Magnesium in PDB 3b8i: Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Enzymatic activity of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
All present enzymatic activity of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.:
4.1.1.3;
Protein crystallography data
The structure of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+., PDB code: 3b8i
was solved by
B.C.Narayanan,
O.Herzberg,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.60 /
1.90
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
260.065,
83.835,
104.874,
90.00,
112.14,
90.00
|
R / Rfree (%)
|
19.1 /
24.9
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
(pdb code 3b8i). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+., PDB code: 3b8i:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 1 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg289
b:27.5
occ:1.00
|
O
|
A:HOH292
|
2.0
|
19.4
|
1.0
|
O
|
A:HOH293
|
2.1
|
20.8
|
1.0
|
OD2
|
A:ASP88
|
2.1
|
20.4
|
1.0
|
O
|
A:HOH294
|
2.2
|
25.8
|
1.0
|
O1
|
A:OXL288
|
2.2
|
31.8
|
1.0
|
O4
|
A:OXL288
|
2.3
|
36.4
|
1.0
|
C1
|
A:OXL288
|
3.0
|
32.8
|
1.0
|
C2
|
A:OXL288
|
3.1
|
35.4
|
1.0
|
CG
|
A:ASP88
|
3.1
|
20.2
|
1.0
|
OD1
|
A:ASP88
|
3.4
|
22.6
|
1.0
|
OD1
|
A:ASP90
|
3.6
|
28.1
|
1.0
|
OD2
|
A:ASP61
|
3.7
|
23.9
|
1.0
|
O
|
A:HOH333
|
3.9
|
35.7
|
1.0
|
O
|
A:HOH437
|
4.0
|
26.1
|
1.0
|
OD1
|
A:ASP61
|
4.2
|
24.3
|
1.0
|
N
|
A:GLY49
|
4.2
|
21.3
|
1.0
|
O3
|
A:OXL288
|
4.2
|
29.8
|
1.0
|
O2
|
A:OXL288
|
4.3
|
38.3
|
1.0
|
N
|
A:SER50
|
4.3
|
21.7
|
1.0
|
CG
|
A:ASP61
|
4.4
|
23.2
|
1.0
|
OE1
|
A:GLU117
|
4.4
|
36.4
|
1.0
|
NH1
|
A:ARG159
|
4.4
|
17.6
|
1.0
|
CA
|
A:GLY49
|
4.5
|
20.8
|
1.0
|
CB
|
A:ASP88
|
4.5
|
21.1
|
1.0
|
CG
|
A:ASP90
|
4.6
|
28.2
|
1.0
|
NH2
|
A:ARG159
|
4.6
|
29.2
|
1.0
|
CZ
|
A:ARG159
|
4.8
|
26.5
|
1.0
|
C
|
A:GLY49
|
4.8
|
21.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 2 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg289
b:37.7
occ:1.00
|
O
|
B:HOH292
|
1.9
|
29.8
|
1.0
|
O
|
B:HOH294
|
2.1
|
45.7
|
1.0
|
OD2
|
B:ASP88
|
2.1
|
30.4
|
1.0
|
O
|
B:HOH293
|
2.2
|
33.5
|
1.0
|
O3
|
B:OXL288
|
2.4
|
47.5
|
1.0
|
O2
|
B:OXL288
|
2.6
|
51.5
|
1.0
|
CG
|
B:ASP88
|
3.1
|
30.5
|
1.0
|
C1
|
B:OXL288
|
3.2
|
48.8
|
1.0
|
C2
|
B:OXL288
|
3.3
|
52.2
|
1.0
|
OD1
|
B:ASP90
|
3.4
|
41.8
|
1.0
|
OD1
|
B:ASP88
|
3.5
|
28.0
|
1.0
|
OD2
|
B:ASP61
|
3.8
|
32.1
|
1.0
|
N
|
B:GLY49
|
4.1
|
26.0
|
1.0
|
OD1
|
B:ASP61
|
4.2
|
30.1
|
1.0
|
N
|
B:SER50
|
4.3
|
25.3
|
1.0
|
CA
|
B:GLY49
|
4.3
|
26.6
|
1.0
|
CG
|
B:ASP90
|
4.3
|
39.1
|
1.0
|
CG
|
B:ASP61
|
4.4
|
31.9
|
1.0
|
CB
|
B:ASP88
|
4.4
|
30.7
|
1.0
|
O1
|
B:OXL288
|
4.4
