Calcium in PDB 2kdu: Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode

The binding sites of Calcium atom in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode (pdb code 2kdu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode, PDB code: 2kdu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:0.0 occ:1.00 OD1 A:ASP20 2.5 0.0 1.0 O A:THR26 2.6 0.0 1.0 OD1 A:ASP24 2.6 0.0 1.0 OE2 A:GLU31 2.6 0.0 1.0 OD2 A:ASP22 2.6 0.0 1.0 OE1 A:GLU31 2.6 0.0 1.0 OD2 A:ASP24 2.7 0.0 1.0 HB2 A:ASP22 2.7 0.0 1.0 CD A:GLU31 2.8 0.0 1.0 HA A:ILE27 2.9 0.0 1.0 H A:THR28 2.9 0.0 1.0 HG22 A:THR28 3.0 0.0 1.0 CG A:ASP24 3.0 0.0 1.0 HG23 A:THR28 3.1 0.0 1.0 CG A:ASP22 3.4 0.0 1.0 CB A:ASP22 3.4 0.0 1.0 CG2 A:THR28 3.5 0.0 1.0 N A:THR28 3.5 0.0 1.0 OG1 A:THR28 3.5 0.0 1.0 CG A:ASP20 3.6 0.0 1.0 C A:THR26 3.6 0.0 1.0 CA A:ILE27 3.7 0.0 1.0 HB3 A:ASP22 3.9 0.0 1.0 C A:ILE27 3.9 0.0 1.0 CB A:THR28 4.0 0.0 1.0 H A:ASP22 4.0 0.0 1.0 HG3 A:GLU31 4.0 0.0 1.0 CG A:GLU31 4.0 0.0 1.0 OD2 A:ASP20 4.1 0.0 1.0 N A:ILE27 4.1 0.0 1.0 H A:ASP24 4.2 0.0 1.0 HG1 A:THR28 4.4 0.0 1.0 HG21 A:THR28 4.4 0.0 1.0 CA A:THR28 4.4 0.0 1.0 H A:THR26 4.5 0.0 1.0 OD1 A:ASP22 4.5 0.0 1.0 CB A:ASP24 4.5 0.0 1.0 HA A:ASP20 4.5 0.0 1.0 OG1 A:THR26 4.6 0.0 1.0 HG1 A:THR26 4.7 0.0 1.0 HG2 A:GLU31 4.7 0.0 1.0 HG23 A:ILE27 4.7 0.0 1.0 N A:ASP22 4.7 0.0 1.0 HZ A:PHE16 4.7 0.0 1.0 CA A:ASP22 4.7 0.0 1.0 HB2 A:GLU31 4.8 0.0 1.0 CB A:ASP20 4.8 0.0 1.0 CA A:THR26 4.8 0.0 1.0 O A:ASP24 4.9 0.0 1.0 O A:ILE27 4.9 0.0 1.0 H A:LYS21 4.9 0.0 1.0 H A:GLY23 4.9 0.0 1.0 N A:THR26 4.9 0.0 1.0 HB3 A:ASP24 4.9 0.0 1.0 HB2 A:ASP20 4.9 0.0 1.0 HB A:THR28 5.0 0.0 1.0

