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Calcium in PDB 1d6y: Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.

Enzymatic activity of Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.

All present enzymatic activity of Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide., PDB code: 1d6y was solved by C.M.Wilmot, J.Hajdu, M.J.Mcpherson, P.F.Knowles, S.E.V.Phillips, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.236, 166.482, 79.628, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.1

Other elements in 1d6y:

The structure of Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. (pdb code 1d6y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide., PDB code: 1d6y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1d6y

Go back to Calcium Binding Sites List in 1d6y
Calcium binding site 1 out of 4 in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.


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 E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:33.5
occ:1.00
 OD1 A:ASP535 2.3 31.7 1.0
O A:ALA679 2.4 27.2 1.0
O A:LEU534 2.4 30.7 1.0
OD1 A:ASP533 2.4 28.6 1.0
OD1 A:ASP678 2.5 34.5 1.0
O A:HOH2140 2.6 36.9 1.0
C A:LEU534 3.3 30.6 1.0
C A:ALA679 3.5 28.6 1.0
NZ A:LYS133 3.5 29.4 1.0
CG A:ASP535 3.6 33.0 1.0
CG A:ASP678 3.6 37.3 1.0
CG A:ASP533 3.6 29.0 1.0
N A:ALA679 3.7 28.7 1.0
C A:ASP533 3.9 30.8 1.0
N A:LEU534 4.0 30.2 1.0
N A:ASP535 4.0 30.1 1.0
CA A:ASP535 4.1 30.6 1.0
CA A:ALA679 4.2 27.9 1.0
O A:ASP533 4.2 31.2 1.0
C A:ASP678 4.2 30.5 1.0
CA A:LEU534 4.3 31.1 1.0
OD2 A:ASP678 4.3 39.3 1.0
OD2 A:ASP533 4.4 28.6 1.0
CA A:ASP533 4.4 29.2 1.0
OD2 A:ASP535 4.4 34.9 1.0
CB A:ASP535 4.4 30.0 1.0
CA A:ASP678 4.4 32.0 1.0
O A:GLU539 4.5 34.2 1.0
N A:VAL680 4.6 29.2 1.0
CB A:ASP533 4.6 28.2 1.0
CB A:ASP678 4.6 34.0 1.0
ND2 A:ASN541 4.7 31.9 1.0
CE A:LYS133 4.8 29.9 1.0
CG2 A:VAL680 4.9 30.6 1.0
CA A:VAL680 4.9 30.0 1.0
O A:ASP678 4.9 29.6 1.0

Calcium binding site 2 out of 4 in 1d6y

Go back to Calcium Binding Sites List in 1d6y
Calcium binding site 2 out of 4 in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.


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 E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:72.4
occ:1.00
 O A:TYR667 2.6 42.9 1.0
OE2 A:GLU573 2.7 46.6 1.0
O A:HOH2293 2.7 36.0 1.0
OE1 A:GLU672 3.1 49.9 1.0
OD2 A:ASP670 3.1 59.8 1.0
CE1 A:HIS644 3.5 63.4 1.0
CD A:GLU573 3.5 44.9 1.0
OE1 A:GLU573 3.5 43.4 1.0
OD1 A:ASP670 3.7 58.6 1.0
C A:TYR667 3.7 42.3 1.0
ND1 A:HIS644 3.8 63.4 1.0
CG A:ASP670 3.8 58.4 1.0
OE1 A:GLU647 3.9 39.5 1.0
O A:HOH2220 4.2 77.2 1.0
CD A:GLU672 4.2 50.6 1.0
N A:ARG642 4.2 38.1 1.0
CB A:ARG642 4.4 44.0 1.0
OE2 A:GLU647 4.4 46.6 1.0
O A:ARG642 4.4 37.7 1.0
CA A:TYR667 4.4 41.6 1.0
CB A:THR641 4.5 35.4 1.0
NE2 A:HIS644 4.5 63.3 1.0
CD A:GLU647 4.6 41.8 1.0
CB A:TYR667 4.7 41.2 1.0
N A:SER668 4.8 43.4 1.0
CG A:GLU672 4.8 47.5 1.0
CA A:ARG642 4.8 40.0 1.0
CG A:GLU573 4.9 43.9 1.0
CA A:SER668 5.0 44.8 1.0
CG A:HIS644 5.0 59.4 1.0
CG2 A:THR641 5.0 34.9 1.0

Calcium binding site 3 out of 4 in 1d6y

Go back to Calcium Binding Sites List in 1d6y
Calcium binding site 3 out of 4 in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.


