Magnesium in PDB 3uxk: P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
Enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
All present enzymatic activity of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate:
5.1.2.2;
Protein crystallography data
The structure of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate, PDB code: 3uxk
was solved by
A.D.Lietzan,
E.Pellmann,
M.St Maurice,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
148.309,
148.309,
169.552,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.2 /
19.3
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
(pdb code 3uxk). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate, PDB code: 3uxk:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 3uxk
Go back to
Magnesium Binding Sites List in 3uxk
Magnesium binding site 1 out
of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg360
b:11.4
occ:1.00
|
OE1
|
A:GLU221
|
2.0
|
13.2
|
1.0
|
O
|
A:HOH722
|
2.1
|
9.5
|
1.0
|
O1
|
A:BHO361
|
2.1
|
35.6
|
1.0
|
OD1
|
A:ASP195
|
2.2
|
9.9
|
1.0
|
OE1
|
A:GLU247
|
2.2
|
12.2
|
1.0
|
O2
|
A:BHO361
|
2.4
|
31.5
|
1.0
|
C
|
A:BHO361
|
2.7
|
36.5
|
1.0
|
N
|
A:BHO361
|
2.7
|
35.1
|
1.0
|
CD
|
A:GLU247
|
3.0
|
12.3
|
1.0
|
OE2
|
A:GLU247
|
3.2
|
13.6
|
1.0
|
CG
|
A:ASP195
|
3.2
|
10.4
|
1.0
|
CD
|
A:GLU221
|
3.2
|
11.9
|
1.0
|
OD2
|
A:ASP195
|
3.6
|
10.5
|
1.0
|
NZ
|
A:LYS166
|
3.8
|
18.6
|
1.0
|
ND2
|
A:ASN197
|
4.0
|
12.9
|
1.0
|
NZ
|
A:LYS164
|
4.0
|
9.9
|
1.0
|
OE2
|
A:GLU221
|
4.1
|
11.8
|
1.0
|
CG
|
A:GLU221
|
4.1
|
11.2
|
1.0
|
NE2
|
A:HIS297
|
4.2
|
12.4
|
1.0
|
C1
|
A:BHO361
|
4.2
|
38.7
|
1.0
|
CD2
|
A:HIS297
|
4.2
|
11.6
|
1.0
|
O
|
A:HOH373
|
4.3
|
7.9
|
1.0
|
OE2
|
A:GLU222
|
4.4
|
11.1
|
1.0
|
CG
|
A:GLU247
|
4.4
|
11.7
|
1.0
|
CB
|
A:ASP195
|
4.5
|
9.9
|
1.0
|
CE
|
A:LYS164
|
4.6
|
10.0
|
1.0
|
CE
|
A:MET268
|
4.6
|
9.1
|
1.0
|
CG
|
A:ASN197
|
4.9
|
12.8
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 3uxk
Go back to
Magnesium Binding Sites List in 3uxk
Magnesium binding site 2 out
of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg360
b:14.5
occ:1.00
|
OE1
|
B:GLU221
|
2.0
|
18.7
|
1.0
|
OE1
|
B:GLU247
|
2.1
|
15.7
|
1.0
|
O
|
B:HOH723
|
2.2
|
13.8
|
1.0
|
OD1
|
B:ASP195
|
2.2
|
14.4
|
1.0
|
O2
|
B:BHO361
|
2.3
|
39.9
|
1.0
|
O1
|
B:BHO361
|
2.3
|
40.4
|
1.0
|
N
|
B:BHO361
|
2.7
|
44.1
|
1.0
|
C
|
B:BHO361
|
2.8
|
43.6
|
1.0
|
CD
|
B:GLU247
|
3.0
|
16.2
|
1.0
|
CD
|
B:GLU221
|
3.2
|
17.2
|
1.0
|
CG
|
B:ASP195
|
3.2
|
14.9
|
1.0
|
OE2
|
B:GLU247
|
3.2
|
17.8
|
1.0
|
OD2
|
B:ASP195
|
3.5
|
14.6
|
1.0
|
NZ
|
B:LYS166
|
3.9
|
25.4
|
1.0
|
NZ
|
B:LYS164
|
4.0
|
18.8
|
1.0
|
CG
|
B:GLU221
|
4.0
|
14.8
|
1.0
|
OE2
|
B:GLU221
|
4.1
|
17.2
|
1.0
|
ND2
|
B:ASN197
|
4.1
|
18.4
|
1.0
|
C1
|
B:BHO361
|
4.3
|
46.7
|
1.0
|
NE2
|
B:HIS297
|
4.3
|
15.0
|
1.0
|
O
|
B:HOH362
|
4.3
|
13.1
|
1.0
|
OE2
|
B:GLU222
|
4.4
|
17.9
|
1.0
|
CD2
|
B:HIS297
|
4.4
|
14.3
|
1.0
|
CG
|
B:GLU247
|
4.4
|
14.4
|
1.0
|
CE
|
B:MET268
|
4.5
|
13.7
|
1.0
|
CB
|
B:ASP195
|
4.5
|
15.4
|
1.0
|
CE
|
B:LYS164
