Calcium in PDB 1spu: Structure of Oxidoreductase

All present enzymatic activity of Structure of Oxidoreductase:
1.4.3.6;

The structure of Structure of Oxidoreductase, PDB code: 1spu was solved by C.M.Wilmot, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	134.460, 166.070, 79.410, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / n/a

The structure of Structure of Oxidoreductase also contains other interesting chemical elements:

Copper

(Cu)

2 atoms

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

Calcium binding site 1 out of 4 in the Structure of Oxidoreductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:19.7 occ:1.00 OD1 A:ASP678 2.2 14.9 1.0 O A:ALA679 2.3 12.6 1.0 OD1 A:ASP535 2.3 11.5 1.0 OD1 A:ASP533 2.4 16.5 1.0 O A:LEU534 2.5 19.9 1.0 O A:HOH1044 2.7 11.7 1.0 C A:ALA679 3.4 16.7 1.0 C A:LEU534 3.4 18.8 1.0 CG A:ASP678 3.4 26.1 1.0 CG A:ASP535 3.6 20.4 1.0 N A:ALA679 3.6 10.0 1.0 NZ A:LYS133 3.6 13.2 1.0 CG A:ASP533 3.6 14.4 1.0 N A:ASP535 4.0 12.8 1.0 CA A:ASP535 4.0 5.8 1.0 C A:ASP533 4.1 21.9 1.0 CA A:ALA679 4.1 11.2 1.0 OD2 A:ASP678 4.1 21.3 1.0 O A:ASP533 4.2 12.9 1.0 N A:LEU534 4.2 18.3 1.0 C A:ASP678 4.2 18.3 1.0 OD2 A:ASP533 4.2 16.9 1.0 O A:GLU539 4.3 11.5 1.0 CA A:ASP678 4.4 14.6 1.0 CB A:ASP535 4.4 14.5 1.0 OD2 A:ASP535 4.5 16.4 1.0 CB A:ASP678 4.5 16.9 1.0 CA A:LEU534 4.5 22.4 1.0 CA A:ASP533 4.5 14.2 1.0 N A:VAL680 4.5 13.7 1.0 CB A:ASP533 4.7 10.9 1.0 ND2 A:ASN541 4.8 10.1 1.0 CG2 A:VAL680 4.9 7.7 1.0 CB A:ALA679 4.9 18.4 1.0 CA A:VAL680 4.9 15.7 1.0 CE A:LYS133 5.0 8.1 1.0

Calcium binding site 2 out of 4 in the Structure of Oxidoreductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:56.7 occ:1.00 O A:TYR667 2.3 20.0 1.0 OE2 A:GLU672 2.4 51.8 1.0 O A:HOH1068 2.4 17.9 1.0 O A:HOH1073 2.7 28.6 1.0 OE2 A:GLU573 2.7 23.3 1.0 OE1 A:GLU573 3.1 16.6 1.0 CD A:GLU573 3.2 25.9 1.0 C A:TYR667 3.6 16.6 1.0 CD A:GLU672 3.6 56.2 1.0 CE1 A:HIS644 4.0 67.3 1.0 ND1 A:HIS644 4.2 69.4 1.0 CG A:GLU672 4.3 51.8 1.0 N A:ARG642 4.4 19.6 1.0 CA A:TYR667 4.5 15.4 1.0 CA A:SER668 4.5 27.1 1.0 N A:SER668 4.5 21.8 1.0 OE1 A:GLU647 4.5 27.5 1.0 OE1 A:GLU672 4.5 56.8 1.0 CG A:GLU573 4.7 14.2 1.0 CB A:THR641 4.7 15.8 1.0 OE2 A:GLU647 4.7 33.7 1.0 CB A:ARG642 4.7 25.6 1.0 CB A:GLU672 4.9 41.6 1.0 O A:ARG642 4.9 19.8 1.0 CB A:TYR667 5.0 17.6 1.0

