Magnesium in PDB 5fju: N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
Enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
All present enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine:
4.2.1.113;
Protein crystallography data
The structure of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine, PDB code: 5fju
was solved by
G.Sanchez Carron,
D.Campopiano,
G.Grogan,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
107.35 /
2.52
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
216.900,
216.900,
261.630,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
15.6 /
19
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
(pdb code 5fju). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine, PDB code: 5fju:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5fju
Go back to
Magnesium Binding Sites List in 5fju
Magnesium binding site 1 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1369
b:50.1
occ:1.00
|
OD2
|
A:ASP239
|
2.3
|
41.6
|
1.0
|
OE2
|
A:GLU214
|
2.4
|
54.3
|
1.0
|
OD2
|
A:ASP189
|
2.5
|
42.2
|
1.0
|
OXT
|
A:5CR1370
|
2.5
|
49.4
|
1.0
|
O
|
A:5CR1370
|
3.0
|
56.9
|
1.0
|
CD
|
A:GLU214
|
3.0
|
47.6
|
1.0
|
OD1
|
A:ASP189
|
3.1
|
45.6
|
1.0
|
CG
|
A:ASP189
|
3.1
|
37.8
|
1.0
|
C
|
A:5CR1370
|
3.1
|
51.8
|
1.0
|
CG
|
A:ASP239
|
3.3
|
35.6
|
1.0
|
ND2
|
A:ASN191
|
3.4
|
43.8
|
1.0
|
CG
|
A:GLU214
|
3.7
|
38.4
|
1.0
|
CB
|
A:ASP239
|
3.7
|
32.5
|
1.0
|
OE1
|
A:GLU214
|
3.8
|
46.8
|
1.0
|
OE1
|
A:GLU240
|
3.8
|
41.3
|
1.0
|
NZ
|
A:LYS263
|
4.0
|
62.8
|
1.0
|
CG
|
A:ASN191
|
4.2
|
44.1
|
1.0
|
NZ
|
A:LYS163
|
4.3
|
45.8
|
1.0
|
NZ
|
A:LYS161
|
4.3
|
42.4
|
1.0
|
OD1
|
A:ASP239
|
4.4
|
40.7
|
1.0
|
OD1
|
A:ASN191
|
4.5
|
50.5
|
1.0
|
CB
|
A:ASP189
|
4.6
|
34.8
|
1.0
|
CD
|
A:GLU240
|
4.6
|
42.4
|
1.0
|
CA
|
A:5CR1370
|
4.7
|
46.4
|
1.0
|
OE2
|
A:GLU240
|
4.7
|
44.0
|
1.0
|
CB
|
A:GLU214
|
4.7
|
34.9
|
1.0
|
ND2
|
A:ASN261
|
4.7
|
51.9
|
1.0
|
CE2
|
A:TYR55
|
5.0
|
43.4
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5fju
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Magnesium Binding Sites List in 5fju
Magnesium binding site 2 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1368
b:56.0
occ:1.00
|
OD2
|
B:ASP239
|
2.5
|
47.5
|
1.0
|
OD2
|
B:ASP189
|
2.7
|
37.4
|
1.0
|
OXT
|
B:5CR1369
|
2.7
|
57.2
|
1.0
|
OD1
|
B:ASP189
|
2.8
|
40.0
|
1.0
|
OE2
|
B:GLU214
|
2.8
|
47.5
|
1.0
|
CG
|
B:ASP189
|
3.1
|
35.7
|
1.0
|
ND2
|
B:ASN191
|
3.1
|
47.0
|
1.0
|
OE1
|
B:GLU240
|
3.3
|
43.9
|
1.0
|
CD
|
B:GLU214
|
3.3
|
50.6
|
1.0
|
CG
|
B:ASP239
|
3.4
|
50.1
|
1.0
|
CB
|
B:ASP239
|
3.6
|
40.0
|
1.0
|
CG
|
B:GLU214
|
3.6
|
44.6
|
1.0
|
C
|
B:5CR1369
|
3.7
|
53.8
|
1.0
|
CG
|
B:ASN191
|
3.9
|
48.3
|
1.0
|
O
|
B:5CR1369
|
3.9
|
59.7
|
1.0
|
CD
|
B:GLU240
|
4.1
|
47.4
|
1.0
|
OE2
|
B:GLU240
|
4.1
|
54.6
|
1.0
|
OE1
|
B:GLU214
|
4.2
|
51.9
|
1.0
|
OD1
|
B:ASN191
|
4.3
|
46.9
|
1.0
|
CB
|
B:GLN215
|
4.5
|
33.5
|
1.0
|
CA
|
B:ASN191
|
4.5
|
38.1
|
1.0
|
NZ
|
B:LYS163
|
4.5
|
43.6
|
1.0
|
OD1
|
B:ASP239
|
4.5
|
45.6
|
1.0
|
N
|
B:ASN191
|
4.5
|
35.7
|
1.0
|
NZ
|
B:LYS263
|
4.5
|
65.4
|
1.0
|
