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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:

Chlorine (Cl) 2 atoms
Zinc (Zn) 1 atom

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

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