Magnesium in PDB 5fjr: N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine
Enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp. Ts-1-60: Q26A M50I G291D F323Y Mutant in Complex with N-Acetyl Napthylalanine
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 Napthylalanine:
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 Napthylalanine, PDB code: 5fjr
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)
|
107.89 /
2.44
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
217.670,
217.670,
263.150,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.222 /
22.052
|
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 Napthylalanine
(pdb code 5fjr). 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 Napthylalanine, PDB code: 5fjr:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5fjr
Go back to
Magnesium Binding Sites List in 5fjr
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 Napthylalanine
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 Napthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1370
b:42.3
occ:1.00
|
OD2
|
A:ASP239
|
2.2
|
43.9
|
1.0
|
OE2
|
A:GLU214
|
2.3
|
38.8
|
1.0
|
OD2
|
A:ASP189
|
2.5
|
40.3
|
1.0
|
OXT
|
A:NPQ1369
|
2.7
|
38.4
|
1.0
|
O
|
A:NPQ1369
|
2.8
|
42.1
|
1.0
|
CD
|
A:GLU214
|
3.1
|
38.1
|
1.0
|
C
|
A:NPQ1369
|
3.1
|
44.5
|
1.0
|
CG
|
A:ASP189
|
3.2
|
36.4
|
1.0
|
CG
|
A:ASP239
|
3.3
|
35.5
|
1.0
|
OD1
|
A:ASP189
|
3.4
|
40.2
|
1.0
|
ND2
|
A:ASN191
|
3.6
|
41.6
|
1.0
|
CB
|
A:ASP239
|
3.8
|
33.0
|
1.0
|
CG
|
A:GLU214
|
3.8
|
31.4
|
1.0
|
OE1
|
A:GLU214
|
3.8
|
43.0
|
1.0
|
NZ
|
A:LYS161
|
3.9
|
35.1
|
1.0
|
NZ
|
A:LYS263
|
3.9
|
42.6
|
1.0
|
NZ
|
A:LYS163
|
4.1
|
38.1
|
1.0
|
OE1
|
A:GLU240
|
4.2
|
44.9
|
1.0
|
OD1
|
A:ASP239
|
4.4
|
37.4
|
1.0
|
CG
|
A:ASN191
|
4.4
|
44.7
|
1.0
|
ND2
|
A:ASN261
|
4.6
|
42.2
|
1.0
|
CB
|
A:ASP189
|
4.6
|
29.6
|
1.0
|
CA
|
A:NPQ1369
|
4.7
|
42.2
|
1.0
|
OD1
|
A:ASN191
|
4.7
|
41.7
|
1.0
|
CE
|
A:LYS263
|
4.7
|
32.7
|
1.0
|
CB
|
A:GLU214
|
4.8
|
31.9
|
1.0
|
O
|
A:HOH2137
|
4.8
|
44.2
|
1.0
|
OE2
|
A:GLU240
|
4.9
|
38.9
|
1.0
|
CE1
|
A:TYR55
|
4.9
|
36.6
|
1.0
|
CE
|
A:LYS161
|
4.9
|
33.5
|
1.0
|
CD
|
A:GLU240
|
4.9
|
45.0
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5fjr
Go back to
Magnesium Binding Sites List in 5fjr
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 Napthylalanine
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 Napthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1369
b:58.6
occ:1.00
|
OD2
|
B:ASP239
|
2.3
|
50.5
|
1.0
|
O
|
B:HOH2080
|
2.3
|
46.7
|
1.0
|
OE2
|
B:GLU214
|
2.4
|
54.2
|
1.0
|
OD2
|
B:ASP189
|
2.5
|
51.2
|
1.0
|
O
|
B:NPQ1368
|
2.7
|
50.0
|
1.0
|
OXT
|
B:NPQ1368
|
2.9
|
57.6
|
1.0
|
CD
|
B:GLU214
|
3.1
|
53.7
|
1.0
|
C
|
B:NPQ1368
|
3.2
|
61.4
|
1.0
|
CG
|
B:ASP189
|
3.2
|
41.1
|
1.0
|
OD1
|
B:ASP189
|
3.3
|
45.9
|
1.0
|
CG
|
B:ASP239
|
3.4
|
48.1
|
1.0
|
CG
|
B:GLU214
|
3.6
|
44.6
|
1.0
|
ND2
|
B:ASN191
|
3.7
|
44.5
|
1.0
|
NZ
|
B:LYS161
|
3.8
|
47.5
|
1.0
|
CB
|
B:ASP239
|
3.8
|
41.3
|
1.0
|
OE1
|
B:GLU214
|
3.9
|
60.0
|
1.0
|
NZ
|
B:LYS263
|
4.0
|
52.8
|
1.0
|
NZ
|
B:LYS163
|
4.1
|
52.9
|
1.0
|
OE1
|
B:GLU240
|
4.2
|
46.9
|
1.0
|
CG
|
B:ASN191
|
4.4
|
43.5
|
