Magnesium in PDB 1upc: Carboxyethylarginine Synthase From Streptomyces Clavuligerus
Protein crystallography data
The structure of Carboxyethylarginine Synthase From Streptomyces Clavuligerus, PDB code: 1upc
was solved by
M.E.C.Caines,
J.M.Elkins,
K.S.Hewitson,
C.J.Schofield,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
38.00 /
2.45
|
|
Space group
|
P 21 21 2
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
123.073,
187.196,
198.615,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
17.6 /
21.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
(pdb code 1upc). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Carboxyethylarginine Synthase From Streptomyces Clavuligerus, PDB code: 1upc:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 1 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg601
b:14.7
occ:1.00
|
O3B
|
A:TPP600
|
2.0
|
26.2
|
1.0
|
|
O1A
|
A:TPP600
|
2.1
|
24.2
|
1.0
|
|
O
|
A:HOH2121
|
2.2
|
25.5
|
1.0
|
|
OD1
|
A:ASP463
|
2.2
|
22.6
|
1.0
|
|
O
|
A:THR492
|
2.2
|
28.8
|
1.0
|
|
OD1
|
A:ASN490
|
2.2
|
31.7
|
1.0
|
|
PA
|
A:TPP600
|
3.3
|
23.2
|
1.0
|
|
PB
|
A:TPP600
|
3.3
|
28.6
|
1.0
|
|
CG
|
A:ASP463
|
3.3
|
25.7
|
1.0
|
|
CG
|
A:ASN490
|
3.4
|
31.9
|
1.0
|
|
C
|
A:THR492
|
3.4
|
28.4
|
1.0
|
|
O3A
|
A:TPP600
|
3.6
|
27.8
|
1.0
|
|
OD2
|
A:ASP463
|
3.8
|
25.6
|
1.0
|
|
O7
|
A:TPP600
|
3.8
|
24.8
|
1.0
|
|
N
|
A:THR492
|
4.0
|
29.5
|
1.0
|
|
N
|
A:GLY494
|
4.0
|
26.9
|
1.0
|
|
O1B
|
A:TPP600
|
4.0
|
31.1
|
1.0
|
|
N
|
A:ASP463
|
4.1
|
26.8
|
1.0
|
|
N
|
A:ASN490
|
4.1
|
31.2
|
1.0
|
|
ND2
|
A:ASN490
|
4.1
|
32.9
|
1.0
|
|
CA
|
A:THR492
|
4.2
|
29.1
|
1.0
|
|
O
|
A:VAL488
|
4.3
|
31.0
|
1.0
|
|
N
|
A:GLY464
|
4.3
|
27.0
|
1.0
|
|
N
|
A:ASN493
|
4.4
|
27.8
|
1.0
|
|
O2B
|
A:TPP600
|
4.5
|
27.1
|
1.0
|
|
CB
|
A:ASN490
|
4.5
|
31.2
|
1.0
|
|
CB
|
A:ASP463
|
4.5
|
26.1
|
1.0
|
|
O2A
|
A:TPP600
|
4.6
|
23.9
|
1.0
|
|
CB
|
A:THR492
|
4.6
|
28.9
|
1.0
|
|
CA
|
A:ASN493
|
4.6
|
27.2
|
1.0
|
|
CA
|
A:ASN490
|
4.7
|
31.0
|
1.0
|
|
C
|
A:ASN490
|
4.7
|
31.1
|
1.0
|
|
CA
