Calcium in PDB 1yut: Solution Structure of Calcium-S100A13 (Minimized Mean Structure)

The binding sites of Calcium atom in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure) (pdb code 1yut). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure), PDB code: 1yut:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure)


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Solution Structure of Calcium-S100A13 (Minimized Mean Structure) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca197 b:10.0 occ:1.00 OE2 A:GLU37 2.3 10.0 1.0 O A:ALA24 2.3 10.0 1.0 O A:SER32 2.3 10.0 1.0 OE1 A:GLU37 2.4 10.0 1.0 O A:GLY28 2.4 10.0 1.0 O A:GLU27 2.4 10.0 1.0 O A:ARG29 2.5 10.0 1.0 CD A:GLU37 2.7 10.0 1.0 C A:GLU27 3.3 10.0 1.0 C A:GLY28 3.4 10.0 1.0 H A:GLU27 3.4 10.0 1.0 C A:ALA24 3.5 10.0 1.0 C A:ARG29 3.5 10.0 1.0 C A:SER32 3.6 10.0 1.0 HB2 A:GLU27 3.6 10.0 1.0 HA A:LEU33 3.6 10.0 1.0 H A:SER34 3.8 10.0 1.0 HA A:ALA24 3.8 10.0 1.0 H A:ASP31 3.9 10.0 1.0 HA A:LYS30 4.0 10.0 1.0 HB2 A:ARG29 4.1 10.0 1.0 N A:GLU27 4.1 10.0 1.0 N A:GLY28 4.1 10.0 1.0 N A:ARG29 4.1 10.0 1.0 CA A:GLU27 4.2 10.0 1.0 HA A:ARG25 4.2 10.0 1.0 CG A:GLU37 4.2 10.0 1.0 CA A:ARG29 4.3 10.0 1.0 CA A:ALA24 4.3 10.0 1.0 CA A:GLY28 4.3 10.0 1.0 CB A:GLU27 4.4 10.0 1.0 N A:LEU33 4.4 10.0 1.0 CA A:LEU33 4.4 10.0 1.0 N A:ARG25 4.4 10.0 1.0 N A:LYS30 4.4 10.0 1.0 H A:SER32 4.5 10.0 1.0 HD13 A:LEU33 4.5 10.0 1.0 CA A:SER32 4.5 10.0 1.0 N A:SER34 4.6 10.0 1.0 N A:SER32 4.6 10.0 1.0 O A:PHE23 4.6 10.0 1.0 C A:ARG25 4.6 10.0 1.0 HG2 A:GLU37 4.6 10.0 1.0 CA A:ARG25 4.7 10.0 1.0 OG A:SER32 4.7 10.0 1.0 H A:GLN26 4.7 10.0 1.0 CB A:ARG29 4.7 10.0 1.0 N A:GLN26 4.7 10.0 1.0 HB2 A:SER32 4.8 10.0 1.0 HG3 A:GLU37 4.8 10.0 1.0 CA A:LYS30 4.8 10.0 1.0 HB1 A:ALA24 4.8 10.0 1.0 N A:ASP31 4.9 10.0 1.0 HA3 A:GLY28 4.9 10.0 1.0 C A:LEU33 4.9 10.0 1.0 CB A:SER32 4.9 10.0 1.0 HB3 A:GLU27 4.9 10.0 1.0 H A:GLY28 4.9 10.0 1.0 HB3 A:GLU37 5.0 10.0 1.0 HB2 A:SER34 5.0 10.0 1.0

Calcium binding site 2 out of 4 in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure)


