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Calcium in PDB 1dyu: The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.

Enzymatic activity of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.

All present enzymatic activity of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.:
1.4.3.4;

Protein crystallography data

The structure of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants., PDB code: 1dyu was solved by J.M.Murray, C.M.Wilmot, C.G.Saysell, J.Jaeger, P.F.Knowles, S.E.V.Phillips, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20 / 2.04
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.050, 167.170, 79.920, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.7

Other elements in 1dyu:

The structure of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. (pdb code 1dyu). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants., PDB code: 1dyu:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1dyu

Go back to Calcium Binding Sites List in 1dyu
Calcium binding site 1 out of 4 in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca802

b:23.6
occ:1.00
 OD1 A:ASP535 2.3 18.8 1.0
O A:LEU534 2.3 22.9 1.0
O A:ALA679 2.4 17.9 1.0
OD1 A:ASP678 2.4 17.8 1.0
OD1 A:ASP533 2.4 22.9 1.0
O A:HOH2667 2.5 14.9 1.0
C A:LEU534 3.3 24.5 1.0
C A:ALA679 3.5 18.7 1.0
CG A:ASP535 3.5 22.2 1.0
NZ A:LYS133 3.6 21.1 1.0
CG A:ASP678 3.6 25.8 1.0
N A:ALA679 3.6 19.7 1.0
CG A:ASP533 3.6 23.2 1.0
N A:ASP535 3.9 22.2 1.0
CA A:ASP535 3.9 20.5 1.0
C A:ASP533 4.0 23.1 1.0
N A:LEU534 4.0 26.8 1.0
CA A:ALA679 4.1 18.1 1.0
OD2 A:ASP678 4.2 22.9 1.0
C A:ASP678 4.3 20.3 1.0
O A:ASP533 4.3 20.5 1.0
OD2 A:ASP533 4.3 22.2 1.0
CA A:LEU534 4.3 25.2 1.0
CB A:ASP535 4.4 21.7 1.0
OD2 A:ASP535 4.4 22.4 1.0
CA A:ASP533 4.5 22.1 1.0
CA A:ASP678 4.5 23.1 1.0
O A:GLU539 4.5 23.5 1.0
N A:VAL680 4.6 15.9 1.0
CB A:ASP533 4.6 23.4 1.0
CB A:ASP678 4.7 21.0 1.0
ND2 A:ASN541 4.9 17.8 1.0
CE A:LYS133 4.9 26.9 1.0
CA A:VAL680 4.9 23.2 1.0
CB A:ALA679 5.0 19.4 1.0

Calcium binding site 2 out of 4 in 1dyu

Go back to Calcium Binding Sites List in 1dyu
Calcium binding site 2 out of 4 in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca803

b:54.3
occ:1.00
 O A:TYR667 2.4 26.1 1.0
OE2 A:GLU573 2.5 25.6 1.0
O A:HOH2767 2.6 33.7 1.0
OE1 A:GLU672 2.7 46.8 1.0
OD2 A:ASP670 2.9 55.2 1.0
OE1 A:GLU573 3.1 26.6 1.0
CD A:GLU573 3.1 28.4 1.0
OD1 A:ASP670 3.6 53.2 1.0
C A:TYR667 3.6 24.1 1.0
CE1 A:HIS644 3.7 47.3 1.0
CG A:ASP670 3.7 52.3 1.0
CD A:GLU672 3.9 49.7 1.0
ND1 A:HIS644 4.0 51.9 1.0
OE1 A:GLU647 4.2 27.7 1.0
N A:ARG642 4.3 24.8 1.0
CG A:GLU672 4.4 44.9 1.0
O A:HOH2795 4.4 79.2 1.0
OE2 A:GLU647 4.5 30.7 1.0
CA A:TYR667 4.5 23.8 1.0
CB A:ARG642 4.5 34.9 1.0
N A:SER668 4.5 26.0 1.0
CB A:THR641 4.6 24.0 1.0
CG A:GLU573 4.6 27.2 1.0
O A:ARG642 4.7 26.1 1.0
CA A:SER668 4.7 29.9 1.0
CB A:GLU672 4.8 37.7 1.0
CB A:TYR667 4.8 23.8 1.0
CD A:GLU647 4.8 30.1 1.0
NE2 A:HIS644 4.9 50.0 1.0
OE2 A:GLU672 4.9 52.0 1.0
CA A:ARG642 4.9 25.8 1.0

