Calcium in PDB 1l7z: Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide

The structure of Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide, PDB code: 1l7z was solved by M.Matsubara, T.Nakatsu, E.Yamauchi, H.Kato, H.Taniguchi, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	40.600, 40.600, 173.639, 90.00, 90.00, 120.00
R / Rfree (%)	23.9 / 26.4

The binding sites of Calcium atom in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide (pdb code 1l7z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide, PDB code: 1l7z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca300 b:48.2 occ:1.00 OD1 A:ASP20 2.2 44.5 1.0 O A:THR26 2.2 47.4 1.0 OD1 A:ASP24 2.4 50.5 1.0 OE1 A:GLU31 2.4 43.2 1.0 OD1 A:ASP22 2.4 55.3 1.0 OE2 A:GLU31 2.5 43.2 1.0 CD A:GLU31 2.8 40.4 1.0 CG A:ASP22 3.2 56.3 1.0 OD2 A:ASP22 3.3 58.3 1.0 CG A:ASP24 3.3 51.9 1.0 CG A:ASP20 3.4 45.9 1.0 C A:THR26 3.4 46.5 1.0 OD2 A:ASP24 3.8 50.1 1.0 OG1 A:THR26 4.0 55.2 1.0 CA A:ASP20 4.0 44.6 1.0 CB A:ASP20 4.1 43.3 1.0 N A:THR26 4.2 48.9 1.0 N A:ASP24 4.2 53.4 1.0 CG A:GLU31 4.3 38.9 1.0 OD2 A:ASP20 4.3 46.3 1.0 CA A:THR26 4.3 48.3 1.0 C A:ASP20 4.3 45.7 1.0 N A:ILE27 4.4 43.4 1.0 CB A:ASP24 4.4 51.9 1.0 CA A:ILE27 4.4 42.5 1.0 N A:ASP22 4.4 56.3 1.0 O A:HOH1004 4.5 42.2 1.0 N A:LYS21 4.5 49.2 1.0 CB A:ASP22 4.5 56.9 1.0 N A:GLY23 4.5 55.3 1.0 CA A:ASP24 4.7 52.2 1.0 N A:THR28 4.7 42.6 1.0 CB A:THR26 4.8 51.4 1.0 CG2 A:THR28 4.8 41.1 1.0 CA A:ASP22 4.9 56.5 1.0 N A:GLY25 4.9 50.9 1.0 O A:ASP20 4.9 44.3 1.0 C A:ILE27 5.0 43.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:61.4 occ:1.00 OD1 A:ASN60 2.1 58.2 1.0 OD1 A:ASP58 2.1 72.2 1.0 OD1 A:ASP56 2.2 61.9 1.0 OE1 A:GLU67 2.3 58.9 1.0 O A:THR62 2.4 56.9 1.0 O A:HOH1052 2.4 59.7 1.0 O A:HOH1027 2.6 51.6 1.0 OE2 A:GLU67 2.7 58.7 1.0 CD A:GLU67 2.8 57.0 1.0 CG A:ASN60 3.1 58.7 1.0 CG A:ASP58 3.2 70.4 1.0 CG A:ASP56 3.5 63.6 1.0 C A:THR62 3.6 56.3 1.0 ND2 A:ASN60 3.7 59.5 1.0 OD2 A:ASP58 3.7 70.3 1.0 OD2 A:ASP64 4.2 59.9 1.0 N A:ASN60 4.2 63.7 1.0 CB A:ASN60 4.3 59.8 1.0 OD2 A:ASP56 4.3 62.5 1.0 CG A:GLU67 4.3 55.2 1.0 N A:THR62 4.3 56.8 1.0 CA A:ASP56 4.4 64.6 1.0 N A:ASP58 4.4 68.4 1.0 O A:HOH1056 4.4 63.1 1.0 CA A:ILE63 4.4 52.8 1.0 CB A:ASP56 4.4 62.5 1.0 N A:ILE63 4.4 55.8 1.0 CB A:ASP58 4.5 69.7 1.0 CA A:THR62 4.5 55.9 1.0 N A:ASP64 4.6 51.2 1.0 C A:ASP56 4.6 65.5 1.0 OG1 A:THR62 4.6 53.6 1.0 CA A:ASN60 4.7 61.4 1.0 N A:GLY59 4.7 67.5 1.0 CG A:ASP64 4.7 55.3 1.0 N A:GLY61 4.8 59.8 1.0 N A:ALA57 4.8 66.4 1.0 CA A:ASP58 4.8 68.8 1.0 C A:ASP58 4.8 69.1 1.0 C A:ILE63 5.0 51.4 1.0 C A:ASN60 5.0 60.7 1.0 CD1 A:ILE63 5.0 53.