Calcium in PDB 1iwq: Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin

The structure of Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin, PDB code: 1iwq was solved by E.Yamauchi, T.Nakatsu, M.Matsubara, 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 / 2.00
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.229, 40.229, 343.468, 90.00, 90.00, 120.00
R / Rfree (%)	22.3 / 26.7

The binding sites of Calcium atom in the Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin (pdb code 1iwq). 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 Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin, PDB code: 1iwq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin


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 Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:34.6 occ:1.00 OD1 A:ASP20 2.2 42.7 1.0 O A:HOH1076 2.3 39.4 1.0 O A:THR26 2.3 36.0 1.0 OE2 A:GLU31 2.4 31.2 1.0 OE1 A:GLU31 2.4 31.7 1.0 OD1 A:ASP22 2.5 42.0 1.0 OD1 A:ASP24 2.5 43.2 1.0 CD A:GLU31 2.7 29.6 1.0 CG A:ASP22 3.3 46.6 1.0 CG A:ASP24 3.4 45.0 1.0 CG A:ASP20 3.4 40.7 1.0 OD2 A:ASP22 3.4 42.0 1.0 C A:THR26 3.5 35.6 1.0 OD2 A:ASP24 3.9 43.8 1.0 N A:ASP24 4.1 48.0 1.0 CA A:ASP20 4.1 40.0 1.0 OD2 A:ASP20 4.1 44.2 1.0 OG1 A:THR26 4.1 38.8 1.0 N A:THR26 4.2 38.7 1.0 CB A:ASP20 4.2 41.0 1.0 CG A:GLU31 4.2 32.2 1.0 CB A:ASP24 4.3 45.7 1.0 N A:ASP22 4.4 47.9 1.0 C A:ASP20 4.4 42.7 1.0 N A:ILE27 4.4 33.5 1.0 CA A:THR26 4.4 37.4 1.0 CA A:ILE27 4.5 33.0 1.0 N A:GLY23 4.5 49.7 1.0 CB A:ASP22 4.6 48.1 1.0 CA A:ASP24 4.6 46.1 1.0 N A:LYS21 4.7 44.9 1.0 O A:HOH1050 4.7 32.3 1.0 O A:HOH1040 4.8 53.0 1.0 CA A:ASP22 4.9 48.2 1.0 N A:THR28 4.9 31.5 1.0 O A:ASP20 4.9 42.8 1.0 C A:ASP22 4.9 49.0 1.0 CG2 A:THR28 4.9 32.1 1.0 N A:GLY25 4.9 42.7 1.0 CB A:THR26 5.0 37.4 1.0 C A:ASP24 5.0 44.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin


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 Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:35.8 occ:1.00 OD1 A:ASP56 2.0 42.0 1.0 O A:HOH1077 2.1 43.5 1.0 O A:THR62 2.4 33.5 1.0 OE1 A:GLU67 2.4 38.0 1.0 OD1 A:ASN60 2.5 41.6 1.0 OD1 A:ASP58 2.5 43.7 1.0 OE2 A:GLU67 2.6 39.2 1.0 CD A:GLU67 2.8 37.3 1.0 CG A:ASP56 3.3 42.4 1.0 CG A:ASP58 3.4 45.7 1.0 CG A:ASN60 3.5 40.8 1.0 C A:THR62 3.6 37.4 1.0 OD2 A:ASP58 3.6 41.1 1.0 ND2 A:ASN60 3.9 41.8 1.0 OD2 A:ASP56 4.0 44.4 1.0 CA A:ASP56 4.2 43.7 1.0 CB A:ASP56 4.2 43.1 1.0 N A:THR62 4.2 39.0 1.0 N A:ASN60 4.3 43.6 1.0 CG A:GLU67 4.3 34.4 1.0 CA A:ILE63 4.4 36.3 1.0 N A:ILE63 4.5 35.7 1.0 N A:ASP64 4.5 35.0 1.0 C A:ASP56 4.5 45.1 1.0 CA A:THR62 4.6 37.2 1.0 N A:ASP58 4.6 46.3 1.0 CB A:ASN60 4.6 41.6 1.0 N A:GLY59 4.7 46.1 1.0 OG1 A:THR62 4.7 38.2 1.0 CB A:ASP58 4.7 46.5 1.0 N A:GLY61 4.7 40.5 1.0 CA A:ASN60 4.8 42.4 1.0 N A:ALA57 4.8 46.0 1.0 C A:ILE63 4.9 35.4 1.0 OD2 A:ASP64 4.9 44.4 1.0 C A:ASN60 4.9 41.6 1.0 CG A:ASP64 4.9 35.3 1.0 O A:ASP56 5.0 46.0 1.0 CA A:ASP58 5.0 47.0 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin


