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Calcium in PDB 1d6z: Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase.

Enzymatic activity of Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase.

All present enzymatic activity of Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase.:
1.4.3.6;

Protein crystallography data

The structure of Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase., PDB code: 1d6z 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 / 2.10
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 (%) 19.3 / 23.7

Other elements in 1d6z:

The structure of Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. (pdb code 1d6z). 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 the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase., PDB code: 1d6z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1d6z

Go back to Calcium Binding Sites List in 1d6z
Calcium binding site 1 out of 4 in the Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine 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 the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:23.9
occ:1.00
 O A:ALA679 2.3 15.3 1.0
OD1 A:ASP535 2.4 19.8 1.0
OD1 A:ASP678 2.4 24.4 1.0
OD1 A:ASP533 2.4 21.1 1.0
O A:LEU534 2.5 19.5 1.0
O A:HOH2141 2.6 20.1 1.0
C A:LEU534 3.4 19.0 1.0
C A:ALA679 3.5 18.3 1.0
CG A:ASP678 3.5 25.8 1.0
NZ A:LYS133 3.6 19.2 1.0
CG A:ASP535 3.6 20.3 1.0
CG A:ASP533 3.6 20.4 1.0
N A:ALA679 3.6 19.1 1.0
C A:ASP533 4.0 19.6 1.0
N A:LEU534 4.1 19.6 1.0
N A:ASP535 4.1 17.7 1.0
CA A:ALA679 4.1 18.0 1.0
CA A:ASP535 4.1 17.6 1.0
C A:ASP678 4.1 21.0 1.0
OD2 A:ASP678 4.2 27.7 1.0
O A:ASP533 4.3 20.9 1.0
OD2 A:ASP533 4.3 21.8 1.0
CA A:LEU534 4.4 19.5 1.0
OD2 A:ASP535 4.4 22.9 1.0
CA A:ASP678 4.4 22.4 1.0
CA A:ASP533 4.5 19.9 1.0
CB A:ASP535 4.5 17.8 1.0
O A:GLU539 4.5 23.5 1.0
N A:VAL680 4.5 18.2 1.0
CB A:ASP678 4.6 22.9 1.0
CB A:ASP533 4.7 19.2 1.0
ND2 A:ASN541 4.8 18.0 1.0
CG2 A:VAL680 4.8 18.9 1.0
CA A:VAL680 4.8 19.6 1.0
O A:ASP678 4.9 19.8 1.0
CE A:LYS133 4.9 21.7 1.0
CB A:ALA679 5.0 18.9 1.0

Calcium binding site 2 out of 4 in 1d6z

Go back to Calcium Binding Sites List in 1d6z
Calcium binding site 2 out of 4 in the Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine 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 the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:60.2
occ:1.00
 OE2 A:GLU573 2.5 31.6 1.0
O A:TYR667 2.6 28.2 1.0
O A:HOH2292 2.7 30.6 1.0
OE1 A:GLU672 2.8 39.2 1.0
OD2 A:ASP670 3.0 49.7 1.0
OE1 A:GLU573 3.3 29.3 1.0
CD A:GLU573 3.3 31.8 1.0
CE1 A:HIS644 3.5 50.7 1.0
OD1 A:ASP670 3.7 47.6 1.0
CG A:ASP670 3.8 47.3 1.0
C A:TYR667 3.8 28.3 1.0
ND1 A:HIS644 3.9 51.7 1.0
CD A:GLU672 4.0 40.2 1.0
OE1 A:GLU647 4.1 26.8 1.0
N A:ARG642 4.1 26.1 1.0
CB A:ARG642 4.3 32.8 1.0
NE2 A:HIS644 4.4 51.2 1.0
CB A:THR641 4.5 24.3 1.0
O A:ARG642 4.5 22.4 1.0
OE2 A:GLU647 4.5 33.0 1.0
CA A:TYR667 4.6 28.9 1.0
CG A:GLU672 4.6 38.2 1.0
CA A:ARG642 4.7 27.5 1.0
CD A:GLU647 4.7 29.0 1.0
CG A:GLU573 4.7 28.8 1.0
CB A:GLU672 4.8 34.7 1.0
N A:SER668 4.8 29.6 1.0
CA A:SER668 4.9 31.2 1.0
CB A:TYR667 4.9 28.4 1.0
OE2 A:GLU672 5.0 44.0 1.0
CG A:HIS644 5.0 47.3 1.0
CA A:THR641 5.0 24.9 1.0