CB
|
B:ASP189
|
4.6
|
32.6
|
1.0
|
CB
|
B:GLU214
|
4.6
|
43.5
|
1.0
|
CB
|
B:ASN191
|
4.8
|
41.0
|
1.0
|
NZ
|
B:LYS161
|
4.9
|
49.4
|
1.0
|
CE2
|
B:TYR55
|
4.9
|
45.4
|
1.0
|
O
|
B:GLU214
|
5.0
|
37.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5fju
Go back to
Magnesium Binding Sites List in 5fju
Magnesium binding site 3 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1368
b:51.8
occ:1.00
|
OD2
|
C:ASP239
|
2.4
|
56.9
|
1.0
|
OXT
|
C:5CR1370
|
2.6
|
56.6
|
1.0
|
OD2
|
C:ASP189
|
2.7
|
50.7
|
1.0
|
OE2
|
C:GLU214
|
2.7
|
44.2
|
1.0
|
OD1
|
C:ASP189
|
2.9
|
54.2
|
1.0
|
CG
|
C:ASP189
|
3.1
|
49.0
|
1.0
|
ND2
|
C:ASN191
|
3.2
|
54.7
|
1.0
|
CD
|
C:GLU214
|
3.2
|
51.5
|
1.0
|
OE1
|
C:GLU240
|
3.3
|
41.6
|
1.0
|
CG
|
C:ASP239
|
3.3
|
41.0
|
1.0
|
CB
|
C:ASP239
|
3.5
|
40.8
|
1.0
|
CG
|
C:GLU214
|
3.6
|
42.1
|
1.0
|
C
|
C:5CR1370
|
3.7
|
52.5
|
1.0
|
CG
|
C:ASN191
|
4.0
|
52.0
|
1.0
|
O
|
C:5CR1370
|
4.0
|
69.9
|
1.0
|
OE1
|
C:GLU214
|
4.1
|
49.4
|
1.0
|
CD
|
C:GLU240
|
4.1
|
41.6
|
1.0
|
OE2
|
C:GLU240
|
4.2
|
41.8
|
1.0
|
OD1
|
C:ASP239
|
4.4
|
41.8
|
1.0
|
OD1
|
C:ASN191
|
4.4
|
48.0
|
1.0
|
NZ
|
C:LYS263
|
4.5
|
55.5
|
1.0
|
CB
|
C:GLN215
|
4.5
|
38.8
|
1.0
|
CB
|
C:GLU214
|
4.6
|
36.7
|
1.0
|
NZ
|
C:LYS163
|
4.6
|
52.7
|
1.0
|
CB
|
C:ASP189
|
4.6
|
47.8
|
1.0
|
CA
|
C:ASN191
|
4.6
|
44.7
|
1.0
|
N
|
C:ASN191
|
4.6
|
40.1
|
1.0
|
NZ
|
C:LYS161
|
4.9
|
52.0
|
1.0
|
CB
|
C:ASN191
|
4.9
|
49.2
|
1.0
|
CE2
|
C:TYR55
|
5.0
|
49.9
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5fju
Go back to
Magnesium Binding Sites List in 5fju
Magnesium binding site 4 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Phenylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1368
b:51.7
occ:1.00
|
O
|
D:HOH2063
|
2.2
|
36.9
|
1.0
|
OD1
|
D:ASP189
|
2.6
|
44.8
|
1.0
|
OD2
|
D:ASP239
|
2.8
|
47.6
|
1.0
|
OE1
|
D:GLU240
|
2.9
|
38.2
|
1.0
|
ND2
|
D:ASN191
|
3.0
|
43.1
|
1.0
|
OD2
|
D:ASP189
|
3.0
|
46.5
|
1.0
|
CG
|
D:ASP189
|
3.2
|
40.5
|
1.0
|
OE2
|
D:GLU214
|
3.3
|
53.2
|
1.0
|
CG
|
D:ASP239
|
3.6
|
47.0
|
1.0
|
OXT
|
D:5CR1370
|
3.6
|
45.4
|
1.0
|
CD
|
D:GLU214
|
3.6
|
50.8
|
1.0
|
CB
|
D:ASP239
|
3.7
|
43.6
|
1.0
|
CG
|
D:GLU214
|
3.7
|
43.7
|
1.0
|
CG
|
D:ASN191
|
3.7
|
43.0
|
1.0
|
CD
|
D:GLU240
|
3.7
|
42.5
|
1.0
|
OE2
|
D:GLU240
|
3.8
|
43.0
|
1.0
|
CB
|
D:GLN215
|
3.9
|
38.9
|
1.0
|
CA
|
D:ASN191
|
4.0
|
37.6
|
1.0
|
N
|
D:ASN191
|
4.0
|
34.0
|
1.0
|
OD1
|
D:ASN191
|
4.3
|
48.1
|
1.0
|
CB
|
D:ASN191
|
4.5
|
43.3
|
1.0
|
O
|
D:GLU214
|
4.5
|
33.9
|
1.0
|
OE1
|
D:GLU214
|
4.5
|
49.0
|
1.0
|
CB
|
D:GLU214
|
4.5
|
40.8
|
1.0
|
C
|
D:5CR1370
|
4.6
|
53.4
|
1.0
|
CB
|
D:ASP189
|
4.6
|
40.7
|
1.0
|
C
|
D:GLU214
|
4.6
|
35.6
|
1.0
|
CG
|
D:GLN215
|
4.7
|
36.0
|
1.0
|
OD1
|
D:ASP239
|
4.7
|
46.9
|
1.0
|
O
|
D:5CR1370
|
4.9
|
57.7
|
1.0
|
NZ
|
D:LYS163
|
4.9
|
47.3
|
1.0
|
N
|
D:GLN215
|
4.9
|
39.5
|
1.0
|
CA
|
D:GLN215
|
5.0
|
37.8
|
1.0
|
|
Reference:
G.Sanchez-Carron,
D.Campopiano,
G.Grogan.
Structure of N-Acylamino Acid Racemase Mutants in Complex with Substrates To Be Published.
Page generated: Sun Sep 29 04:19:06 2024
|