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 E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:39.4
occ:1.00
 OD1 B:ASP533 2.2 30.9 1.0
OD1 B:ASP535 2.2 35.6 1.0
O B:ALA679 2.4 38.7 1.0
OD1 B:ASP678 2.4 38.3 1.0
O B:LEU534 2.5 35.1 1.0
O B:HOH3171 2.6 34.6 1.0
C B:LEU534 3.4 35.1 1.0
CG B:ASP535 3.4 34.6 1.0
CG B:ASP533 3.5 34.1 1.0
C B:ALA679 3.5 38.0 1.0
CG B:ASP678 3.5 39.5 1.0
NZ B:LYS133 3.6 40.3 1.0
N B:ALA679 3.6 37.0 1.0
C B:ASP533 4.0 33.4 1.0
N B:LEU534 4.0 34.2 1.0
N B:ASP535 4.1 34.9 1.0
CA B:ALA679 4.1 37.3 1.0
CA B:ASP535 4.1 35.2 1.0
OD2 B:ASP533 4.1 31.0 1.0
OD2 B:ASP678 4.2 40.9 1.0
OD2 B:ASP535 4.2 34.5 1.0
O B:ASP533 4.2 34.1 1.0
C B:ASP678 4.2 37.8 1.0
CA B:LEU534 4.3 35.0 1.0
CB B:ASP535 4.4 34.9 1.0
CA B:ASP533 4.4 32.8 1.0
CA B:ASP678 4.5 38.6 1.0
CB B:ASP533 4.5 33.3 1.0
N B:VAL680 4.6 38.3 1.0
O B:GLU539 4.6 46.9 1.0
CB B:ASP678 4.6 38.9 1.0
ND2 B:ASN541 4.7 41.2 1.0
CE B:LYS133 4.8 40.6 1.0
CA B:VAL680 4.9 37.6 1.0
CB B:ALA679 4.9 37.8 1.0
CG2 B:VAL680 4.9 38.6 1.0

Calcium binding site 4 out of 4 in 1d6y

Go back to Calcium Binding Sites List in 1d6y
Calcium binding site 4 out of 4 in the Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of E. Coli Copper-Containing Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine and Complexed with Nitric Oxide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:74.3
occ:1.00
 O B:TYR667 2.4 47.5 1.0
OE2 B:GLU573 2.4 48.1 1.0
O B:HOH3195 2.5 53.1 1.0
OE1 B:GLU573 2.7 50.5 1.0
O B:HOH3199 2.9 46.3 1.0
OE2 B:GLU672 2.9 63.4 1.0
CD B:GLU573 2.9 49.6 1.0
O B:HOH3245 2.9 65.1 1.0
C B:TYR667 3.7 48.4 1.0
CD B:GLU672 3.7 61.7 1.0
CG B:GLU672 3.9 59.0 1.0
CB B:GLU672 4.3 54.2 1.0
N B:ARG642 4.4 43.8 1.0
CD2 B:HIS644 4.4 69.0 1.0
CG B:GLU573 4.4 48.9 1.0
OE1 B:GLU647 4.5 45.7 1.0
CA B:SER668 4.5 51.4 1.0
NE2 B:HIS644 4.5 70.1 1.0
CB B:ARG642 4.5 48.5 1.0
N B:SER668 4.5 49.5 1.0
CA B:TYR667 4.6 48.4 1.0
CB B:THR641 4.6 41.0 1.0
OE1 B:GLU672 4.9 63.0 1.0
OE2 B:GLU647 4.9 49.7 1.0
N B:GLU672 5.0 53.9 1.0

Reference:

C.M.Wilmot, J.Hajdu, M.J.Mcpherson, P.F.Knowles, S.E.Phillips. Visualization of Dioxygen Bound to Copper During Enzyme Catalysis. Science V. 286 1724 1999.
ISSN: ISSN 0036-8075
PubMed: 10576737
DOI: 10.1126/SCIENCE.286.5445.1724
Page generated: Mon Jul 7 14:18:52 2025

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