Atomistry » Calcium » PDB 1cxk-1dds » 1d6u
Atomistry »
  Calcium »
    PDB 1cxk-1dds »
      1d6u »

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: Wed Oct 28 07:02:54 2020

Last articles

Xe in 6AYK
Xe in 6QII
Xe in 6ASM
Xe in 5NSW
Xe in 6FY9
Xe in 5O1K
Xe in 5O27
Xe in 5M69
Xe in 5KPU
Xe in 5I63
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy