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:
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
|