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Calcium in PDB 1qak: 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: 1qak was solved by J.M.Murray, C.M.Wilmot, C.G.Saysell, J.Jaeger, P.F.Knowles, S.E.Phillips, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 134.660, 166.170, 79.090, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.4

Other elements in 1qak:

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 1qak). 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: 1qak:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1qak

Go back to Calcium Binding Sites List in 1qak
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:21.3
occ:1.00
 O A:ALA679 2.4 13.9 1.0
OD1 A:ASP533 2.4 13.0 1.0
OD1 A:ASP535 2.4 18.9 1.0
O A:LEU534 2.4 15.6 1.0
OD1 A:ASP678 2.4 19.7 1.0
O A:HOH949 2.6 15.3 1.0
C A:LEU534 3.4 18.8 1.0
C A:ALA679 3.5 15.0 1.0
N A:ALA679 3.6 15.8 1.0
CG A:ASP533 3.6 14.2 1.0
CG A:ASP535 3.6 14.7 1.0
NZ A:LYS133 3.6 17.2 1.0
CG A:ASP678 3.7 24.4 1.0
CA A:ASP535 4.0 13.1 1.0
C A:ASP533 4.0 17.0 1.0
N A:ASP535 4.0 16.6 1.0
CA A:ALA679 4.1 17.3 1.0
N A:LEU534 4.1 17.8 1.0
C A:ASP678 4.2 18.7 1.0
O A:ASP533 4.2 17.1 1.0
OD2 A:ASP533 4.2 16.1 1.0
OD2 A:ASP678 4.3 23.1 1.0
CA A:LEU534 4.4 19.8 1.0
CB A:ASP535 4.4 16.8 1.0
CA A:ASP533 4.4 14.9 1.0
CA A:ASP678 4.4 18.5 1.0
OD2 A:ASP535 4.5 18.6 1.0
N A:VAL680 4.6 14.2 1.0
O A:GLU539 4.6 20.9 1.0
CB A:ASP533 4.6 14.0 1.0
CB A:ASP678 4.7 19.0 1.0
ND2 A:ASN541 4.8 15.8 1.0
CB A:ALA679 4.8 17.1 1.0
CA A:VAL680 4.8 17.2 1.0
CG2 A:VAL680 4.9 15.0 1.0
O A:ASP678 5.0 19.5 1.0

Calcium binding site 2 out of 4 in 1qak

Go back to Calcium Binding Sites List in 1qak
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:42.0
occ:1.00
 O A:TYR667 2.4 17.7 1.0
OE2 A:GLU573 2.5 21.6 1.0
O A:HOH975 2.6 26.0 1.0
OE1 A:GLU672 2.6 36.2 1.0
OD2 A:ASP670 2.8 48.9 1.0
OE1 A:GLU573 2.9 23.8 1.0
CD A:GLU573 3.0 24.9 1.0
OD1 A:ASP670 3.2 50.4 1.0
CG A:ASP670 3.4 49.6 1.0
C A:TYR667 3.6 22.9 1.0
CD A:GLU672 3.7 42.3 1.0
CE1 A:HIS644 4.0 41.1 1.0
O A:HOH1033 4.2 43.4 1.0
CG A:GLU672 4.2 36.6 1.0
ND1 A:HIS644 4.2 45.4 1.0
OE1 A:GLU647 4.4 26.8 1.0
N A:ARG642 4.4 22.2 1.0
CA A:TYR667 4.4 21.6 1.0
CA A:SER668 4.5 24.4 1.0
N A:SER668 4.5 24.9 1.0
CG A:GLU573 4.5 20.8 1.0
OE2 A:GLU647 4.6 25.4 1.0
CB A:THR641 4.6 19.6 1.0
CB A:ARG642 4.6 31.5 1.0
CB A:GLU672 4.7 32.3 1.0
O A:ARG642 4.8 21.2 1.0
OE2 A:GLU672 4.8 44.7 1.0
CB A:TYR667 4.9 20.7 1.0
CB A:ASP670 4.9 42.3 1.0
CD A:GLU647 4.9 24.1 1.0