Calcium binding site 2 out of 4 in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:0.0 occ:1.00 HB2 A:ASP56 2.4 0.0 1.0 OD1 A:ASN60 2.5 0.0 1.0 OE1 A:GLU67 2.5 0.0 1.0 OD2 A:ASP56 2.6 0.0 1.0 OD2 A:ASP58 2.6 0.0 1.0 OE2 A:GLU67 2.6 0.0 1.0 O A:THR62 2.6 0.0 1.0 CD A:GLU67 2.8 0.0 1.0 H A:ASN60 2.8 0.0 1.0 CG A:ASN60 2.9 0.0 1.0 HD22 A:ASN60 3.0 0.0 1.0 O A:ALA57 3.0 0.0 1.0 ND2 A:ASN60 3.1 0.0 1.0 CG A:ASP56 3.2 0.0 1.0 CB A:ASP56 3.2 0.0 1.0 H A:GLY59 3.5 0.0 1.0 H A:THR62 3.5 0.0 1.0 CG A:ASP58 3.6 0.0 1.0 HA A:ILE63 3.7 0.0 1.0 N A:ASN60 3.7 0.0 1.0 C A:THR62 3.8 0.0 1.0 HB3 A:ASN60 3.8 0.0 1.0 HD21 A:ASN60 3.8 0.0 1.0 H A:ASP64 3.9 0.0 1.0 HB3 A:ASP56 3.9 0.0 1.0 CB A:ASN60 3.9 0.0 1.0 C A:ASP56 4.1 0.0 1.0 C A:ALA57 4.2 0.0 1.0 CA A:ASP56 4.2 0.0 1.0 N A:GLY59 4.2 0.0 1.0 OD1 A:ASP58 4.2 0.0 1.0 H A:GLY61 4.2 0.0 1.0 CG A:GLU67 4.3 0.0 1.0 OD1 A:ASP56 4.3 0.0 1.0 O A:ASP56 4.3 0.0 1.0 N A:ALA57 4.3 0.0 1.0 OG1 A:THR62 4.3 0.0 1.0 N A:THR62 4.4 0.0 1.0 OD2 A:ASP64 4.4 0.0 1.0 CA A:ASN60 4.4 0.0 1.0 HB3 A:ASP58 4.5 0.0 1.0 HB3 A:GLU67 4.5 0.0 1.0 H A:ALA57 4.5 0.0 1.0 HG2 A:GLU67 4.6 0.0 1.0 HA2 A:GLY59 4.6 0.0 1.0 CA A:ILE63 4.6 0.0 1.0 CB A:ASP58 4.6 0.0 1.0 HA A:ASP56 4.6 0.0 1.0 CA A:THR62 4.7 0.0 1.0 N A:ILE63 4.7 0.0 1.0 CG A:ASP64 4.7 0.0 1.0 C A:GLY59 4.7 0.0 1.0 N A:ASP64 4.7 0.0 1.0 N A:GLY61 4.8 0.0 1.0 CA A:GLY59 4.8 0.0 1.0 HB2 A:ASN60 4.8 0.0 1.0 CB A:GLU67 4.8 0.0 1.0 OD1 A:ASP64 4.9 0.0 1.0 HB2 A:GLU67 4.9 0.0 1.0 CA A:ALA57 4.9 0.0 1.0 C A:ASN60 4.9 0.0 1.0 HG3 A:GLU67 5.0 0.0 1.0

Calcium binding site 3 out of 4 in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca503 b:0.0 occ:1.00 HB2 A:ASP93 2.3 0.0 1.0 HD22 A:ASN97 2.4 0.0 1.0 OE2 A:GLU104 2.6 0.0 1.0 O A:TYR99 2.6 0.0 1.0 HB3 A:ASP93 2.6 0.0 1.0 OD1 A:ASN97 2.6 0.0 1.0 OD2 A:ASP93 2.7 0.0 1.0 OE1 A:GLU104 2.7 0.0 1.0 CB A:ASP93 2.7 0.0 1.0 OD2 A:ASP95 2.8 0.0 1.0 CD A:GLU104 3.0 0.0 1.0 CG A:ASP93 3.1 0.0 1.0 ND2 A:ASN97 3.1 0.0 1.0 CG A:ASN97 3.3 0.0 1.0 HB2 A:TYR99 3.5 0.0 1.0 HB2 A:ASP95 3.7 0.0 1.0 H A:TYR99 3.7 0.0 1.0 C A:TYR99 3.7 0.0 1.0 CG A:ASP95 3.9 0.0 1.0 HD21 A:ASN97 4.0 0.0 1.0 HA A:ILE100 4.2 0.0 1.0 CA A:ASP93 4.2 0.0 1.0 CB A:ASP95 4.2 0.0 1.0 OD1 A:ASP93 4.2 0.0 1.0 N A:TYR99 4.4 0.0 1.0 CB A:TYR99 4.4 0.0 1.0 HB3 A:ASP95 4.4 0.0 1.0 CA A:TYR99 4.4 0.0 1.0 H A:SER101 4.4 0.0 1.0 HA A:ASP93 4.4 0.0 1.0 CG A:GLU104 4.5 0.0 1.0 HB2 A:SER101 4.6 0.0 1.0 N A:ILE100 4.7 0.0 1.0 O A:ASP93 4.8 0.0 1.0 CB A:ASN97 4.8 0.0 1.0 HB3 A:TYR99 4.8 0.0 1.0 HG2 A:GLU104 4.9 0.0 1.0 CA A:ILE100 4.9 0.0 1.0 HD2 A:TYR99 4.9 0.0 1.0 C A:ASP93 4.9 0.0 1.0 OD1 A:ASP95 5.0 0.0 1.0 H A:ASN97 5.0 0.0 1.0

