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Calcium in PDB 1d6u: Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine

Enzymatic activity of Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine

All present enzymatic activity of Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine, PDB code: 1d6u 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 / 23.9

Other elements in 1d6u:

The structure of Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine 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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine (pdb code 1d6u). 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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine, PDB code: 1d6u:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1d6u

Go back to Calcium Binding Sites List in 1d6u
Calcium binding site 1 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine


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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:20.5
occ:1.00
 OD1 A:ASP535 2.3 21.1 1.0
O A:ALA679 2.3 18.9 1.0
O A:LEU534 2.3 21.9 1.0
OD1 A:ASP533 2.5 18.7 1.0
OD1 A:ASP678 2.5 24.6 1.0
O A:HOH2140 2.6 20.1 1.0
C A:LEU534 3.3 21.6 1.0
C A:ALA679 3.5 19.3 1.0
CG A:ASP535 3.5 19.1 1.0
NZ A:LYS133 3.5 25.9 1.0
N A:ALA679 3.6 17.1 1.0
CG A:ASP533 3.6 20.0 1.0
CG A:ASP678 3.7 27.4 1.0
N A:LEU534 4.0 24.2 1.0
C A:ASP533 4.0 22.7 1.0
N A:ASP535 4.0 19.9 1.0
CA A:ASP535 4.1 19.2 1.0
CA A:ALA679 4.1 18.2 1.0
C A:ASP678 4.2 22.4 1.0
CA A:LEU534 4.2 25.6 1.0
O A:ASP533 4.3 22.8 1.0
OD2 A:ASP533 4.3 22.1 1.0
OD2 A:ASP535 4.4 19.4 1.0
CB A:ASP535 4.4 15.6 1.0
OD2 A:ASP678 4.4 27.4 1.0
CA A:ASP533 4.4 18.1 1.0
CA A:ASP678 4.5 23.5 1.0
N A:VAL680 4.5 19.3 1.0
O A:GLU539 4.6 23.5 1.0
ND2 A:ASN541 4.7 25.8 1.0
CB A:ASP533 4.7 17.8 1.0
CB A:ASP678 4.7 25.5 1.0
CA A:VAL680 4.9 20.8 1.0
CE A:LYS133 4.9 24.1 1.0
CG2 A:VAL680 4.9 22.3 1.0

Calcium binding site 2 out of 4 in 1d6u

Go back to Calcium Binding Sites List in 1d6u
Calcium binding site 2 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine


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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:65.5
occ:1.00
 OE2 A:GLU573 2.7 38.9 1.0
O A:TYR667 2.7 32.4 1.0
O A:HOH2297 2.8 42.4 1.0
OE1 A:GLU672 3.0 45.8 1.0
CD A:GLU573 3.5 37.0 1.0
OD2 A:ASP670 3.5 60.0 1.0
OE1 A:GLU573 3.5 37.7 1.0
CE1 A:HIS644 3.6 60.6 1.0
ND1 A:HIS644 3.8 63.4 1.0
OE1 A:GLU647 3.9 29.4 1.0
C A:TYR667 3.9 32.1 1.0
OD1 A:ASP670 4.0 60.2 1.0
N A:ARG642 4.1 28.3 1.0
CG A:ASP670 4.2 59.9 1.0
CB A:ARG642 4.2 39.2 1.0
CD A:GLU672 4.2 50.2 1.0
O A:ARG642 4.3 30.0 1.0
OE2 A:GLU647 4.3 42.4 1.0
CB A:THR641 4.4 25.5 1.0
CA A:TYR667 4.5 32.7 1.0
CD A:GLU647 4.5 32.4 1.0
NE2 A:HIS644 4.6 60.5 1.0
CA A:ARG642 4.6 32.3 1.0
CB A:TYR667 4.8 33.3 1.0
CG A:GLU672 4.8 45.3 1.0
CG A:GLU573 4.9 34.6 1.0
CG A:HIS644 4.9 56.6 1.0
N A:SER668 4.9 33.5 1.0
C A:ARG642 4.9 28.9 1.0
CA A:THR641 5.0 26.7 1.0
CB A:GLU672 5.0 39.3 1.0
C A:THR641 5.0 28.5 1.0