|
A:GLY494
|
4.7
|
26.7
|
1.0
|
|
CA
|
A:ASP463
|
4.7
|
26.6
|
1.0
|
|
N
|
A:ASP491
|
4.8
|
31.5
|
1.0
|
|
CA
|
A:GLY462
|
4.8
|
27.4
|
1.0
|
|
C
|
A:GLY462
|
4.8
|
27.0
|
1.0
|
|
C
|
A:ASN493
|
4.9
|
26.9
|
1.0
|
|
OH
|
A:TYR561
|
4.9
|
43.7
|
1.0
|
|
CE2
|
A:TYR561
|
5.0
|
45.4
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 2 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg601
b:13.4
occ:1.00
|
O
|
B:HOH2182
|
2.1
|
19.1
|
1.0
|
|
O
|
B:THR492
|
2.1
|
27.7
|
1.0
|
|
OD1
|
B:ASN490
|
2.1
|
32.0
|
1.0
|
|
O3B
|
B:TPP600
|
2.1
|
28.1
|
1.0
|
|
OD1
|
B:ASP463
|
2.3
|
27.0
|
1.0
|
|
O1A
|
B:TPP600
|
2.3
|
27.0
|
1.0
|
|
CG
|
B:ASP463
|
3.3
|
26.9
|
1.0
|
|
C
|
B:THR492
|
3.3
|
28.4
|
1.0
|
|
CG
|
B:ASN490
|
3.4
|
31.9
|
1.0
|
|
PB
|
B:TPP600
|
3.4
|
29.8
|
1.0
|
|
PA
|
B:TPP600
|
3.5
|
25.7
|
1.0
|
|
OD2
|
B:ASP463
|
3.8
|
26.3
|
1.0
|
|
O3A
|
B:TPP600
|
3.8
|
28.7
|
1.0
|
|
N
|
B:THR492
|
3.9
|
30.1
|
1.0
|
|
O7
|
B:TPP600
|
4.0
|
24.7
|
1.0
|
|
N
|
B:GLY494
|
4.0
|
26.9
|
1.0
|
|
N
|
B:ASP463
|
4.0
|
27.2
|
1.0
|
|
CA
|
B:THR492
|
4.1
|
29.3
|
1.0
|
|
ND2
|
B:ASN490
|
4.1
|
32.5
|
1.0
|
|
O1B
|
B:TPP600
|
4.1
|
29.5
|
1.0
|
|
N
|
B:ASN490
|
4.1
|
31.0
|
1.0
|
|
N
|
B:GLY464
|
4.3
|
27.0
|
1.0
|
|
N
|
B:ASN493
|
4.4
|
27.2
|
1.0
|
|
O
|
B:VAL488
|
4.5
|
30.3
|
1.0
|
|
CB
|
B:THR492
|
4.5
|
29.2
|
1.0
|
|
CB
|
B:ASN490
|
4.5
|
31.2
|
1.0
|
|
CB
|
B:ASP463
|
4.5
|
26.6
|
1.0
|
|
O2B
|
B:TPP600
|
4.5
|
28.0
|
1.0
|
|
CA
|
B:ASN493
|
4.6
|
26.8
|
1.0
|
|
CA
|
B:ASN490
|
4.6
|
30.9
|
1.0
|
|
CA
|
B:GLY494
|
4.7
|
27.3
|
1.0
|
|
N
|
B:ASP491
|
4.7
|
31.6
|
1.0
|
|
C
|
B:ASN490
|
4.7
|
30.9
|
1.0
|
|
OH
|
B:TYR561
|
4.7
|
42.6
|
1.0
|
|
CA
|
B:ASP463
|
4.7
|
27.1
|
1.0
|
|
O2A
|
B:TPP600
|
4.8
|
25.8
|
1.0
|
|
C
|
B:GLY462
|
4.8
|
26.8
|
1.0
|
|
C
|
B:ASN493
|
4.8
|
26.3
|
1.0
|
|
CE2
|
B:TYR561
|
4.9
|
43.8
|
1.0
|
|
CA
|
B:GLY462
|
4.9
|
26.8
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 3 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg601
b:12.7
occ:1.00
|
O3B
|
C:TPP600
|
