Magnesium in PDB 5fjp: N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
Enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
All present enzymatic activity of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine:
4.2.1.113;
Protein crystallography data
The structure of N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine, PDB code: 5fjp
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)
|
76.44 /
2.58
|
Space group
|
H 3 2
|
Cell size a, b, c (Å), α, β, γ (°)
|
217.290,
217.290,
262.220,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
17.926 /
20.834
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
(pdb code 5fjp). 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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine, PDB code: 5fjp:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 5fjp
Go back to
Magnesium Binding Sites List in 5fjp
Magnesium binding site 1 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1370
b:34.2
occ:1.00
|
O
|
A:HOH2062
|
2.3
|
19.7
|
1.0
|
OD2
|
A:ASP239
|
2.3
|
33.0
|
1.0
|
OD2
|
A:ASP189
|
2.4
|
32.8
|
1.0
|
OE2
|
A:GLU214
|
2.4
|
31.8
|
1.0
|
OXT
|
A:NPQ1369
|
2.5
|
35.3
|
1.0
|
O
|
A:NPQ1369
|
2.7
|
30.8
|
1.0
|
C
|
A:NPQ1369
|
3.0
|
39.2
|
1.0
|
CD
|
A:GLU214
|
3.2
|
34.4
|
1.0
|
CG
|
A:ASP189
|
3.3
|
31.0
|
1.0
|
CG
|
A:ASP239
|
3.5
|
31.2
|
1.0
|
ND2
|
A:ASN191
|
3.6
|
37.9
|
1.0
|
NZ
|
A:LYS161
|
3.6
|
32.2
|
1.0
|
OD1
|
A:ASP189
|
3.7
|
29.2
|
1.0
|
NZ
|
A:LYS263
|
3.8
|
34.6
|
1.0
|
NZ
|
A:LYS163
|
3.9
|
43.5
|
1.0
|
CB
|
A:ASP239
|
3.9
|
28.2
|
1.0
|
OE1
|
A:GLU214
|
3.9
|
33.8
|
1.0
|
CG
|
A:GLU214
|
4.0
|
32.5
|
1.0
|
ND2
|
A:ASN261
|
4.2
|
31.1
|
1.0
|
CG
|
A:ASN191
|
4.4
|
42.5
|
1.0
|
OE1
|
A:GLU240
|
4.4
|
27.3
|
1.0
|
O
|
A:HOH2055
|
4.4
|
26.1
|
1.0
|
OD1
|
A:ASN191
|
4.5
|
45.5
|
1.0
|
CE
|
A:LYS263
|
4.5
|
31.9
|
1.0
|
CA
|
A:NPQ1369
|
4.5
|
39.3
|
1.0
|
OD1
|
A:ASP239
|
4.5
|
31.5
|
1.0
|
CB
|
A:ASP189
|
4.6
|
28.9
|
1.0
|
CE
|
A:LYS161
|
4.7
|
30.6
|
1.0
|
N
|
A:NPQ1369
|
4.7
|
39.9
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 5fjp
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Magnesium Binding Sites List in 5fjp
Magnesium binding site 2 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1370
b:35.4
occ:1.00
|
OD2
|
B:ASP239
|
2.2
|
34.0
|
1.0
|
OE2
|
B:GLU214
|
2.2
|
33.1
|
1.0
|
O
|
B:HOH2056
|
2.2
|
26.3
|
1.0
|
OD2
|
B:ASP189
|
2.4
|
31.5
|
1.0
|
OXT
|
B:NPQ1369
|
2.7
|
40.0
|
1.0
|
O
|
B:NPQ1369
|
2.7
|
34.5
|
1.0
|
CD
|
B:GLU214
|
3.1
|
34.6
|
1.0
|
C
|
B:NPQ1369
|
3.1
|
42.6
|
1.0
|
CG
|
B:ASP239
|
3.3
|
35.5
|
1.0
|
CG
|
B:ASP189
|
3.3
|
29.1
|
1.0
|
OD1
|
B:ASP189
|
3.6
|
31.5
|
1.0
|
CB
|
B:ASP239
|
3.7
|
30.9
|
1.0
|
ND2
|
B:ASN191
|
3.7
|
34.8
|
1.0
|
NZ
|
B:LYS161
|
3.7
|
35.3
|
1.0
|
CG
|
B:GLU214
|
3.8
|
33.6
|
1.0
|
OE1
|
B:GLU214
|
3.8
|
36.6
|
1.0
|
NZ
|
B:LYS263
|
3.9
|
38.9
|
1.0
|
NZ
|
B:LYS163
|
4.1
|
51.5
|
1.0
|
ND2
|
B:ASN261
|
4.1
|
40.0
|
1.0
|
OE1
|
B:GLU240
|
4.2
|
30.5
|
1.0
|
OD1
|
B:ASP239
|
4.4
|
35.6
|
1.0
|
O
|
B:HOH2051
|
4.4
|
32.1
|
1.0
|
CG
|
B:ASN191
|
4.5
|
33.5
|
1.0
|
CE
|
B:LYS263
|
4.6
|
37.8
|
1.0
|
CB
|
B:ASP189
|
4.6
