Calcium in PDB 1qal: 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: 1qal
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 (°)
|
135.050,
166.520,
79.320,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.2 /
24.1
|
Other elements in 1qal:
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 1qal). 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: 1qal:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 1qal
Go back to
Calcium Binding Sites List in 1qal
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:25.4
occ:1.00
|
O
|
A:ALA679
|
2.3
|
17.0
|
1.0
|
OD1
|
A:ASP533
|
2.4
|
18.9
|
1.0
|
OD1
|
A:ASP535
|
2.4
|
17.5
|
1.0
|
OD1
|
A:ASP678
|
2.4
|
21.9
|
1.0
|
O
|
A:LEU534
|
2.5
|
19.9
|
1.0
|
O
|
A:HOH940
|
2.7
|
19.0
|
1.0
|
C
|
A:LEU534
|
3.4
|
20.9
|
1.0
|
C
|
A:ALA679
|
3.4
|
16.7
|
1.0
|
CG
|
A:ASP535
|
3.5
|
18.7
|
1.0
|
NZ
|
A:LYS133
|
3.6
|
19.4
|
1.0
|
CG
|
A:ASP533
|
3.6
|
17.3
|
1.0
|
CG
|
A:ASP678
|
3.6
|
22.6
|
1.0
|
N
|
A:ALA679
|
3.7
|
21.2
|
1.0
|
C
|
A:ASP533
|
3.9
|
22.3
|
1.0
|
N
|
A:LEU534
|
4.0
|
21.2
|
1.0
|
N
|
A:ASP535
|
4.0
|
20.9
|
1.0
|
CA
|
A:ASP535
|
4.0
|
17.4
|
1.0
|
O
|
A:ASP533
|
4.1
|
17.8
|
1.0
|
CA
|
A:ALA679
|
4.2
|
19.3
|
1.0
|
C
|
A:ASP678
|
4.2
|
21.5
|
1.0
|
OD2
|
A:ASP678
|
4.2
|
24.5
|
1.0
|
OD2
|
A:ASP533
|
4.3
|
18.6
|
1.0
|
CA
|
A:LEU534
|
4.3
|
23.8
|
1.0
|
CA
|
A:ASP533
|
4.3
|
17.5
|
1.0
|
CB
|
A:ASP535
|
4.4
|
19.4
|
1.0
|
N
|
A:VAL680
|
4.4
|
17.7
|
1.0
|
OD2
|
A:ASP535
|
4.5
|
20.3
|
1.0
|
CA
|
A:ASP678
|
4.5
|
21.3
|
1.0
|
CB
|
A:ASP533
|
4.6
|
16.0
|
1.0
|
O
|
A:GLU539
|
4.7
|
19.2
|
1.0
|
CB
|
A:ASP678
|
4.7
|
19.2
|
1.0
|
CA
|
A:VAL680
|
4.8
|
20.4
|
1.0
|
ND2
|
A:ASN541
|
4.9
|
16.1
|
1.0
|
CE
|
A:LYS133
|
4.9
|
20.4
|
1.0
|
CG2
|
A:VAL680
|
4.9
|
18.0
|
1.0
|
O
|
A:ASP678
|
4.9
|
19.1
|
1.0
|
CB
|
A:ALA679
|
4.9
|
14.9
|
1.0
|
|
Calcium binding site 2 out
of 4 in 1qal
Go back to
Calcium Binding Sites List in 1qal
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:47.1
occ:1.00
|
O
|
A:TYR667
|
2.4
|
20.6
|
1.0
|
OE2
|
A:GLU573
|
2.6
|
22.0
|
1.0
|
OE1
|
A:GLU672
|
2.6
|
34.0
|
1.0
|
O
|
A:HOH1601
|
2.6
|
28.6
|
1.0
|
O
|
A:HOH1096
|
2.7
|
30.6
|
1.0
|
OE1
|
A:GLU573
|
2.9
|
23.7
|
1.0
|
OD2
|
A:ASP670
|
2.9
|
51.2
|
1.0
|
OD1
|
A:ASP670
|
3.1
|
54.5
|
1.0
|
CD
|
A:GLU573
|
3.1
|
24.9
|
1.0
|
CG
|
A:ASP670
|
3.4
|
52.8
|
1.0
|
C
|
A:TYR667
|
3.6
|
23.4
|
1.0
|
CD
|
A:GLU672
|
3.7
|
40.1
|
1.0
|
CE1
|
A:HIS644
|
3.9
|
43.3
|
1.0
|
CG
|
A:GLU672
|
4.1
|
38.4
|
1.0
|
O
|
A:HOH1023
|
4.2
|
71.9
|
1.0
|
ND1
|
A:HIS644
|
4.2
|
46.8
|
1.0
|
CB
|
A:ARG642
|
4.4
|
36.8
|
1.0
|
OE1
|
A:GLU647
|
4.4
|
29.2
|
1.0
|
CA
|
A:TYR667
|
4.5
|
26.0
|
1.0
|
N
|
A:SER668
|
4.5
|
28.1
|
1.0
|
CB
|
A:GLU672
|
4.5
|
33.8
|
1.0
|
CA
|
A:SER668
|
4.5
|
26.5
|
1.0
|
N
|
A:ARG642
|
4.6
|
25.5
