Calcium in PDB 3gdc: Crystal Structure of Multicopper Oxidase

All present enzymatic activity of Crystal Structure of Multicopper Oxidase:
1.10.3.2;

The structure of Crystal Structure of Multicopper Oxidase, PDB code: 3gdc was solved by I.S.Macpherson, W.C.Lee, T.I.Liang, M.E.P.Murphy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	128.00 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.956, 50.705, 134.667, 90.00, 107.86, 90.00
R / Rfree (%)	19.1 / 22.5

The structure of Crystal Structure of Multicopper Oxidase also contains other interesting chemical elements:

Copper

(Cu)

12 atoms

The binding sites of Calcium atom in the Crystal Structure of Multicopper Oxidase (pdb code 3gdc). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Multicopper Oxidase, PDB code: 3gdc:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Multicopper Oxidase


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 Multicopper Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca401 b:24.6 occ:1.00 OD1 A:ASP190 2.4 28.3 1.0 O A:GLY187 2.4 29.4 1.0 OD1 A:ASN184 2.4 19.0 1.0 O A:ASP190 2.4 22.8 1.0 OD1 A:ASP186 2.5 30.5 1.0 OE2 A:GLU192 2.5 22.8 1.0 OE1 A:GLU192 2.5 22.4 1.0 CD A:GLU192 2.9 22.1 1.0 CG A:ASN184 3.3 20.4 1.0 CG A:ASP190 3.4 27.6 1.0 C A:ASP190 3.4 23.7 1.0 C A:GLY187 3.5 29.4 1.0 CG A:ASP186 3.6 29.1 1.0 N A:GLY187 3.9 28.6 1.0 ND2 A:ASN184 4.0 21.3 1.0 N A:ASP186 4.0 25.7 1.0 N A:ASP190 4.0 27.0 1.0 CA A:ASP190 4.1 25.5 1.0 OD2 A:ASP190 4.1 30.4 1.0 C A:ASP186 4.2 28.1 1.0 OD2 A:ASP186 4.2 31.0 1.0 CB A:ASP190 4.3 26.3 1.0 CA A:GLY187 4.3 29.2 1.0 CG A:GLU192 4.3 20.2 1.0 CA A:ASN184 4.3 19.3 1.0 CB A:ASN184 4.4 19.1 1.0 CA A:ASP186 4.4 27.3 1.0 N A:THR185 4.4 21.1 1.0 N A:ASN191 4.4 22.0 1.0 N A:GLY188 4.5 29.9 1.0 C A:ASN184 4.6 20.0 1.0 CB A:ASP186 4.6 27.6 1.0 C A:GLY188 4.6 30.3 1.0 CA A:GLY188 4.7 30.1 1.0 CA A:ASN191 4.7 20.8 1.0 O A:ASP186 4.7 28.4 1.0 O A:GLY188 4.8 30.6 1.0 C A:ASN191 4.8 20.1 1.0 N A:GLU192 5.0 19.1 1.0 N A:ASP189 5.0 29.8 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Multicopper Oxidase


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 Multicopper Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca401 b:24.1 occ:1.00 OD1 B:ASP186 2.3 34.4 1.0 O B:ASP190 2.3 27.9 1.0 OD1 B:ASN184 2.3 25.5 1.0 OD1 B:ASP190 2.4 32.2 1.0 OE2 B:GLU192 2.5 30.8 1.0 OE1 B:GLU192 2.6 27.0 1.0 O B:GLY188 2.7 36.6 1.0 CD B:GLU192 2.9 27.7 1.0 CG B:ASN184 3.3 26.0 1.0 C B:ASP190 3.4 28.7 1.0 CG B:ASP190 3.4 32.7 1.0 CG B:ASP186 3.5 35.6 1.0 N B:ASP190 3.6 32.3 1.0 C B:GLY188 3.7 36.4 1.0 O B:ASP186 3.9 35.1 1.0 CA B:ASP190 4.0 30.3 1.0 C B:ASP186 4.1 34.8 1.0 OD2 B:ASP190 4.1 35.5 1.0 N B:ASP186 4.1 32.5 1.0 OD2 B:ASP186 4.1 37.7 1.0 N B:GLY188 4.1 36.5 1.0 ND2 B:ASN184 4.1 27.9 1.0 CB B:ASN184 4.2 24.6 1.0 CB B:ASP190 4.3 30.9 1.0 CA B:GLY188 4.3 36.5 1.0 CA B:ASN184 4.3 24.7 1.0 CG B:GLU192 4.4 25.6 1.0 CA B:ASP186 4.4 34.0 1.0 N B:ASN191 4.4 26.8 1.0 N B:GLY187 4.5 35.2 1.0 CB B:ASP186 4.5 34.2 1.0 N B:THR185 4.6 27.7 1.0 C B:GLY187 4.6 36.4 1.0 C B:ASN184 4.6 25.7 1.0 N B:ASP189 4.7 35.9 1.0 CA B:ASN191 4.7 24.9 1.0 C B:ASP189 4.8 34.1 1.0 N B:GLU192 4.8 23.6 1.0 C B:ASN191 4.8 24.4 1.0 O B:HOH386 4.9 40.9 1.0 CA B:ASP189 5.0 35.3 1.0 O B:GLY187 5.0 37.2 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Multicopper Oxidase


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 Multicopper Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca401 b:27.8 occ:1.00 OD1 C:ASP190 2.3 32.3 1.0 OD1 C:ASP186 2.4 35.5 1.0 O C:GLY187 2.4 38.4 1.0 O C:ASP190 2.4 29.7 1.0 OD1 C:ASN184 2.5 28.2 1.0 OE1 C:GLU192 2.5 29.1 1.0 OE2 C:GLU192 2.5 29.5 1.0 CD C:GLU192 2.8 28.3 1.0 CG C:ASN184 3.3 28.3 1.0 C C:ASP190 3.4 30.2 1.0 CG C:ASP190 3.4 32.8 1.0 CG C:ASP186 3.5 36.6 1.0 C C:GLY187 3.5 38.4 1.0 ND2 C:ASN184 3.8 31.0 1.0 N C:GLY187 3.9 37.7 1.0 N C:ASP190 4.0 34.0 1.0 CA C:ASP190 4.0 31.9 1.0 OD2 C:ASP186 4.1 37.5 1.0 C C:ASP186 4.2 37.0 1.0 N C:ASP186 4.2 35.1 1.0 OD2 C:ASP190 4.2 34.4 1.0 CB C:ASP190 4.3 32.1 1.0 CA C:GLY187 4.3 38.2 1.0 CG C:GLU192 4.3 25.6 1.0 N C:ASN191 4.4 27.9 1.0 CB C:ASN184 4.4 28.5 1.0 CA C:ASN184 4.4 28.1 1.0 CA C:ASP186 4.5 36.3 1.0 N C:THR185 4.6 30.8 1.0 N C:GLY188 4.6 38.4 1.0 CB C:ASP186 4.6 36.3 1.0 O C:ASP186 4.6 37.6 1.0 CA C:ASN191 4.7 26.1 1.0 C C:ASN184 4.7 29.3 1.0 C C:GLY188 4.7 38.2 1.0 CA C:GLY188 4.8 38.2 1.0 C C:ASN191 4.8 25.3 1.0 O C:GLY188 4.8 38.7 1.0 N C:GLU192 4.9 24.2 1.0

I.S.Macpherson, W.C.Lee, T.I.Liang, M.E.P.Murphy. A Trimeric Multicopper Oxidase Provides An Evolutionary Link to Nitrite Reductase To Be Published.