|
28.4
|
1.0
|
OD1
|
B:ASN191
|
4.6
|
32.6
|
1.0
|
CA
|
B:NPQ1369
|
4.7
|
43.7
|
1.0
|
CE
|
B:LYS161
|
4.7
|
33.4
|
1.0
|
N
|
B:NPQ1369
|
4.9
|
43.4
|
1.0
|
CD
|
B:GLU240
|
5.0
|
31.1
|
1.0
|
CB
|
B:GLU214
|
5.0
|
35.8
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 5fjp
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Magnesium Binding Sites List in 5fjp
Magnesium binding site 3 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1369
b:40.2
occ:1.00
|
O
|
C:HOH2037
|
2.1
|
33.2
|
1.0
|
OD2
|
C:ASP239
|
2.2
|
31.0
|
1.0
|
OE2
|
C:GLU214
|
2.3
|
33.8
|
1.0
|
OD2
|
C:ASP189
|
2.4
|
35.1
|
1.0
|
O
|
C:NPQ1368
|
2.6
|
45.0
|
1.0
|
OXT
|
C:NPQ1368
|
3.0
|
56.8
|
1.0
|
CD
|
C:GLU214
|
3.1
|
33.7
|
1.0
|
C
|
C:NPQ1368
|
3.2
|
50.6
|
1.0
|
CG
|
C:ASP239
|
3.3
|
34.0
|
1.0
|
CG
|
C:ASP189
|
3.4
|
34.4
|
1.0
|
ND2
|
C:ASN191
|
3.6
|
48.4
|
1.0
|
OD1
|
C:ASP189
|
3.6
|
38.0
|
1.0
|
CB
|
C:ASP239
|
3.7
|
31.9
|
1.0
|
CG
|
C:GLU214
|
3.8
|
32.0
|
1.0
|
NZ
|
C:LYS161
|
3.8
|
38.9
|
1.0
|
OE1
|
C:GLU214
|
3.9
|
32.0
|
1.0
|
NZ
|
C:LYS263
|
3.9
|
46.0
|
1.0
|
NZ
|
C:LYS163
|
4.1
|
48.5
|
1.0
|
OE1
|
C:GLU240
|
4.2
|
30.1
|
1.0
|
ND2
|
C:ASN261
|
4.2
|
34.9
|
1.0
|
CG
|
C:ASN191
|
4.4
|
48.0
|
1.0
|
OD1
|
C:ASP239
|
4.4
|
27.1
|
1.0
|
OD1
|
C:ASN191
|
4.6
|
44.8
|
1.0
|
CB
|
C:ASP189
|
4.6
|
30.9
|
1.0
|
CE
|
C:LYS263
|
4.7
|
39.8
|
1.0
|
CA
|
C:NPQ1368
|
4.7
|
52.4
|
1.0
|
CE
|
C:LYS161
|
4.8
|
37.6
|
1.0
|
N
|
C:NPQ1368
|
4.9
|
57.1
|
1.0
|
CD
|
C:GLU240
|
4.9
|
30.9
|
1.0
|
OE2
|
C:GLU240
|
5.0
|
32.4
|
1.0
|
CB
|
C:GLU214
|
5.0
|
30.1
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 5fjp
Go back to
Magnesium Binding Sites List in 5fjp
Magnesium binding site 4 out
of 4 in the N-Acyl Amino Acid Racemase From Amycolatopsis Sp Ts-1-60: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine
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: G291D F323Y I293G Mutant in Complex with N-Acetyl Naphthylalanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1369
b:55.6
occ:1.00
|
OE2
|
D:GLU214
|
2.0
|
39.1
|
1.0
|
O
|
D:HOH2031
|
2.2
|
32.9
|
1.0
|
OD2
|
D:ASP239
|
2.3
|
35.0
|
1.0
|
OD2
|
D:ASP189
|
2.4
|
36.0
|
1.0
|
OXT
|
D:NPQ1368
|
2.6
|
50.1
|
1.0
|
O
|
D:NPQ1368
|
2.9
|
50.4
|
1.0
|
CD
|
D:GLU214
|
3.0
|
38.2
|
1.0
|
C
|
D:NPQ1368
|
3.1
|
52.1
|
1.0
|
CG
|
D:ASP189
|
3.3
|
40.8
|
1.0
|
CG
|
D:ASP239
|
3.4
|
38.6
|
1.0
|
OD1
|
D:ASP189
|
3.6
|
44.6
|
1.0
|
NZ
|
D:LYS161
|
3.7
|
44.2
|
1.0
|
OE1
|
D:GLU214
|
3.7
|
32.1
|
1.0
|
CB
|
D:ASP239
|
3.7
|
38.5
|
1.0
|
CG
|
D:GLU214
|
3.8
|
35.8
|
1.0
|
ND2
|
D:ASN191
|
3.8
|
43.0
|
1.0
|
NZ
|
D:LYS263
|
3.9
|
42.9
|
1.0
|
NZ
|
D:LYS163
|
4.1
|
50.5
|
1.0
|
ND2
|
D:ASN261
|
4.1
|
46.2
|
1.0
|
OE1
|
D:GLU240
|
4.3
|
37.6
|
1.0
|
OD1
|
D:ASP239
|
4.5
|
36.5
|
1.0
|
CG
|
D:ASN191
|
4.5
|
46.6
|
1.0
|
CB
|
D:ASP189
|
4.5
|
40.5
|
1.0
|
O
|
D:HOH2028
|
4.6
|
38.0
|
1.0
|
CE
|
D:LYS263
|
4.6
|
38.6
|
1.0
|
CE
|
D:LYS161
|
4.7
|
39.1
|
1.0
|
OD1
|
D:ASN191
|
4.7
|
46.2
|
1.0
|
CA
|
D:NPQ1368
|
4.7
|
53.1
|
1.0
|
CB
|
D:GLU214
|
4.8
|
32.9
|
1.0
|
N
|
D:NPQ1368
|
4.9
|
49.3
|
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
|