Calcium binding site 3 out of 4 in 1dyu

Go back to Calcium Binding Sites List in 1dyu
Calcium binding site 3 out of 4 in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca802

b:25.8
occ:1.00
 OD1 B:ASP533 2.3 22.0 1.0
OD1 B:ASP535 2.3 23.9 1.0
O B:ALA679 2.3 26.6 1.0
OD1 B:ASP678 2.4 18.8 1.0
O B:HOH2574 2.4 26.4 1.0
O B:LEU534 2.5 21.8 1.0
C B:ALA679 3.4 30.2 1.0
C B:LEU534 3.5 29.3 1.0
N B:ALA679 3.5 31.7 1.0
CG B:ASP535 3.5 25.2 1.0
CG B:ASP533 3.5 23.5 1.0
CG B:ASP678 3.6 27.3 1.0
NZ B:LYS133 3.8 23.7 1.0
CA B:ALA679 4.0 30.5 1.0
CA B:ASP535 4.0 26.3 1.0
C B:ASP533 4.0 23.8 1.0
N B:ASP535 4.1 27.9 1.0
C B:ASP678 4.2 33.7 1.0
N B:LEU534 4.2 26.9 1.0
OD2 B:ASP533 4.2 23.4 1.0
O B:ASP533 4.2 23.6 1.0
OD2 B:ASP678 4.3 28.2 1.0
OD2 B:ASP535 4.3 25.3 1.0
CB B:ASP535 4.4 25.1 1.0
CA B:ASP678 4.4 29.4 1.0
CA B:ASP533 4.5 23.9 1.0
CA B:LEU534 4.5 27.6 1.0
O B:GLU539 4.5 28.7 1.0
N B:VAL680 4.5 23.8 1.0
CB B:ASP678 4.6 27.5 1.0
CB B:ASP533 4.6 22.6 1.0
ND2 B:ASN541 4.7 21.5 1.0
CB B:ALA679 4.8 32.1 1.0
CG2 B:VAL680 4.9 22.2 1.0
CA B:VAL680 4.9 23.7 1.0
CE B:LYS133 5.0 23.3 1.0
O B:ASP678 5.0 30.4 1.0

Calcium binding site 4 out of 4 in 1dyu

Go back to Calcium Binding Sites List in 1dyu
Calcium binding site 4 out of 4 in the The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca803

b:51.9
occ:1.00
 O B:TYR667 2.3 28.7 1.0
OE2 B:GLU573 2.5 29.5 1.0
O B:HOH2679 2.6 31.6 1.0
O B:HOH2678 2.7 38.9 1.0
OE2 B:GLU672 2.8 54.8 1.0
OE1 B:GLU573 2.8 36.2 1.0
CD B:GLU573 3.1 37.0 1.0
O B:HOH2699 3.2 54.7 1.0
C B:TYR667 3.6 27.5 1.0
CD B:GLU672 3.8 52.8 1.0
NE2 B:HIS644 4.0 60.9 1.0
CD2 B:HIS644 4.2 59.7 1.0
CG B:GLU672 4.2 48.2 1.0
OE1 B:GLU647 4.2 30.9 1.0
CA B:TYR667 4.4 29.7 1.0
N B:ARG642 4.5 32.0 1.0
N B:SER668 4.5 31.4 1.0
CA B:SER668 4.5 33.0 1.0
CG B:GLU573 4.6 30.8 1.0
CB B:GLU672 4.6 41.9 1.0
OE2 B:GLU647 4.7 34.8 1.0
CB B:THR641 4.7 28.1 1.0
CB B:ARG642 4.7 41.1 1.0
CB B:TYR667 4.9 29.1 1.0
CD B:GLU647 4.9 34.6 1.0
O B:ARG642 4.9 27.9 1.0
OE1 B:GLU672 4.9 54.6 1.0
CG2 B:THR641 5.0 27.6 1.0
O B:HOH2672 5.0 68.3 1.0

Reference:

J.M.Murray, C.M.Wilmot, C.G.Saysell, J.Jaeger, P.F.Knowles, S.E.V.Phillips, M.J.Mcpherson. The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase : X-Ray Crystallographicstudies with Mutational Variants Biochemistry V. 38 8217 1999.
ISSN: ISSN 0006-2960
PubMed: 10387067
DOI: 10.1021/BI9900469
Page generated: Thu Jul 11 07:41:53 2024

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