|
48.5
|
1.0
|
O4
|
B:OXL288
|
4.5
|
52.2
|
1.0
|
NH2
|
B:ARG159
|
4.5
|
43.4
|
1.0
|
NH1
|
B:ARG159
|
4.6
|
40.2
|
1.0
|
C
|
B:GLY49
|
4.7
|
26.5
|
1.0
|
OD2
|
B:ASP90
|
4.7
|
43.6
|
1.0
|
OE1
|
B:GLU117
|
4.7
|
47.8
|
1.0
|
CZ
|
B:ARG159
|
4.9
|
41.5
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 3 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg289
b:39.3
occ:1.00
|
O
|
C:HOH291
|
1.9
|
37.7
|
1.0
|
O
|
C:HOH290
|
2.0
|
32.3
|
1.0
|
O
|
C:HOH477
|
2.0
|
26.8
|
1.0
|
OD2
|
C:ASP88
|
2.0
|
29.2
|
1.0
|
O2
|
C:OXL288
|
2.3
|
39.5
|
1.0
|
O3
|
C:OXL288
|
2.7
|
48.5
|
1.0
|
CG
|
C:ASP88
|
3.0
|
27.3
|
1.0
|
C2
|
C:OXL288
|
3.1
|
43.6
|
1.0
|
C1
|
C:OXL288
|
3.2
|
48.5
|
1.0
|
OD1
|
C:ASP88
|
3.4
|
31.2
|
1.0
|
OD1
|
C:ASP90
|
3.7
|
37.6
|
1.0
|
OD2
|
C:ASP61
|
3.9
|
29.6
|
1.0
|
N
|
C:GLY49
|
4.1
|
26.2
|
1.0
|
CA
|
C:GLY49
|
4.3
|
25.7
|
1.0
|
O4
|
C:OXL288
|
4.3
|
45.2
|
1.0
|
CB
|
C:ASP88
|
4.3
|
28.4
|
1.0
|
NH2
|
C:ARG159
|
4.4
|
31.1
|
1.0
|
O1
|
C:OXL288
|
4.4
|
51.9
|
1.0
|
N
|
C:SER50
|
4.4
|
26.7
|
1.0
|
OD1
|
C:ASP61
|
4.4
|
30.2
|
1.0
|
CG
|
C:ASP90
|
4.5
|
33.6
|
1.0
|
NH1
|
C:ARG159
|
4.5
|
31.3
|
1.0
|
CG
|
C:ASP61
|
4.6
|
30.9
|
1.0
|
OE1
|
C:GLU117
|
4.6
|
38.8
|
1.0
|
CZ
|
C:ARG159
|
4.7
|
28.8
|
1.0
|
C
|
C:GLY49
|
4.8
|
25.6
|
1.0
|
OD2
|
C:ASP90
|
4.9
|
40.2
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 4 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg289
b:49.8
occ:1.00
|
O
|
D:HOH293
|
1.7
|
40.8
|
1.0
|
O
|
D:HOH291
|
1.9
|
52.8
|
1.0
|
O
|
D:HOH292
|
2.0
|
41.1
|
1.0
|
OD1
|
D:ASP88
|
2.1
|
36.7
|
1.0
|
O1
|
D:OXL288
|
2.5
|
48.1
|
1.0
|
O4
|
D:OXL288
|
2.7
|
51.8
|
1.0
|
CG
|
D:ASP88
|
3.0
|
34.2
|
1.0
|
C1
|
D:OXL288
|
3.3
|
51.6
|
1.0
|
OD2
|
D:ASP88
|
3.3
|
33.7
|
1.0
|
C2
|
D:OXL288
|
3.3
|
52.0
|
1.0
|
OD2
|
D:ASP90
|
3.6
|
39.3
|
1.0
|
OD2
|
D:ASP61
|
3.8
|
40.7
|
1.0
|
N
|
D:GLY49
|
4.1
|
33.5
|
1.0
|
CA
|
D:GLY49
|
4.3
|
32.6
|
1.0
|
O
|
D:HOH457
|
4.3
|
42.3
|
1.0
|
CB
|
D:ASP88
|
4.4
|
32.7
|
1.0
|
NH2
|
D:ARG159
|
4.4
|
43.2
|
1.0
|
N
|
D:SER50
|
4.4
|
32.5
|
1.0
|
OE1
|
D:GLU117
|
4.4
|
42.3
|
1.0
|
O3
|
D:OXL288
|
4.5
|
49.5
|
1.0
|
OD1
|
D:ASP61
|
4.5
|
42.0
|
1.0
|
O2
|
D:OXL288
|
4.5
|
53.1
|
1.0
|
CG
|
D:ASP90
|
4.5
|
35.4
|
1.0
|
CG
|
D:ASP61
|
4.6
|
40.5
|
1.0
|
CZ
|
D:ARG159
|
4.8
|
41.9
|
1.0
|
C
|
D:GLY49
|
4.8
|
33.0
|
1.0
|
NH1
|
D:ARG159
|
4.8
|
42.1
|
1.0
|
OD1
|
D:ASP90
|
4.9
|
38.7
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 5 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg289
b:29.4
occ:1.00
|
O
|
E:HOH631
|
2.0
|
21.0
|
1.0
|
O
|
E:HOH632
|
2.0
|
14.1
|
1.0
|
O
|
E:HOH633
|
2.1
|
23.2
|