Calcium binding site 4 out of 4 in the Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis of the MUNC13-1/CA2+-Calmodulin Interaction: A Novel 1-26 Calmodulin Binding Motif with A Bipartite Binding Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.0 occ:1.00 HB2 A:ASP131 2.5 0.0 1.0 HA A:ASP129 2.6 0.0 1.0 OD1 A:ASP133 2.6 0.0 1.0 OD1 A:ASP129 2.6 0.0 1.0 OE2 A:GLU140 2.6 0.0 1.0 O A:GLN135 2.6 0.0 1.0 OE1 A:GLU140 2.6 0.0 1.0 OD2 A:ASP131 2.6 0.0 1.0 OD2 A:ASP133 2.8 0.0 1.0 CD A:GLU140 2.8 0.0 1.0 CG A:ASP133 2.9 0.0 1.0 H A:ASP131 3.0 0.0 1.0 CB A:ASP131 3.3 0.0 1.0 CG A:ASP131 3.4 0.0 1.0 H A:ASP133 3.4 0.0 1.0 HA A:VAL136 3.4 0.0 1.0 H A:ASN137 3.5 0.0 1.0 CA A:ASP129 3.5 0.0 1.0 CG A:ASP129 3.6 0.0 1.0 H A:ILE130 3.7 0.0 1.0 C A:GLN135 3.8 0.0 1.0 H A:GLN135 3.8 0.0 1.0 N A:ASP131 3.8 0.0 1.0 H A:GLY132 3.9 0.0 1.0 HB2 A:ASN137 3.9 0.0 1.0 CB A:ASP129 4.0 0.0 1.0 CG A:GLU140 4.1 0.0 1.0 N A:ILE130 4.1 0.0 1.0 C A:ASP129 4.1 0.0 1.0 HG3 A:GLU140 4.1 0.0 1.0 CA A:ASP131 4.1 0.0 1.0 HB3 A:ASP131 4.1 0.0 1.0 HB2 A:ASP129 4.2 0.0 1.0 CA A:VAL136 4.3 0.0 1.0 N A:ASN137 4.3 0.0 1.0 CB A:ASP133 4.3 0.0 1.0 N A:ASP133 4.3 0.0 1.0 N A:GLY132 4.4 0.0 1.0 HB3 A:ASP133 4.5 0.0 1.0 N A:VAL136 4.5 0.0 1.0 OD1 A:ASP131 4.5 0.0 1.0 N A:GLN135 4.5 0.0 1.0 C A:ASP131 4.6 0.0 1.0 O A:ALA128 4.6 0.0 1.0 HB2 A:GLN135 4.6 0.0 1.0 OD2 A:ASP129 4.6 0.0 1.0 N A:ASP129 4.6 0.0 1.0 HG2 A:GLU140 4.7 0.0 1.0 C A:VAL136 4.8 0.0 1.0 CA A:GLN135 4.8 0.0 1.0 HD13 A:ILE130 4.8 0.0 1.0 H A:GLY134 4.8 0.0 1.0 CB A:ASN137 4.8 0.0 1.0 CA A:ASP133 4.9 0.0 1.0 C A:ILE130 4.9 0.0 1.0 O A:ASP129 4.9 0.0 1.0 HB3 A:GLU140 5.0 0.0 1.0

F.Rodriguez-Castaneda, M.Maestre-Martinez, N.Coudevylle, K.Dimova, H.Junge, N.Lipstein, D.Lee, S.Becker, N.Brose, O.Jahn, T.Carlomagno, C.Griesinger. Modular Architecture of MUNC13/Calmodulin Complexes: Dual Regulation By CA2+ and Possible Function in Short-Term Synaptic Plasticity. Embo J. V. 29 680 2010.
ISSN: ISSN 0261-4189
PubMed: 20010694
DOI: 10.1038/EMBOJ.2009.373