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Calcium in PDB 3gdc: Crystal Structure of Multicopper Oxidase

Enzymatic activity of Crystal Structure of Multicopper Oxidase

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

Protein crystallography data

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

Other elements in 3gdc:

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

Copper (Cu) 12 atoms

Calcium Binding Sites:

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 3gdc

Go back to Calcium Binding Sites List in 3gdc
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 3gdc

Go back to Calcium Binding Sites List in 3gdc
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 3gdc

Go back to Calcium Binding Sites List in 3gdc
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

Reference:

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.
Page generated: Sat Dec 12 04:12:49 2020

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