Calcium binding site 3 out of 4 in 1d6z

Go back to Calcium Binding Sites List in 1d6z
Calcium binding site 3 out of 4 in the Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine 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 the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:28.2
occ:1.00
 OD1 B:ASP535 2.3 24.7 1.0
OD1 B:ASP533 2.3 19.7 1.0
O B:ALA679 2.4 28.9 1.0
OD1 B:ASP678 2.4 27.9 1.0
O B:HOH3175 2.5 23.3 1.0
O B:LEU534 2.6 22.7 1.0
C B:LEU534 3.4 23.5 1.0
C B:ALA679 3.5 28.6 1.0
CG B:ASP535 3.5 24.8 1.0
CG B:ASP678 3.5 30.2 1.0
CG B:ASP533 3.5 22.2 1.0
NZ B:LYS133 3.6 25.4 1.0
N B:ALA679 3.6 27.9 1.0
C B:ASP533 4.0 21.3 1.0
N B:LEU534 4.1 22.7 1.0
N B:ASP535 4.1 24.3 1.0
CA B:ALA679 4.1 27.7 1.0
CA B:ASP535 4.1 23.7 1.0
C B:ASP678 4.2 28.1 1.0
OD2 B:ASP678 4.2 25.9 1.0
O B:ASP533 4.2 19.6 1.0
OD2 B:ASP533 4.2 23.2 1.0
OD2 B:ASP535 4.3 26.9 1.0
CB B:ASP535 4.4 25.3 1.0
CA B:ASP533 4.4 21.0 1.0
CA B:LEU534 4.4 23.2 1.0
CA B:ASP678 4.4 28.6 1.0
O B:GLU539 4.5 32.4 1.0
N B:VAL680 4.5 28.0 1.0
CB B:ASP533 4.6 21.9 1.0
CB B:ASP678 4.6 28.3 1.0
CG2 B:VAL680 4.8 25.5 1.0
ND2 B:ASN541 4.8 23.9 1.0
CA B:VAL680 4.9 26.5 1.0
CE B:LYS133 4.9 26.9 1.0
O B:ASP678 4.9 27.4 1.0
CB B:ALA679 5.0 26.0 1.0

Calcium binding site 4 out of 4 in 1d6z

Go back to Calcium Binding Sites List in 1d6z
Calcium binding site 4 out of 4 in the Crystal Structure of the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase.


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 the Aerobically Freeze Trapped Rate-Determining Catalytic Intermediate of E. Coli Copper-Containing Amine Oxidase. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:64.5
occ:1.00
 OE2 B:GLU573 2.5 33.8 1.0
O B:HOH3199 2.5 46.2 1.0
O B:TYR667 2.5 33.9 1.0
OE2 B:GLU672 2.6 52.2 1.0
OE1 B:GLU573 2.8 36.3 1.0
O B:HOH3203 3.0 40.4 1.0
CD B:GLU573 3.0 35.8 1.0
O B:HOH3250 3.2 64.0 1.0
CD B:GLU672 3.5 50.7 1.0
CG B:GLU672 3.7 47.3 1.0
C B:TYR667 3.8 34.2 1.0
CB B:GLU672 4.3 41.2 1.0
NE2 B:HIS644 4.3 59.5 1.0
CD2 B:HIS644 4.3 58.0 1.0
N B:ARG642 4.3 31.1 1.0
CB B:ARG642 4.4 34.6 1.0
CG B:GLU573 4.5 33.9 1.0
OE1 B:GLU647 4.5 35.0 1.0
OE1 B:GLU672 4.5 52.2 1.0
CA B:SER668 4.6 37.0 1.0
N B:SER668 4.6 35.0 1.0
CA B:TYR667 4.7 33.7 1.0
CB B:THR641 4.7 29.2 1.0
O B:HOH3324 4.7 76.6 1.0
OE2 B:GLU647 4.9 38.4 1.0
O B:ARG642 4.9 29.3 1.0
CA B:ARG642 5.0 31.9 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: Thu Jul 11 07:24:34 2024

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