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Solution Structure of Calcium-S100A13 (Minimized Mean Structure) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca198 b:10.0 occ:1.00 OD1 A:ASP64 2.2 10.0 1.0 OD1 A:ASP68 2.3 10.0 1.0 OE2 A:GLU75 2.3 10.0 1.0 OE1 A:GLU75 2.3 10.0 1.0 O A:GLU70 2.3 10.0 1.0 OD1 A:ASN66 2.4 10.0 1.0 OD2 A:ASP68 2.4 10.0 1.0 CG A:ASP68 2.6 10.0 1.0 CD A:GLU75 2.7 10.0 1.0 HD22 A:ASN66 3.2 10.0 1.0 CG A:ASP64 3.2 10.0 1.0 CG A:ASN66 3.4 10.0 1.0 HE2 A:LYS72 3.4 10.0 1.0 H A:ASP68 3.5 10.0 1.0 HZ1 A:LYS72 3.5 10.0 1.0 H A:GLU70 3.5 10.0 1.0 C A:GLU70 3.5 10.0 1.0 H A:LYS72 3.6 10.0 1.0 OD2 A:ASP64 3.7 10.0 1.0 ND2 A:ASN66 3.7 10.0 1.0 HA A:LEU71 3.7 10.0 1.0 HB2 A:GLU70 3.9 10.0 1.0 HE3 A:LYS72 4.0 10.0 1.0 CB A:ASP68 4.0 10.0 1.0 HA A:ASP64 4.0 10.0 1.0 CE A:LYS72 4.1 10.0 1.0 HB3 A:ASP68 4.2 10.0 1.0 CG A:GLU75 4.2 10.0 1.0 NZ A:LYS72 4.2 10.0 1.0 N A:ASP68 4.3 10.0 1.0 N A:GLU70 4.3 10.0 1.0 CB A:ASP64 4.3 10.0 1.0 H A:ASN66 4.4 10.0 1.0 H A:SER69 4.4 10.0 1.0 CA A:GLU70 4.4 10.0 1.0 N A:LEU71 4.4 10.0 1.0 HD13 A:LEU71 4.5 10.0 1.0 HB2 A:LYS72 4.5 10.0 1.0 HB3 A:GLU75 4.5 10.0 1.0 CA A:LEU71 4.5 10.0 1.0 CB A:GLU70 4.5 10.0 1.0 HB2 A:ASP64 4.5 10.0 1.0 N A:LYS72 4.6 10.0 1.0 HB3 A:GLU70 4.6 10.0 1.0 HB2 A:GLU75 4.6 10.0 1.0 CA A:ASP64 4.6 10.0 1.0 CA A:ASP68 4.6 10.0 1.0 HG2 A:GLU75 4.7 10.0 1.0 HD21 A:ASN66 4.7 10.0 1.0 CB A:GLU75 4.7 10.0 1.0 HB2 A:ASP68 4.7 10.0 1.0 CB A:ASN66 4.7 10.0 1.0 HG3 A:GLU75 4.7 10.0 1.0 HZ3 A:LYS72 4.7 10.0 1.0 H A:GLN67 4.8 10.0 1.0 N A:SER69 5.0 10.0 1.0 HD21 A:LEU71 5.0 10.0 1.0 HB2 A:ASN66 5.0 10.0 1.0 HZ2 A:LYS72 5.0 10.0 1.0

Calcium binding site 3 out of 4 in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure)


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Solution Structure of Calcium-S100A13 (Minimized Mean Structure) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca199 b:10.0 occ:1.00 OE1 B:GLU37 2.3 10.0 1.0 OE2 B:GLU37 2.3 10.0 1.0 O B:GLY28 2.3 10.0 1.0 O B:ALA24 2.3 10.0 1.0 O B:SER32 2.3 10.0 1.0 O B:ARG29 2.4 10.0 1.0 OG B:SER34 2.4 10.0 1.0 CD B:GLU37 2.7 10.0 1.0 HG B:SER34 3.1 10.0 1.0 H B:SER34 3.3 10.0 1.0 HB2 B:SER34 3.3 10.0 1.0 CB B:SER34 3.5 10.0 1.0 C B:ALA24 3.5 10.0 1.0 C B:ARG29 3.5 10.0 1.0 C B:GLY28 3.5 10.0 1.0 C B:SER32 3.6 10.0 1.0 HA B:LEU33 3.6 10.0 1.0 HA B:ALA24 3.7 10.0 1.0 N B:SER34 3.7 10.0 1.0 HB3 B:ALA24 3.7 10.0 1.0 H B:GLU27 3.7 10.0 1.0 H B:GLY28 3.8 10.0 1.0 HB3 B:ARG29 3.9 10.0 1.0 H B:SER32 4.0 10.0 1.0 HA B:LYS30 4.0 10.0 1.0 CA B:ALA24 4.1 10.0 1.0 C B:LEU33 4.1 10.0 1.0 HB2 B:GLU27 4.1 10.0 1.0 CG B:GLU37 4.2 10.0 1.0 CA B:LEU33 4.2 10.0 1.0 CA B:ARG29 4.3 10.0 1.0 N B:ARG29 4.3 10.0 1.0 CA B:SER34 4.3 10.0 1.0 HB3 B:SER34 4.3 10.0 1.0 OG B:SER32 4.3 10.0 1.0 N B:LEU33 4.3 10.0 1.0 N B:LYS30 4.4 10.0 1.0 CB B:ALA24 4.4 10.0 1.0 N B:GLY28 4.5 10.0 1.0 CA B:GLY28 4.5 10.0 1.0 CB B:ARG29 4.6 10.0 1.0 HG2 B:GLU37 4.6 10.0 1.0 N B:GLU27 4.6 10.0 1.0 N B:ARG25 4.6 10.0 1.0 C B:ARG25 4.6 10.0 1.0 CA B:SER32 4.6 10.0 1.0 HA B:ARG25 4.7 10.0 1.0 CA B:LYS30 4.7 10.0 1.0 N B:GLN26 4.7 10.0 1.0 N B:SER32 4.7 10.0 1.0 HA3 B:GLY28 4.7 10.0 1.0 HG3 B:GLU37 4.7 10.0 1.0 HB2 B:GLU37 4.7 10.0 1.0 HD12 B:LEU33 4.8 10.0 1.0 H B:GLN26 4.8 10.0 1.0 O B:LYS30 4.8 10.0 1.0 C B:LYS30 4.9 10.0 1.0 CA B:ARG25 4.9 10.0 1.0 HA B:SER34 4.9 10.0 1.0 O B:ARG25 4.9 10.0 1.0 O B:LEU33 4.9 10.0 1.0 CB B:GLU37 5.0 10.0 1.0 HB2 B:ARG29 5.0 10.0 1.0