Calcium binding site 3 out of 4 in 1qak

Go back to Calcium Binding Sites List in 1qak
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:23.0
occ:1.00
 OD1 B:ASP533 2.4 16.2 1.0
OD1 B:ASP535 2.4 21.1 1.0
O B:LEU534 2.4 16.2 1.0
OD1 B:ASP678 2.4 22.3 1.0
O B:ALA679 2.5 22.8 1.0
O B:HOH970 2.7 18.8 1.0
C B:LEU534 3.4 22.9 1.0
C B:ALA679 3.6 24.9 1.0
CG B:ASP533 3.6 20.4 1.0
CG B:ASP535 3.6 22.9 1.0
N B:ALA679 3.6 24.1 1.0
CG B:ASP678 3.6 25.8 1.0
NZ B:LYS133 3.7 20.9 1.0
C B:ASP533 4.0 20.1 1.0
CA B:ASP535 4.0 19.4 1.0
N B:LEU534 4.1 21.9 1.0
N B:ASP535 4.1 21.3 1.0
CA B:ALA679 4.1 23.2 1.0
C B:ASP678 4.1 25.0 1.0
OD2 B:ASP533 4.2 21.0 1.0
O B:ASP533 4.3 21.6 1.0
OD2 B:ASP678 4.3 18.8 1.0
CA B:ASP533 4.4 21.4 1.0
CB B:ASP535 4.4 15.4 1.0
CA B:ASP678 4.4 27.9 1.0
OD2 B:ASP535 4.4 27.3 1.0
CA B:LEU534 4.5 21.1 1.0
O B:GLU539 4.5 23.7 1.0
CB B:ASP533 4.6 20.7 1.0
CB B:ASP678 4.6 20.4 1.0
N B:VAL680 4.6 22.0 1.0
ND2 B:ASN541 4.7 20.6 1.0
CB B:ALA679 4.8 24.8 1.0
O B:ASP678 4.9 26.6 1.0
CA B:VAL680 4.9 21.6 1.0
CE B:LYS133 5.0 22.4 1.0

Calcium binding site 4 out of 4 in 1qak

Go back to Calcium Binding Sites List in 1qak
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:49.1
occ:1.00
 O B:TYR667 2.4 24.0 1.0
OE2 B:GLU573 2.6 22.9 1.0
O B:HOH999 2.7 29.7 1.0
OE2 B:GLU672 2.8 43.4 1.0
OE1 B:GLU573 2.8 27.3 1.0
OD1 B:ASP670 3.0 56.6 1.0
CD B:GLU573 3.0 25.5 1.0
OD2 B:ASP670 3.5 59.3 1.0
CG B:GLU672 3.6 42.3 1.0
CD B:GLU672 3.6 46.2 1.0
C B:TYR667 3.7 24.4 1.0
CG B:ASP670 3.7 57.4 1.0
NE2 B:HIS644 4.1 48.0 1.0
CD2 B:HIS644 4.3 51.0 1.0
CB B:GLU672 4.4 37.9 1.0
OE1 B:GLU647 4.4 28.9 1.0
CA B:SER668 4.4 24.9 1.0
N B:ARG642 4.5 27.6 1.0
N B:SER668 4.5 21.2 1.0
CG B:GLU573 4.5 21.8 1.0
CA B:TYR667 4.5 24.8 1.0
OE2 B:GLU647 4.6 30.6 1.0
CB B:ARG642 4.6 35.2 1.0
CB B:THR641 4.8 24.0 1.0
OE1 B:GLU672 4.8 46.9 1.0
N B:GLU672 5.0 33.1 1.0
O B:ARG642 5.0 26.2 1.0
CD B:GLU647 5.0 25.9 1.0
CB B:TYR667 5.0 25.2 1.0

Reference:

J.M.Murray, C.G.Saysell, C.M.Wilmot, W.S.Tambyrajah, J.Jaeger, P.F.Knowles, S.E.Phillips, M.J.Mcpherson. The Active Site Base Controls Cofactor Reactivity in Escherichia Coli Amine Oxidase: X-Ray Crystallographic Studies with Mutational Variants. Biochemistry V. 38 8217 1999.
ISSN: ISSN 0006-2960
PubMed: 10387067
DOI: 10.1021/BI9900469
Page generated: Thu Jul 11 14:19:41 2024

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