1.0
|
OD1
|
B:ASP239
|
4.4
|
45.2
|
1.0
|
OD1
|
B:ASN191
|
4.4
|
42.6
|
1.0
|
ND2
|
B:ASN261
|
4.6
|
62.4
|
1.0
|
CB
|
B:ASP189
|
4.6
|
39.8
|
1.0
|
CE
|
B:LYS263
|
4.7
|
46.9
|
1.0
|
CA
|
B:NPQ1368
|
4.8
|
52.3
|
1.0
|
CE
|
B:LYS161
|
4.8
|
39.5
|
1.0
|
CE2
|
B:TYR55
|
4.8
|
46.2
|
1.0
|
CB
|
B:GLU214
|
4.9
|
44.6
|
1.0
|
CD
|
B:GLU240
|
4.9
|
44.7
|
1.0
|
OE2
|
B:GLU240
|
5.0
|
44.1
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5fjr
Go back to
Magnesium Binding Sites List in 5fjr
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 Napthylalanine
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 Napthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1369
b:52.5
occ:1.00
|
O
|
C:HOH2066
|
2.2
|
41.1
|
1.0
|
OE2
|
C:GLU214
|
2.2
|
48.9
|
1.0
|
OD2
|
C:ASP239
|
2.2
|
50.9
|
1.0
|
OD2
|
C:ASP189
|
2.6
|
46.8
|
1.0
|
O
|
C:NPQ1368
|
2.8
|
53.3
|
1.0
|
OXT
|
C:NPQ1368
|
2.9
|
64.6
|
1.0
|
CD
|
C:GLU214
|
3.0
|
46.0
|
1.0
|
C
|
C:NPQ1368
|
3.2
|
59.9
|
1.0
|
CG
|
C:ASP239
|
3.3
|
46.3
|
1.0
|
CG
|
C:ASP189
|
3.3
|
52.1
|
1.0
|
OD1
|
C:ASP189
|
3.4
|
47.8
|
1.0
|
CB
|
C:ASP239
|
3.6
|
37.7
|
1.0
|
ND2
|
C:ASN191
|
3.7
|
46.4
|
1.0
|
CG
|
C:GLU214
|
3.7
|
39.5
|
1.0
|
OE1
|
C:GLU214
|
3.7
|
49.2
|
1.0
|
NZ
|
C:LYS161
|
4.0
|
41.3
|
1.0
|
NZ
|
C:LYS263
|
4.1
|
48.2
|
1.0
|
OE1
|
C:GLU240
|
4.2
|
47.5
|
1.0
|
NZ
|
C:LYS163
|
4.3
|
49.5
|
1.0
|
ND2
|
C:ASN261
|
4.4
|
41.8
|
1.0
|
OD1
|
C:ASP239
|
4.4
|
40.5
|
1.0
|
CG
|
C:ASN191
|
4.5
|
51.2
|
1.0
|
OD1
|
C:ASN191
|
4.6
|
52.4
|
1.0
|
CB
|
C:ASP189
|
4.7
|
41.7
|
1.0
|
CA
|
C:NPQ1368
|
4.7
|
59.2
|
1.0
|
CE
|
C:LYS263
|
4.8
|
39.4
|
1.0
|
CB
|
C:GLU214
|
4.8
|
36.5
|
1.0
|
CE
|
C:LYS161
|
4.9
|
37.9
|
1.0
|
OE2
|
C:GLU240
|
4.9
|
48.5
|
1.0
|
CD
|
C:GLU240
|
4.9
|
48.7
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5fjr
Go back to
Magnesium Binding Sites List in 5fjr
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 Napthylalanine
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 Napthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1369
b:54.1
occ:1.00
|
OE2
|
D:GLU214
|
2.1
|
52.7
|
1.0
|
OD2
|
D:ASP239
|
2.3
|
46.2
|
1.0
|
O
|
D:HOH2059
|
2.4
|
36.7
|
1.0
|
OD2
|
D:ASP189
|
2.5
|
46.1
|
1.0
|
O
|
D:NPQ1368
|
2.8
|
53.4
|
1.0
|
CD
|
D:GLU214
|
2.9
|
52.1
|
1.0
|
OXT
|
D:NPQ1368
|
2.9
|
48.8
|
1.0
|
C
|
D:NPQ1368
|
3.2
|
55.8
|
1.0
|
CG
|
D:ASP189
|
3.2
|
50.3
|
1.0
|
CG
|
D:ASP239
|
3.3
|
49.9
|
1.0
|
OD1
|
D:ASP189
|
3.4
|
51.8
|
1.0
|
CG
|
D:GLU214
|
3.6
|
45.4
|
1.0
|
OE1
|
D:GLU214
|
3.7
|
42.2
|
1.0
|
CB
|
D:ASP239
|
3.7
|
37.3
|
1.0
|
NZ
|
D:LYS161
|
3.7
|
39.4
|
1.0
|
ND2
|
D:ASN191
|
3.9
|
48.4
|
1.0
|
NZ
|
D:LYS263
|
4.1
|
53.0
|
1.0
|
OE1
|
D:GLU240
|
4.3
|
52.2
|
1.0
|
NZ
|
D:LYS163
|
4.3
|
50.7
|
1.0
|
OD1
|
D:ASP239
|
4.4
|
42.5
|
1.0
|
ND2
|
D:ASN261
|
4.5
|
57.6
|
1.0
|
CB
|
D:ASP189
|
4.5
|
42.2
|
1.0
|
CG
|
D:ASN191
|
4.6
|
48.1
|
1.0
|
O
|
D:HOH2051
|
4.7
|
46.6
|
1.0
|
CE
|
D:LYS161
|
4.7
|
33.4
|
1.0
|
OD1
|
D:ASN191
|
4.7
|
44.0
|
1.0
|
CE
|
D:LYS263
|
4.7
|
45.8
|
1.0
|
CB
|
D:GLU214
|
4.8
|
42.3
|
1.0
|
CA
|
D:NPQ1368
|
4.9
|
53.5
|
1.0
|
OE2
|
D:GLU240
|
5.0
|
39.5
|
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
|