Calcium binding site 4 out of 4 in the Solution Structure of Calcium-S100A13 (Minimized Mean Structure)


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Solution Structure of Calcium-S100A13 (Minimized Mean Structure) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca200 b:10.0 occ:1.00 OD1 B:ASP68 2.2 10.0 1.0 OE1 B:GLU75 2.3 10.0 1.0 OD1 B:ASP64 2.3 10.0 1.0 OE2 B:GLU75 2.3 10.0 1.0 OD2 B:ASP64 2.4 10.0 1.0 OD1 B:ASN66 2.4 10.0 1.0 O B:GLU70 2.4 10.0 1.0 CG B:ASP64 2.6 10.0 1.0 CD B:GLU75 2.7 10.0 1.0 O B:ASP64 2.8 10.0 1.0 CG B:ASP68 3.1 10.0 1.0 H B:SER69 3.2 10.0 1.0 H B:ASP68 3.3 10.0 1.0 H B:GLU70 3.3 10.0 1.0 HA B:ASP64 3.4 10.0 1.0 C B:GLU70 3.4 10.0 1.0 CG B:ASN66 3.5 10.0 1.0 OD2 B:ASP68 3.5 10.0 1.0 H B:LYS72 3.5 10.0 1.0 H B:GLN67 3.6 10.0 1.0 HB2 B:LYS72 3.6 10.0 1.0 HA B:LEU71 3.6 10.0 1.0 HD22 B:ASN66 3.7 10.0 1.0 C B:ASP64 3.7 10.0 1.0 CB B:ASP64 3.8 10.0 1.0 CA B:ASP64 3.8 10.0 1.0 N B:SER69 4.0 10.0 1.0 ND2 B:ASN66 4.0 10.0 1.0 N B:GLU70 4.0 10.0 1.0 N B:ASP68 4.0 10.0 1.0 HB2 B:GLU70 4.1 10.0 1.0 H B:ASN66 4.1 10.0 1.0 CG B:GLU75 4.2 10.0 1.0 N B:GLN67 4.3 10.0 1.0 N B:LEU71 4.3 10.0 1.0 CB B:ASP68 4.3 10.0 1.0 CA B:GLU70 4.3 10.0 1.0 HE3 B:LYS72 4.3 10.0 1.0 HD11 B:LEU71 4.4 10.0 1.0 CA B:LEU71 4.4 10.0 1.0 N B:LYS72 4.4 10.0 1.0 HZ3 B:LYS72 4.4 10.0 1.0 HA B:SER69 4.4 10.0 1.0 HB3 B:ASP64 4.4 10.0 1.0 CA B:ASP68 4.5 10.0 1.0 HD2 B:LYS72 4.5 10.0 1.0 HD21 B:LEU71 4.5 10.0 1.0 HA B:GLN67 4.5 10.0 1.0 HB2 B:ASP64 4.5 10.0 1.0 C B:ASP68 4.6 10.0 1.0 HG2 B:GLU75 4.6 10.0 1.0 CB B:LYS72 4.6 10.0 1.0 HB2 B:GLU75 4.6 10.0 1.0 CA B:SER69 4.6 10.0 1.0 CB B:ASN66 4.7 10.0 1.0 C B:SER69 4.7 10.0 1.0 CB B:GLU70 4.7 10.0 1.0 HB3 B:ASP68 4.7 10.0 1.0 HG3 B:GLU75 4.7 10.0 1.0 C B:GLN67 4.8 10.0 1.0 CA B:GLN67 4.8 10.0 1.0 N B:ASN66 4.8 10.0 1.0 HB3 B:LYS72 4.9 10.0 1.0 CB B:GLU75 4.9 10.0 1.0 C B:ASN66 4.9 10.0 1.0 C B:LEU71 4.9 10.0 1.0 HB3 B:ASN66 5.0 10.0 1.0 HD21 B:ASN66 5.0 10.0 1.0 N B:VAL65 5.0 10.0 1.0 HB3 B:GLU75 5.0 10.0 1.0

F.Arnesano, L.Banci, I.Bertini, A.Fantoni, L.Tenori, M.S.Viezzoli. Structural Interplay Between Calcium(II) and Copper(II) Binding to S100A13 Protein Angew.Chem.Int.Ed.Engl. V. 44 6341 2005.
ISSN: ISSN 1433-7851
PubMed: 16145699
DOI: 10.1002/ANIE.200500540