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:39.3 occ:1.00 OD1 A:ASP133 2.2 32.7 0.0 OD1 A:ASP129 2.2 34.1 1.0 O A:GLN135 2.3 31.8 1.0 OD1 A:ASP131 2.3 36.6 1.0 O A:HOH1014 2.4 29.6 1.0 OE1 A:GLU140 2.5 43.9 1.0 OE2 A:GLU140 2.6 44.9 1.0 CD A:GLU140 2.9 42.2 1.0 CG A:ASP133 3.0 30.3 1.0 CG A:ASP131 3.2 39.0 1.0 C A:GLN135 3.3 32.9 1.0 CG A:ASP129 3.3 35.2 1.0 OD2 A:ASP133 3.4 37.3 1.0 OD2 A:ASP131 3.4 41.1 1.0 N A:GLN135 4.0 31.5 1.0 OD2 A:ASP129 4.1 36.5 1.0 N A:VAL136 4.2 34.8 1.0 CA A:GLN135 4.2 32.5 1.0 N A:ASP133 4.2 33.9 1.0 CA A:VAL136 4.2 35.2 1.0 N A:ILE130 4.3 42.0 1.0 CB A:ASP129 4.3 36.5 1.0 CB A:ASP133 4.3 32.5 1.0 N A:ASP131 4.3 40.6 1.0 CA A:ASP129 4.3 40.0 1.0 CG A:GLU140 4.4 43.8 1.0 N A:ASN137 4.5 33.7 1.0 N A:GLY132 4.5 36.0 1.0 CB A:ASP131 4.5 37.8 1.0 N A:GLY134 4.6 32.1 1.0 CB A:GLN135 4.7 32.4 1.0 CA A:ASP133 4.7 31.9 1.0 CA A:ASP131 4.8 39.4 1.0 C A:ASP129 4.8 40.6 1.0 C A:VAL136 4.8 33.2 1.0 C A:ASP133 4.9 32.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of CA2+/Calmodulin Complexed with Myristoylated Cap-23/Nap-22 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:39.4 occ:1.00 OD1 A:ASP93 2.2 32.0 1.0 OD1 A:ASN97 2.2 36.6 1.0 O A:HOH1015 2.2 36.6 1.0 O A:TYR99 2.3 36.4 1.0 OE1 A:GLU104 2.4 44.6 1.0 OD1 A:ASP95 2.5 49.1 1.0 OE2 A:GLU104 2.7 44.8 1.0 CD A:GLU104 2.8 43.8 1.0 CG A:ASP95 3.0 49.0 1.0 OD2 A:ASP95 3.1 48.3 1.0 CG A:ASN97 3.3 35.8 1.0 CG A:ASP93 3.4 32.7 1.0 C A:TYR99 3.5 32.5 1.0 N A:ASN97 4.0 37.3 1.0 ND2 A:ASN97 4.0 33.7 1.0 O A:HOH1017 4.2 39.2 1.0 CA A:ASP93 4.2 41.6 1.0 N A:TYR99 4.2 31.1 1.0 OD2 A:ASP93 4.2 33.9 1.0 N A:ASP95 4.3 47.8 1.0 CB A:ASP93 4.3 36.3 1.0 CG A:GLU104 4.3 40.8 1.0 CB A:ASN97 4.3 36.0 1.0 CB A:ASP95 4.3 47.7 1.0 CA A:TYR99 4.3 31.6 1.0 N A:ILE100 4.4 33.8 1.0 N A:GLY96 4.5 43.4 1.0 CA A:ILE100 4.5 32.9 1.0 C A:ASP93 4.5 43.5 1.0 CA A:ASN97 4.6 36.5 1.0 CA A:ASP95 4.7 45.9 1.0 N A:LYS94 4.7 46.4 1.0 N A:SER101 4.7 33.6 1.0 CB A:TYR99 4.7 30.7 1.0 N A:GLY98 4.8 33.4 1.0 C A:ASP95 4.8 44.0 1.0 O A:HOH1003 4.9 41.0 1.0 C A:ASN97 5.0 35.9 1.0

M.Matsubara, T.Nakatsu, H.Kato, H.Taniguchi. Crystal Structure of A Myristoylated Cap-23/Nap-22 N-Terminal Domain Complexed with CA2+/Calmodulin Embo J. V. 23 712 2004.
ISSN: ISSN 0261-4189
PubMed: 14765114
DOI: 10.1038/SJ.EMBOJ.7600093