Calcium binding site 3 out of 4 in 1d6u

Go back to Calcium Binding Sites List in 1d6u
Calcium binding site 3 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine


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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:30.6
occ:1.00
 OD1 B:ASP533 2.3 23.8 1.0
OD1 B:ASP535 2.3 29.6 1.0
O B:ALA679 2.3 34.8 1.0
OD1 B:ASP678 2.4 25.3 1.0
O B:LEU534 2.5 30.9 1.0
O B:HOH3165 2.5 25.3 1.0
C B:LEU534 3.4 30.4 1.0
C B:ALA679 3.4 33.0 1.0
CG B:ASP535 3.4 26.6 1.0
CG B:ASP533 3.5 28.1 1.0
CG B:ASP678 3.5 31.1 1.0
NZ B:LYS133 3.6 31.2 1.0
N B:ALA679 3.6 30.9 1.0
C B:ASP533 4.0 27.4 1.0
N B:LEU534 4.0 28.6 1.0
CA B:ALA679 4.1 31.4 1.0
N B:ASP535 4.1 29.5 1.0
CA B:ASP535 4.1 29.5 1.0
C B:ASP678 4.1 32.0 1.0
OD2 B:ASP533 4.2 22.8 1.0
OD2 B:ASP678 4.2 28.0 1.0
OD2 B:ASP535 4.2 27.9 1.0
O B:ASP533 4.3 29.8 1.0
CA B:LEU534 4.4 31.3 1.0
CB B:ASP535 4.4 28.1 1.0
CA B:ASP678 4.4 31.6 1.0
CA B:ASP533 4.4 26.0 1.0
N B:VAL680 4.5 30.9 1.0
O B:GLU539 4.5 36.9 1.0
CB B:ASP533 4.6 26.3 1.0
CB B:ASP678 4.6 29.9 1.0
ND2 B:ASN541 4.7 30.4 1.0
CG2 B:VAL680 4.8 29.8 1.0
CA B:VAL680 4.9 30.3 1.0
O B:ASP678 4.9 32.5 1.0
CB B:ALA679 4.9 30.9 1.0
CE B:LYS133 4.9 27.6 1.0

Calcium binding site 4 out of 4 in 1d6u

Go back to Calcium Binding Sites List in 1d6u
Calcium binding site 4 out of 4 in the Crystal Structure of E. Coli Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine


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 Amine Oxidase Anaerobically Reduced with Beta-Phenylethylamine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:61.5
occ:1.00
 OE2 B:GLU573 2.4 37.0 1.0
O B:TYR667 2.5 35.6 1.0
O B:HOH3190 2.6 38.1 1.0
OE1 B:GLU573 2.6 42.8 1.0
OE2 B:GLU672 2.7 61.0 1.0
CD B:GLU573 2.9 41.8 1.0
O B:HOH3194 2.9 47.8 1.0
O B:HOH3241 3.3 52.9 1.0
CD B:GLU672 3.6 58.6 1.0
C B:TYR667 3.7 36.8 1.0
CG B:GLU672 3.8 54.7 1.0
NE2 B:HIS644 4.1 69.6 1.0
N B:ARG642 4.2 35.4 1.0
CB B:GLU672 4.3 46.5 1.0
CB B:ARG642 4.3 44.8 1.0
CD2 B:HIS644 4.3 69.1 1.0
CG B:GLU573 4.4 42.6 1.0
CA B:SER668 4.5 40.8 1.0
OE1 B:GLU647 4.6 39.3 1.0
CB B:THR641 4.6 29.3 1.0
O B:HOH3312 4.6 68.6 1.0
N B:SER668 4.6 37.9 1.0
OE1 B:GLU672 4.7 60.0 1.0
CA B:TYR667 4.7 37.3 1.0
CA B:ARG642 4.8 39.0 1.0
O B:ARG642 4.8 37.5 1.0
CG2 B:THR641 4.9 30.1 1.0
OE2 B:GLU647 5.0 44.6 1.0
N B:GLU672 5.0 43.1 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: Thu Jul 11 07:24:14 2024

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