Zinc in PDB 3uct: Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+

The structure of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+, PDB code: 3uct was solved by F.T.Senguen, Z.Grabarek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.23 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.288, 35.463, 58.343, 90.00, 93.12, 90.00
R / Rfree (%)	20.2 / 23.4

The structure of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ also contains other interesting chemical elements:

Manganese

(Mn)

6 atoms

The binding sites of Zinc atom in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ (pdb code 3uct). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+, PDB code: 3uct:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn104 b:38.1 occ:1.00 OD2 A:ASP64 2.0 40.1 1.0 OE2 A:GLU67 2.0 36.2 1.0 CG A:ASP64 2.8 32.1 1.0 CD A:GLU67 2.8 44.3 1.0 OD1 A:ASP64 2.9 26.1 1.0 CG A:GLU67 3.5 39.9 1.0 OE1 A:GLU67 3.7 41.3 1.0 O A:HOH119 4.0 46.6 1.0 CB A:ASP64 4.2 26.8 1.0 CB A:GLU67 4.7 32.5 1.0 O A:HOH120 4.8 51.9 1.0

Zinc binding site 2 out of 4 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:42.4 occ:1.00 OD2 B:ASP24 2.0 32.4 1.0 OE2 A:GLU45 2.0 44.9 1.0 OD2 B:ASP22 2.0 35.9 1.0 OE1 A:GLU45 2.1 43.2 1.0 O A:HOH110 2.1 33.4 1.0 CD A:GLU45 2.3 39.9 1.0 CG B:ASP22 2.9 38.4 1.0 CG B:ASP24 2.9 33.4 1.0 OD1 B:ASP22 3.2 36.6 1.0 OD1 B:ASP24 3.2 31.5 1.0 MN B:MN100 3.4 29.9 1.0 O A:HOH118 3.7 43.2 1.0 CG A:GLU45 3.8 46.8 1.0 OG1 B:THR26 3.9 31.8 1.0 O A:HOH117 4.3 47.8 1.0 CB B:ASP24 4.3 31.3 1.0 CB B:ASP22 4.3 34.8 1.0 O B:HOH85 4.3 35.8 1.0 O A:HOH131 4.7 43.6 1.0 CG2 B:THR62 4.7 38.5 1.0 O B:HOH92 4.8 43.2 1.0 CB A:GLU45 4.8 40.7 1.0 O B:THR26 4.8 29.5 1.0

Zinc binding site 3 out of 4 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:41.4 occ:1.00 OE2 B:GLU67 2.0 42.2 1.0 OD2 B:ASP64 2.1 45.9 1.0 OD1 B:ASP64 2.4 32.5 1.0 CG B:ASP64 2.6 37.3 1.0 CD B:GLU67 2.8 38.1 1.0 CG B:GLU67 3.5 38.9 1.0 OE1 B:GLU67 3.6 32.1 1.0 O B:HOH94 3.8 42.7 1.0 CB B:ASP64 4.1 31.4 1.0 O B:HOH93 4.2 47.9 1.0 CB B:GLU67 4.6 34.3 1.0 O B:HOH88 4.9 36.3 1.0 N B:ASP64 5.0 28.7 1.0 N B:GLU67 5.0 28.6 1.0

Zinc binding site 4 out of 4 in the Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of MN2+-Bound N-Terminal Domain of Calmodulin in the Presence of ZN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn104 b:46.5 occ:1.00 OE2 B:GLU54 2.0 48.0 1.0 OD1 B:ASP50 2.0 52.5 1.0 OD2 B:ASP50 2.1 57.1 1.0 CG B:ASP50 2.4 52.1 1.0 CD B:GLU54 2.9 53.8 1.0 CG B:GLU54 3.2 46.9 1.0 CB B:ASP50 3.9 50.5 1.0 OE1 B:GLU54 4.1 51.5 1.0 O B:ASP50 4.3 48.6 1.0 C B:ASP50 4.6 49.5 1.0 CA B:ASP50 4.6 48.8 1.0 CB B:GLU54 4.7 47.0 1.0

F.T.Senguen, Z.Grabarek. X-Ray Structures of Magnesium and Manganese Complexes with the N-Terminal Domain of Calmodulin: Insights Into the Mechanism and Specificity of Metal Ion Binding to An Ef-Hand. Biochemistry V. 51 6182 2012.
ISSN: ISSN 0006-2960
PubMed: 22803592
DOI: 10.1021/BI300698H