|
1.0
|
CG
|
A:GLU573
|
4.6
|
20.1
|
1.0
|
OE2
|
A:GLU672
|
4.7
|
42.0
|
1.0
|
CB
|
A:THR641
|
4.7
|
26.7
|
1.0
|
OE2
|
A:GLU647
|
4.8
|
37.3
|
1.0
|
O
|
A:ARG642
|
4.8
|
24.6
|
1.0
|
CB
|
A:ASP670
|
5.0
|
44.8
|
1.0
|
|
Calcium binding site 3 out
of 4 in 1qal
Go back to
Calcium Binding Sites List in 1qal
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:26.0
occ:1.00
|
O
|
B:ALA679
|
2.3
|
27.7
|
1.0
|
OD1
|
B:ASP533
|
2.3
|
18.3
|
1.0
|
OD1
|
B:ASP535
|
2.4
|
21.8
|
1.0
|
O
|
B:LEU534
|
2.4
|
24.1
|
1.0
|
OD1
|
B:ASP678
|
2.5
|
21.6
|
1.0
|
O
|
B:HOH980
|
2.6
|
24.4
|
1.0
|
C
|
B:LEU534
|
3.4
|
25.8
|
1.0
|
C
|
B:ALA679
|
3.4
|
26.6
|
1.0
|
CG
|
B:ASP533
|
3.6
|
21.9
|
1.0
|
CG
|
B:ASP535
|
3.6
|
21.5
|
1.0
|
N
|
B:ALA679
|
3.6
|
25.6
|
1.0
|
NZ
|
B:LYS133
|
3.7
|
23.8
|
1.0
|
CG
|
B:ASP678
|
3.7
|
28.4
|
1.0
|
N
|
B:LEU534
|
4.0
|
24.8
|
1.0
|
C
|
B:ASP533
|
4.0
|
22.0
|
1.0
|
C
|
B:ASP678
|
4.1
|
26.0
|
1.0
|
CA
|
B:ALA679
|
4.1
|
23.5
|
1.0
|
N
|
B:ASP535
|
4.1
|
25.9
|
1.0
|
CA
|
B:ASP535
|
4.2
|
21.4
|
1.0
|
OD2
|
B:ASP533
|
4.3
|
19.4
|
1.0
|
CA
|
B:ASP533
|
4.4
|
24.2
|
1.0
|
CA
|
B:ASP678
|
4.4
|
29.1
|
1.0
|
OD2
|
B:ASP535
|
4.4
|
23.8
|
1.0
|
O
|
B:ASP533
|
4.4
|
23.8
|
1.0
|
CA
|
B:LEU534
|
4.4
|
24.8
|
1.0
|
OD2
|
B:ASP678
|
4.4
|
23.9
|
1.0
|
N
|
B:VAL680
|
4.5
|
25.1
|
1.0
|
CB
|
B:ASP535
|
4.5
|
18.9
|
1.0
|
O
|
B:GLU539
|
4.5
|
27.2
|
1.0
|
CB
|
B:ASP533
|
4.6
|
19.7
|
1.0
|
CB
|
B:ASP678
|
4.7
|
23.7
|
1.0
|
ND2
|
B:ASN541
|
4.7
|
31.3
|
1.0
|
CA
|
B:VAL680
|
4.7
|
24.6
|
1.0
|
CB
|
B:ALA679
|
4.8
|
22.5
|
1.0
|
CG2
|
B:VAL680
|
4.8
|
22.2
|
1.0
|
O
|
B:ASP678
|
4.8
|
31.5
|
1.0
|
|
Calcium binding site 4 out
of 4 in 1qal
Go back to
Calcium Binding Sites List in 1qal
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:45.5
occ:1.00
|
O
|
B:TYR667
|
2.3
|
25.7
|
1.0
|
OE2
|
B:GLU573
|
2.5
|
23.9
|
1.0
|
O
|
B:HOH1007
|
2.6
|
33.1
|
1.0
|
OE2
|
B:GLU672
|
2.6
|
45.6
|
1.0
|
O
|
B:HOH1003
|
2.6
|
31.0
|
1.0
|
OE1
|
B:GLU573
|
2.7
|
29.9
|
1.0
|
O
|
B:HOH1055
|
2.8
|
42.9
|
1.0
|
CD
|
B:GLU573
|
2.9
|
29.0
|
1.0
|
C
|
B:TYR667
|
3.5
|
23.1
|
1.0
|
CD
|
B:GLU672
|
3.6
|
47.0
|
1.0
|
CG
|
B:GLU672
|
3.8
|
40.9
|
1.0
|
CD2
|
B:HIS644
|
4.3
|
48.0
|
1.0
|
NE2
|
B:HIS644
|
4.3
|
46.0
|
1.0
|
OE1
|
B:GLU647
|
4.3
|
33.9
|
1.0
|
CA
|
B:TYR667
|
4.4
|
25.9
|
1.0
|
CA
|
B:SER668
|
4.4
|
31.1
|
1.0
|
N
|
B:SER668
|
4.4
|
27.1
|
1.0
|
CG
|
B:GLU573
|
4.5
|
30.5
|
1.0
|
N
|
B:ARG642
|
4.5
|
29.2
|
1.0
|
CB
|
B:GLU672
|
4.5
|
37.5
|
1.0
|
O
|
B:HOH1125
|
4.6
|
54.8
|
1.0
|
OE1
|
B:GLU672
|
4.7
|
50.3
|
1.0
|
CB
|
B:THR641
|
4.7
|
22.8
|
1.0
|
OE2
|
B:GLU647
|
4.7
|
33.3
|
1.0
|
CB
|
B:ARG642
|
4.8
|
36.7
|
1.0
|
CB
|
B:TYR667
|
4.9
|
24.5
|
1.0
|
O
|
B:ARG642
|
4.9
|
32.0
|
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 14:22:06 2024
|