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 Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:26.2 occ:1.00 O A:TYR99 2.2 25.0 1.0 OD1 A:ASP93 2.3 29.2 1.0 OD1 A:ASN97 2.3 25.9 1.0 O A:HOH1029 2.4 30.3 1.0 OE1 A:GLU104 2.4 23.9 1.0 OD1 A:ASP95 2.5 31.2 1.0 OE2 A:GLU104 2.5 27.5 1.0 CD A:GLU104 2.8 30.4 1.0 CG A:ASP95 3.4 35.1 1.0 CG A:ASN97 3.4 26.4 1.0 C A:TYR99 3.4 23.9 1.0 CG A:ASP93 3.5 26.9 1.0 OD2 A:ASP95 3.7 32.8 1.0 ND2 A:ASN97 4.1 26.9 1.0 N A:TYR99 4.1 22.6 1.0 N A:ASN97 4.1 26.8 1.0 CG A:GLU104 4.2 25.8 1.0 CA A:ASP93 4.2 32.0 1.0 CA A:TYR99 4.3 22.9 1.0 CB A:ASP93 4.3 30.6 1.0 OD2 A:ASP93 4.3 25.6 1.0 N A:ILE100 4.3 23.0 1.0 O A:HOH1018 4.3 27.7 1.0 CA A:ILE100 4.4 22.3 1.0 N A:ASP95 4.4 36.8 1.0 C A:ASP93 4.5 34.3 1.0 CB A:ASN97 4.5 26.3 1.0 N A:SER101 4.6 25.1 1.0 N A:LYS94 4.6 37.7 1.0 CB A:ASP95 4.6 34.8 1.0 CB A:TYR99 4.7 24.3 1.0 N A:GLY96 4.7 31.4 1.0 O A:HOH1017 4.7 36.5 1.0 CA A:ASN97 4.7 25.7 1.0 N A:GLY98 4.8 23.7 1.0 CA A:ASP95 4.8 35.2 1.0 C A:ILE100 4.9 24.5 1.0 O A:ASP93 4.9 33.8 1.0 C A:ASP95 5.0 32.8 1.0 O A:HOH1035 5.0 41.1 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin


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 Marcks Calmodulin Binding Domain Peptide Complexed with CA2+/Calmodulin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:24.6 occ:1.00 O A:GLN135 2.2 25.6 1.0 OD1 A:ASP129 2.4 23.3 1.0 OD2 A:ASP133 2.4 22.4 1.0 OE1 A:GLU140 2.4 24.4 1.0 O A:HOH1006 2.4 27.6 1.0 OD2 A:ASP131 2.4 22.8 1.0 OE2 A:GLU140 2.5 27.8 1.0 CD A:GLU140 2.8 25.9 1.0 CG A:ASP133 3.2 24.6 1.0 CG A:ASP131 3.3 31.3 1.0 C A:GLN135 3.4 24.8 1.0 CG A:ASP129 3.4 26.3 1.0 OD1 A:ASP131 3.6 33.6 1.0 OD1 A:ASP133 3.7 25.6 1.0 N A:GLN135 4.1 24.0 1.0 N A:ASP133 4.2 25.2 1.0 OD2 A:ASP129 4.2 25.6 1.0 N A:ASP131 4.2 30.4 1.0 CA A:ASP129 4.2 28.7 1.0 N A:VAL136 4.2 26.0 1.0 CB A:ASP129 4.3 28.5 1.0 CA A:VAL136 4.3 24.7 1.0 CG A:GLU140 4.3 27.2 1.0 CA A:GLN135 4.3 25.3 1.0 N A:ILE130 4.4 31.5 1.0 CB A:ASP133 4.4 24.5 1.0 N A:GLY132 4.5 26.5 1.0 N A:ASN137 4.5 24.6 1.0 CB A:ASP131 4.6 29.6 1.0 CA A:ASP133 4.7 25.4 1.0 N A:GLY134 4.7 24.6 1.0 C A:ASP129 4.7 30.2 1.0 CA A:ASP131 4.7 30.1 1.0 C A:VAL136 4.9 25.7 1.0 C A:ASP131 4.9 28.9 1.0 CB A:GLN135 4.9 25.2 1.0 C A:ASP133 4.9 24.5 1.0

E.Yamauchi, T.Nakatsu, M.Matsubara, H.Kato, H.Taniguchi. Crystal Structure of A Marcks Peptide Containing the Calmodulin-Binding Domain in Complex with Ca(2+)-Calmodulin Nat.Struct.Biol. V. 10 226 2003.
ISSN: ISSN 1072-8368
PubMed: 12577052
DOI: 10.1038/NSB900