204
b:37.6
occ:1.00
|
O
|
A:TYR100
|
2.2
|
43.7
|
1.0
|
OD1
|
A:ASP94
|
2.3
|
42.0
|
1.0
|
OE1
|
A:GLU105
|
2.3
|
33.2
|
1.0
|
OD1
|
A:ASP96
|
2.4
|
49.9
|
1.0
|
OD1
|
A:ASN98
|
2.4
|
38.8
|
1.0
|
O
|
A:HOH339
|
2.5
|
41.1
|
1.0
|
OE2
|
A:GLU105
|
2.5
|
32.6
|
1.0
|
CD
|
A:GLU105
|
2.7
|
33.2
|
1.0
|
CG
|
A:ASP96
|
3.2
|
42.8
|
1.0
|
CG
|
A:ASN98
|
3.4
|
43.6
|
1.0
|
C
|
A:TYR100
|
3.5
|
44.7
|
1.0
|
CG
|
A:ASP94
|
3.5
|
38.8
|
1.0
|
OD2
|
A:ASP96
|
3.6
|
51.8
|
1.0
|
ND2
|
A:ASN98
|
3.8
|
46.1
|
1.0
|
N
|
A:TYR100
|
4.1
|
34.5
|
1.0
|
N
|
A:ASN98
|
4.2
|
40.5
|
1.0
|
CG
|
A:GLU105
|
4.3
|
30.9
|
1.0
|
CA
|
A:ASP94
|
4.3
|
30.8
|
1.0
|
OD2
|
A:ASP94
|
4.3
|
34.5
|
1.0
|
CA
|
A:TYR100
|
4.3
|
46.6
|
1.0
|
N
|
A:ASP96
|
4.4
|
28.8
|
1.0
|
N
|
A:GLY97
|
4.4
|
39.4
|
1.0
|
N
|
A:ILE101
|
4.4
|
43.4
|
1.0
|
CB
|
A:ASP94
|
4.4
|
37.0
|
1.0
|
CB
|
A:ASP96
|
4.5
|
33.7
|
1.0
|
C
|
A:ASP94
|
4.5
|
30.6
|
1.0
|
CA
|
A:ILE101
|
4.5
|
40.0
|
1.0
|
CB
|
A:ASN98
|
4.5
|
47.5
|
1.0
|
N
|
A:SER102
|
4.5
|
39.0
|
1.0
|
OE1
|
A:GLN136
|
4.7
|
67.1
|
1.0
|
N
|
A:LYS95
|
4.7
|
32.5
|
1.0
|
CA
|
A:ASP96
|
4.8
|
34.9
|
1.0
|
CA
|
A:ASN98
|
4.8
|
43.9
|
1.0
|
N
|
A:GLY99
|
4.8
|
41.4
|
1.0
|
CB
|
A:TYR100
|
4.8
|
49.5
|
1.0
|
C
|
A:ASP96
|
4.9
|
42.0
|
1.0
|
O
|
A:ASP94
|
5.0
|
31.2
|
1.0
|
|
Calcium binding site 4 out
of 4 in 6eeb
Go back to
Calcium Binding Sites List in 6eeb
Calcium binding site 4 out
of 4 in the Calmodulin in Complex with Malbrancheamide
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 Malbrancheamide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca205
b:59.5
occ:1.00
|
O
|
A:GLN136
|
2.3
|
48.5
|
1.0
|
OE1
|
A:GLU141
|
2.3
|
62.9
|
1.0
|
OD1
|
A:ASP130
|
2.4
|
54.9
|
1.0
|
O
|
A:HOH324
|
2.5
|
42.4
|
1.0
|
OD1
|
A:ASP134
|
2.6
|
61.0
|
1.0
|
OE2
|
A:GLU141
|
2.7
|
54.5
|
1.0
|
OD1
|
A:ASP132
|
2.7
|
71.9
|
1.0
|
CD
|
A:GLU141
|
2.9
|
63.9
|
1.0
|
CG
|
A:ASP132
|
3.3
|
74.0
|
1.0
|
C
|
A:GLN136
|
3.5
|
53.3
|
1.0
|
OD2
|
A:ASP132
|
3.5
|
76.1
|
1.0
|
CG
|
A:ASP134
|
3.5
|
64.5
|
1.0
|
CG
|
A:ASP130
|
3.6
|
60.6
|
1.0
|
OD2
|
A:ASP134
|
4.0
|
66.1
|
1.0
|
CA
|
A:ASP130
|
4.1
|
55.6
|
1.0
|
N
|
A:GLN136
|
4.3
|
49.8
|
1.0
|
N
|
A:ASP132
|
4.3
|
66.3
|
1.0
|
N
|
A:ILE131
|
4.3
|
63.2
|
1.0
|
CA
|
A:VAL137
|
4.3
|
48.8
|
1.0
|
N
|
A:ASN138
|
4.3
|
46.9
|
1.0
|
CB
|
A:ASP130
|
4.3
|
55.6
|
1.0
|
N
|
A:VAL137
|
4.3
|
46.5
|
1.0
|
N
|
A:ASP134
|
4.4
|
66.0
|
1.0
|
CG
|
A:GLU141
|
4.4
|
55.7
|
1.0
|
OD2
|
A:ASP130
|
4.4
|
58.3
|
1.0
|
CA
|
A:GLN136
|
4.5
|
47.0
|
1.0
|
C
|
A:ASP130
|
4.5
|
64.9
|
1.0
|
N
|
A:GLY133
|
4.5
|
63.6
|
1.0
|
CB
|
A:ASP134
|
4.6
|
67.1
|
1.0
|
CB
|
A:ASP132
|
4.6
|
73.1
|
1.0
|
C
|
A:VAL137
|
4.8
|
47.8
|
1.0
|
CA
|
A:ASP132
|
4.8
|
70.7
|
1.0
|
ND2
|
A:ASN138
|
4.8
|
48.5
|
1.0
|
CG
|
A:ASN138
|
4.8
|
46.1
|
1.0
|
N
|
A:GLY135
|
4.9
|
59.0
|
1.0
|
C
|
A:ASP132
|
4.9
|
62.2
|
1.0
|
CA
|
A:ASP134
|
4.9
|
64.8
|
1.0
|
|
Reference:
T.S.Beyett,
A.E.Fraley,
E.Labudde,
D.Patra,
R.C.Coleman,
A.Eguchi,
A.Glukhova,
Q.Chen,
R.M.Williams,
W.J.Koch,
D.H.Sherman,
J.J.G.Tesmer.
Perturbation of the Interactions of Calmodulin with GRK5 Using A Natural Product Chemical Probe. Proc.Natl.Acad.Sci.Usa V. 116 15895 2019.
ISSN: ESSN 1091-6490
PubMed: 31337679
DOI: 10.1073/PNAS.1818547116
Page generated: Mon Jul 15 18:16:37 2024
|