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Calcium in PDB 1qaf: 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: 1qaf 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 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.200, 167.000, 79.930, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 24.4

Other elements in 1qaf:

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

Calcium binding site 1 out of 4 in 1qaf

Go back to Calcium Binding Sites List in 1qaf
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:25.1
occ:1.00
 OD1 A:ASP535 2.3 17.9 1.0
OD1 A:ASP678 2.4 22.8 1.0
O A:ALA679 2.4 21.9 1.0
OD1 A:ASP533 2.4 24.9 1.0
O A:LEU534 2.5 23.4 1.0
O A:HOH952 2.6 18.1 1.0
C A:LEU534 3.5 25.8 1.0
NZ A:LYS133 3.5 26.0 1.0
CG A:ASP535 3.5 18.6 1.0
C A:ALA679 3.5 21.6 1.0
N A:ALA679 3.6 17.7 1.0
CG A:ASP678 3.6 31.4 1.0
CG A:ASP533 3.7 25.6 1.0
C A:ASP533 4.1 23.7 1.0
N A:LEU534 4.1 24.8 1.0
CA A:ASP535 4.1 21.7 1.0
CA A:ALA679 4.1 19.5 1.0
N A:ASP535 4.1 21.8 1.0
C A:ASP678 4.2 18.8 1.0
OD2 A:ASP678 4.3 32.1 1.0
O A:ASP533 4.3 21.3 1.0
CB A:ASP535 4.3 21.4 1.0
OD2 A:ASP533 4.3 24.6 1.0
OD2 A:ASP535 4.4 19.2 1.0
CA A:LEU534 4.4 23.9 1.0
CA A:ASP678 4.4 21.3 1.0
CA A:ASP533 4.5 24.1 1.0
O A:GLU539 4.6 22.3 1.0
N A:VAL680 4.6 20.1 1.0
CB A:ASP533 4.7 22.6 1.0
CB A:ASP678 4.7 22.9 1.0
CB A:ALA679 4.8 17.4 1.0
ND2 A:ASN541 4.8 20.1 1.0
CE A:LYS133 4.9 30.6 1.0
CA A:VAL680 4.9 22.3 1.0

Calcium binding site 2 out of 4 in 1qaf

Go back to Calcium Binding Sites List in 1qaf
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:53.3
occ:1.00
 O A:TYR667 2.5 25.2 1.0
OE2 A:GLU573 2.5 28.4 1.0
O A:HOH978 2.5 30.2 1.0
OE1 A:GLU672 2.7 48.8 1.0
O A:HOH983 2.8 40.7 1.0
O A:HOH1547 2.9 41.1 1.0
OE1 A:GLU573 3.0 27.0 1.0
CD A:GLU573 3.1 30.2 1.0
C A:TYR667 3.7 28.3 1.0
CD A:GLU672 3.8 50.0 1.0
CE1 A:HIS644 4.1 62.9 1.0
N A:ARG642 4.2 29.5 1.0
ND1 A:HIS644 4.2 64.0 1.0
OE1 A:GLU647 4.2 28.8 1.0
CG A:GLU672 4.3 46.5 1.0
O A:HOH1037 4.4 43.9 1.0
CB A:THR641 4.6 25.5 1.0
CB A:ARG642 4.6 37.2 1.0
CG A:ARG642 4.6 41.3 1.0
CG A:GLU573 4.6 27.0 1.0
CA A:TYR667 4.6 27.6 1.0
N A:SER668 4.6 34.7 1.0
OE2 A:GLU647 4.6 33.0 1.0
O A:ARG642 4.7 24.7 1.0
CA A:SER668 4.7 35.6 1.0
CB A:GLU672 4.8 42.8 1.0
OE2 A:GLU672 4.9 53.0 1.0
CA A:ARG642 4.9 31.1 1.0
CD A:GLU647 4.9 28.6 1.0
CB A:TYR667 5.0 29.2 1.0
CD A:ARG642 5.0 44.8 1.0

Calcium binding site 3 out of 4 in 1qaf

Go back to Calcium Binding Sites List in 1qaf
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:29.0
occ:1.00
 O B:ALA679 2.3 27.3 1.0
OD1 B:ASP535 2.3 28.8 1.0
OD1 B:ASP533 2.3 15.4 1.0
O B:LEU534 2.4 26.1 1.0
OD1 B:ASP678 2.6 22.4 1.0
O B:HOH1619 2.6 29.8 1.0
C B:LEU534 3.4 30.4 1.0
C B:ALA679 3.4 28.1 1.0
CG B:ASP535 3.5 29.6 1.0
CG B:ASP533 3.6 23.7 1.0
N B:ALA679 3.6 25.0 1.0
NZ B:LYS133 3.7 27.2 1.0
CG B:ASP678 3.8 29.8 1.0
C B:ASP533 4.0 21.7 1.0
N B:LEU534 4.0 28.0 1.0
CA B:ALA679 4.0 25.2 1.0
CA B:ASP535 4.1 29.3 1.0
N B:ASP535 4.1 28.0 1.0
O B:ASP533 4.1 21.3 1.0
C B:ASP678 4.2 30.1 1.0
OD2 B:ASP533 4.2 21.7 1.0
CA B:LEU534 4.4 26.1 1.0
OD2 B:ASP535 4.4 27.3 1.0
CB B:ASP535 4.4 28.3 1.0
CA B:ASP533 4.4 25.0 1.0
N B:VAL680 4.4 27.4 1.0
OD2 B:ASP678 4.4 27.4 1.0
CA B:ASP678 4.5 27.3 1.0
O B:GLU539 4.6 29.1 1.0
CB B:ASP533 4.6 20.6 1.0
CB B:ASP678 4.7 29.1 1.0
ND2 B:ASN541 4.7 33.1 1.0
CA B:VAL680 4.8 29.1 1.0
CG2 B:VAL680 4.8 24.5 1.0
CB B:ALA679 4.8 27.5 1.0
CE B:LYS133 4.9 22.6 1.0
O B:ASP678 4.9 26.9 1.0

Calcium binding site 4 out of 4 in 1qaf

Go back to Calcium Binding Sites List in 1qaf
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:53.9
occ:1.00
 OE2 B:GLU573 2.5 28.5 1.0
O B:TYR667 2.6 29.4 1.0
OE2 B:GLU672 2.7 51.4 1.0
O B:HOH1645 2.8 38.9 1.0
O B:HOH1650 2.8 36.4 1.0
OE1 B:GLU573 2.9 36.1 1.0
CD B:GLU573 3.1 35.4 1.0
CG B:GLU672 3.4 51.2 1.0
CD B:GLU672 3.5 56.3 1.0
O B:HOH1702 3.7 53.1 1.0
C B:TYR667 3.8 26.7 1.0
CD2 B:HIS644 4.2 66.8 1.0
NE2 B:HIS644 4.3 66.3 1.0
CB B:GLU672 4.3 42.6 1.0
CB B:ARG642 4.5 39.4 1.0
N B:ARG642 4.5 31.4 1.0
CG B:GLU573 4.6 31.8 1.0
CA B:SER668 4.6 35.6 1.0
N B:SER668 4.6 31.5 1.0
CA B:TYR667 4.7 29.3 1.0
OE1 B:GLU647 4.7 37.0 1.0
OE1 B:GLU672 4.7 58.6 1.0
OE2 B:GLU647 4.9 38.0 1.0
CG B:ARG642 4.9 44.2 1.0
CB B:THR641 4.9 33.5 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 14:17:17 2024

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