Calcium binding site 3 out of 4 in the Structure of Oxidoreductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca801 b:20.2 occ:1.00 O B:ALA679 2.3 21.4 1.0 OD1 B:ASP678 2.3 15.3 1.0 OD1 B:ASP533 2.3 16.3 1.0 OD1 B:ASP535 2.4 19.4 1.0 O B:HOH1496 2.5 21.8 1.0 O B:LEU534 2.5 19.1 1.0 C B:LEU534 3.4 22.2 1.0 C B:ALA679 3.4 20.6 1.0 CG B:ASP678 3.5 26.0 1.0 N B:ALA679 3.6 23.6 1.0 CG B:ASP533 3.6 22.0 1.0 CG B:ASP535 3.6 24.7 1.0 NZ B:LYS133 3.8 23.0 1.0 N B:ASP535 4.0 24.2 1.0 C B:ASP533 4.1 21.0 1.0 CA B:ALA679 4.1 13.0 1.0 C B:ASP678 4.1 26.7 1.0 CA B:ASP535 4.1 24.8 1.0 N B:LEU534 4.2 22.2 1.0 O B:ASP533 4.2 21.1 1.0 OD2 B:ASP533 4.2 16.1 1.0 OD2 B:ASP678 4.3 19.9 1.0 CA B:ASP678 4.3 25.5 1.0 O B:GLU539 4.4 29.4 1.0 ND2 B:ASN541 4.4 17.4 1.0 CB B:ASP535 4.5 20.8 1.0 OD2 B:ASP535 4.5 25.1 1.0 CA B:LEU534 4.5 21.1 1.0 CB B:ASP678 4.5 25.9 1.0 CA B:ASP533 4.5 24.7 1.0 N B:VAL680 4.5 21.3 1.0 CB B:ASP533 4.6 16.4 1.0 CB B:ALA679 4.8 12.4 1.0 O B:ASP678 4.9 29.0 1.0 CG2 B:VAL680 4.9 9.9 1.0 CA B:VAL680 5.0 24.4 1.0

Calcium binding site 4 out of 4 in the Structure of Oxidoreductase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Oxidoreductase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:71.2 occ:1.00 O B:HOH1279 2.0 78.4 1.0 O B:TYR667 2.2 21.7 1.0 OE2 B:GLU672 2.6 59.7 1.0 OE2 B:GLU573 3.0 25.8 1.0 OE1 B:GLU573 3.2 27.2 1.0 NE2 B:HIS644 3.4 86.5 1.0 CD B:GLU573 3.4 30.2 1.0 C B:TYR667 3.5 18.7 1.0 CD2 B:HIS644 3.7 89.4 1.0 CD B:GLU672 3.7 53.5 1.0 OE1 B:GLU647 4.0 33.9 1.0 CG B:GLU672 4.1 47.4 1.0 OE2 B:GLU647 4.3 37.3 1.0 CA B:TYR667 4.3 25.9 1.0 O B:HOH1375 4.4 63.8 1.0 N B:SER668 4.4 24.8 1.0 CA B:SER668 4.5 32.6 1.0 CD B:GLU647 4.5 37.0 1.0 CE1 B:HIS644 4.6 86.8 1.0 OE1 B:GLU672 4.7 49.7 1.0 N B:ARG642 4.8 28.2 1.0 CB B:GLU672 4.8 36.8 1.0 CB B:ASP670 4.9 75.5 1.0 CB B:TYR667 4.9 20.9 1.0 CG B:GLU573 4.9 24.4 1.0

C.M.Wilmot, J.M.Murray, G.Alton, M.R.Parsons, M.A.Convery, V.Blakeley, A.S.Corner, M.M.Palcic, P.F.Knowles, M.J.Mcpherson, S.E.Phillips. Catalytic Mechanism of the Quinoenzyme Amine Oxidase From Escherichia Coli: Exploring the Reductive Half-Reaction. Biochemistry V. 36 1608 1997.
ISSN: ISSN 0006-2960
PubMed: 9048544
DOI: 10.1021/BI962205J