|
4.5
|
17.7
|
1.0
|
CG
|
B:ASN197
|
4.8
|
18.6
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 3uxk
Go back to
Magnesium Binding Sites List in 3uxk
Magnesium binding site 3 out
of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg360
b:13.7
occ:1.00
|
OE1
|
C:GLU221
|
2.0
|
17.8
|
1.0
|
OE1
|
C:GLU247
|
2.1
|
14.6
|
1.0
|
O
|
C:HOH721
|
2.2
|
13.1
|
1.0
|
OD1
|
C:ASP195
|
2.2
|
14.4
|
1.0
|
O1
|
C:BHO361
|
2.2
|
39.9
|
1.0
|
O2
|
C:BHO361
|
2.4
|
40.3
|
1.0
|
N
|
C:BHO361
|
2.7
|
44.5
|
1.0
|
C
|
C:BHO361
|
2.7
|
43.5
|
1.0
|
CD
|
C:GLU247
|
3.0
|
15.0
|
1.0
|
CG
|
C:ASP195
|
3.2
|
14.9
|
1.0
|
OE2
|
C:GLU247
|
3.2
|
16.2
|
1.0
|
CD
|
C:GLU221
|
3.2
|
16.7
|
1.0
|
OD2
|
C:ASP195
|
3.5
|
14.5
|
1.0
|
NZ
|
C:LYS166
|
3.9
|
25.8
|
1.0
|
NZ
|
C:LYS164
|
4.0
|
18.6
|
1.0
|
ND2
|
C:ASN197
|
4.0
|
17.3
|
1.0
|
CG
|
C:GLU221
|
4.0
|
14.6
|
1.0
|
OE2
|
C:GLU221
|
4.1
|
16.3
|
1.0
|
C1
|
C:BHO361
|
4.2
|
45.6
|
1.0
|
OE2
|
C:GLU222
|
4.3
|
17.5
|
1.0
|
O
|
C:HOH363
|
4.4
|
12.2
|
1.0
|
CG
|
C:GLU247
|
4.4
|
13.6
|
1.0
|
NE2
|
C:HIS297
|
4.4
|
15.2
|
1.0
|
CB
|
C:ASP195
|
4.4
|
15.4
|
1.0
|
CD2
|
C:HIS297
|
4.4
|
14.5
|
1.0
|
CE
|
C:MET268
|
4.6
|
13.7
|
1.0
|
CE
|
C:LYS164
|
4.6
|
17.2
|
1.0
|
CG
|
C:ASN197
|
4.8
|
17.4
|
1.0
|
OD1
|
C:ASN197
|
4.9
|
17.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 3uxk
Go back to
Magnesium Binding Sites List in 3uxk
Magnesium binding site 4 out
of 4 in the P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of P. Putida Mandelate Racemase Co-Crystallized with the Intermediate Analogue Benzohydroxamate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg360
b:11.3
occ:1.00
|
O1
|
D:BHO361
|
2.1
|
31.1
|
1.0
|
OE1
|
D:GLU221
|
2.1
|
13.2
|
1.0
|
O
|
D:HOH724
|
2.2
|
9.0
|
1.0
|
OD1
|
D:ASP195
|
2.2
|
10.4
|
1.0
|
OE1
|
D:GLU247
|
2.2
|
11.9
|
1.0
|
O2
|
D:BHO361
|
2.4
|
30.2
|
1.0
|
C
|
D:BHO361
|
2.6
|
33.4
|
1.0
|
N
|
D:BHO361
|
2.7
|
33.8
|
1.0
|
CD
|
D:GLU247
|
3.0
|
11.9
|
1.0
|
OE2
|
D:GLU247
|
3.1
|
13.1
|
1.0
|
CG
|
D:ASP195
|
3.2
|
10.9
|
1.0
|
CD
|
D:GLU221
|
3.2
|
11.7
|
1.0
|
OD2
|
D:ASP195
|
3.6
|
11.1
|
1.0
|
NZ
|
D:LYS166
|
3.8
|
18.4
|
1.0
|
ND2
|
D:ASN197
|
3.9
|
12.2
|
1.0
|
NZ
|
D:LYS164
|
4.0
|
10.0
|
1.0
|
CG
|
D:GLU221
|
4.1
|
10.9
|
1.0
|
CE1
|
D:HIS297
|
4.1
|
12.2
|
1.0
|
OE2
|
D:GLU221
|
4.1
|
11.6
|
1.0
|
C1
|
D:BHO361
|
4.1
|
36.8
|
1.0
|
ND1
|
D:HIS297
|
4.3
|
12.1
|
1.0
|
O
|
D:HOH384
|
4.4
|
7.6
|
1.0
|
OE2
|
D:GLU222
|
4.4
|
11.8
|
1.0
|
CG
|
D:GLU247
|
4.4
|
11.3
|
1.0
|
CB
|
D:ASP195
|
4.5
|
10.4
|
1.0
|
CE
|
D:MET268
|
4.5
|
9.3
|
1.0
|
CE
|
D:LYS164
|
4.6
|
10.0
|
1.0
|
CG
|
D:ASN197
|
4.8
|
12.4
|
1.0
|
C6
|
D:BHO361
|
4.9
|
37.7
|
1.0
|
CE
|
D:LYS166
|
5.0
|
18.6
|
1.0
|
|
Reference:
A.D.Lietzan,
M.Nagar,
E.A.Pellmann,
J.R.Bourque,
S.L.Bearne,
M.St Maurice.
Structure of Mandelate Racemase with Bound Intermediate Analogues Benzohydroxamate and Cupferron. Biochemistry V. 51 1160 2012.
ISSN: ISSN 0006-2960
PubMed: 22264153
DOI: 10.1021/BI2018514
Page generated: Thu Aug 15 12:40:07 2024
|