1.0
|
OD2
|
E:ASP88
|
2.2
|
21.7
|
1.0
|
O3
|
E:OXL288
|
2.3
|
27.0
|
1.0
|
O2
|
E:OXL288
|
2.6
|
35.8
|
1.0
|
C1
|
E:OXL288
|
3.1
|
33.1
|
1.0
|
CG
|
E:ASP88
|
3.2
|
18.9
|
1.0
|
C2
|
E:OXL288
|
3.2
|
37.2
|
1.0
|
OD1
|
E:ASP88
|
3.4
|
21.6
|
1.0
|
OD2
|
E:ASP61
|
3.7
|
22.5
|
1.0
|
O
|
E:HOH757
|
3.8
|
42.5
|
1.0
|
O
|
E:HOH677
|
3.9
|
28.5
|
1.0
|
OD1
|
E:ASP90
|
4.1
|
36.6
|
1.0
|
N
|
E:GLY49
|
4.3
|
18.0
|
1.0
|
OD1
|
E:ASP61
|
4.3
|
23.9
|
1.0
|
OD2
|
E:ASP90
|
4.3
|
26.1
|
1.0
|
O1
|
E:OXL288
|
4.3
|
34.8
|
1.0
|
NH1
|
E:ARG159
|
4.4
|
21.2
|
1.0
|
NH2
|
E:ARG159
|
4.4
|
18.8
|
1.0
|
N
|
E:SER50
|
4.4
|
18.4
|
1.0
|
O4
|
E:OXL288
|
4.4
|
40.1
|
1.0
|
CA
|
E:GLY49
|
4.4
|
18.6
|
1.0
|
CG
|
E:ASP61
|
4.5
|
22.5
|
1.0
|
CG
|
E:ASP90
|
4.5
|
25.8
|
1.0
|
OE1
|
E:GLU117
|
4.5
|
26.3
|
1.0
|
CB
|
E:ASP88
|
4.5
|
19.2
|
1.0
|
CZ
|
E:ARG159
|
4.6
|
15.6
|
1.0
|
C
|
E:GLY49
|
4.8
|
17.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 3b8i
Go back to
Magnesium Binding Sites List in 3b8i
Magnesium binding site 6 out
of 6 in the Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Oxaloacetate Decarboxylase From Pseudomonas Aeruginosa (PA4872) in Complex with Oxalate and MG2+. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg289
b:49.1
occ:1.00
|
O
|
F:HOH292
|
1.9
|
39.0
|
1.0
|
OD2
|
F:ASP88
|
2.1
|
26.1
|
1.0
|
O
|
F:HOH291
|
2.1
|
26.3
|
1.0
|
O
|
F:HOH293
|
2.2
|
48.6
|
1.0
|
O4
|
F:OXL288
|
2.2
|
42.5
|
1.0
|
O1
|
F:OXL288
|
2.6
|
44.7
|
1.0
|
CG
|
F:ASP88
|
3.1
|
27.7
|
1.0
|
C2
|
F:OXL288
|
3.1
|
44.7
|
1.0
|
C1
|
F:OXL288
|
3.2
|
46.8
|
1.0
|
OD1
|
F:ASP88
|
3.4
|
31.1
|
1.0
|
OD1
|
F:ASP90
|
3.7
|
38.6
|
1.0
|
OD2
|
F:ASP61
|
4.0
|
36.4
|
1.0
|
N
|
F:GLY49
|
4.2
|
27.8
|
1.0
|
O2
|
F:OXL288
|
4.3
|
44.6
|
1.0
|
OE1
|
F:GLU117
|
4.3
|
47.5
|
1.0
|
OD1
|
F:ASP61
|
4.3
|
38.9
|
1.0
|
CA
|
F:GLY49
|
4.4
|
27.4
|
1.0
|
O3
|
F:OXL288
|
4.4
|
46.7
|
1.0
|
CB
|
F:ASP88
|
4.4
|
26.7
|
1.0
|
CG
|
F:ASP90
|
4.4
|
36.0
|
1.0
|
N
|
F:SER50
|
4.5
|
27.0
|
1.0
|
NH1
|
F:ARG159
|
4.5
|
45.3
|
1.0
|
CG
|
F:ASP61
|
4.6
|
36.0
|
1.0
|
NH2
|
F:ARG159
|
4.7
|
44.1
|
1.0
|
OD2
|
F:ASP90
|
4.7
|
44.9
|
1.0
|
CZ
|
F:ARG159
|
4.8
|
45.0
|
1.0
|
C
|
F:GLY49
|
4.9
|
27.8
|
1.0
|
|
Reference:
B.C.Narayanan,
W.Niu,
Y.Han,
J.Zou,
P.S.Mariano,
D.Dunaway-Mariano,
O.Herzberg.
Structure and Function of PA4872 From Pseudomonas Aeruginosa, A Novel Class of Oxaloacetate Decarboxylase From the Pep Mutase/Isocitrate Lyase Superfamily. Biochemistry V. 47 167 2008.
ISSN: ISSN 0006-2960
PubMed: 18081320
DOI: 10.1021/BI701954P
Page generated: Wed Aug 14 08:53:51 2024
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