2.1
|
27.5
|
1.0
|
|
OD1
|
C:ASP463
|
2.1
|
24.8
|
1.0
|
|
O
|
C:HOH2105
|
2.2
|
25.6
|
1.0
|
|
O
|
C:THR492
|
2.2
|
29.5
|
1.0
|
|
OD1
|
C:ASN490
|
2.2
|
32.9
|
1.0
|
|
O1A
|
C:TPP600
|
2.4
|
25.7
|
1.0
|
|
CG
|
C:ASP463
|
3.3
|
27.2
|
1.0
|
|
PB
|
C:TPP600
|
3.3
|
28.8
|
1.0
|
|
PA
|
C:TPP600
|
3.4
|
26.2
|
1.0
|
|
C
|
C:THR492
|
3.4
|
29.5
|
1.0
|
|
CG
|
C:ASN490
|
3.4
|
32.0
|
1.0
|
|
O3A
|
C:TPP600
|
3.6
|
28.6
|
1.0
|
|
OD2
|
C:ASP463
|
3.8
|
24.6
|
1.0
|
|
O7
|
C:TPP600
|
3.9
|
27.2
|
1.0
|
|
N
|
C:GLY494
|
4.0
|
26.8
|
1.0
|
|
N
|
C:ASP463
|
4.0
|
27.6
|
1.0
|
|
N
|
C:THR492
|
4.0
|
30.4
|
1.0
|
|
O1B
|
C:TPP600
|
4.1
|
31.3
|
1.0
|
|
N
|
C:ASN490
|
4.1
|
31.7
|
1.0
|
|
CA
|
C:THR492
|
4.2
|
29.9
|
1.0
|
|
ND2
|
C:ASN490
|
4.2
|
29.9
|
1.0
|
|
N
|
C:GLY464
|
4.4
|
27.5
|
1.0
|
|
CB
|
C:ASN490
|
4.4
|
32.0
|
1.0
|
|
N
|
C:ASN493
|
4.4
|
29.1
|
1.0
|
|
O
|
C:VAL488
|
4.4
|
30.7
|
1.0
|
|
CB
|
C:ASP463
|
4.5
|
27.1
|
1.0
|
|
O2B
|
C:TPP600
|
4.5
|
25.4
|
1.0
|
|
CB
|
C:THR492
|
4.6
|
30.1
|
1.0
|
|
CA
|
C:ASN493
|
4.6
|
27.9
|
1.0
|
|
OH
|
C:TYR561
|
4.6
|
42.5
|
1.0
|
|
CA
|
C:ASN490
|
4.6
|
31.6
|
1.0
|
|
CA
|
C:GLY494
|
4.6
|
26.4
|
1.0
|
|
CA
|
C:ASP463
|
4.7
|
27.7
|
1.0
|
|
C
|
C:ASN490
|
4.7
|
31.9
|
1.0
|
|
O2A
|
C:TPP600
|
4.7
|
27.4
|
1.0
|
|
CE2
|
C:TYR561
|
4.8
|
43.7
|
1.0
|
|
C
|
C:ASN493
|
4.8
|
27.5
|
1.0
|
|
N
|
C:ASP491
|
4.8
|
32.0
|
1.0
|
|
C
|
C:GLY462
|
4.9
|
28.2
|
1.0
|
|
CA
|
C:GLY462
|
4.9
|
28.3
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 4 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg601
b:15.5
occ:1.00
|
O
|
D:THR492
|
2.1
|
28.8
|
1.0
|
|
O
|
D:HOH2144
|
2.1
|
23.0
|
1.0
|
|
O3B
|
D:TPP600
|
2.1
|
29.3
|
1.0
|
|
O1A
|
D:TPP600
|
2.2
|
27.9
|
1.0
|
|
OD1
|
D:ASN490
|
2.3
|
32.1
|
1.0
|
|
OD1
|
D:ASP463
|
2.3
|
25.0
|
1.0
|
|
C
|
D:THR492
|
3.3
|
29.1
|
1.0
|
|
PA
|
D:TPP600
|
3.3
|
25.8
|
1.0
|
|
PB
|
D:TPP600
|
3.4
|
30.5
|
1.0
|
|
CG
|
D:ASP463
|
3.4
|
27.3
|
1.0
|
|
CG
|
D:ASN490
|
3.4
|
31.3
|
1.0
|
|
O3A
|
D:TPP600
|
3.6
|
28.4
|
1.0
|
|
O7
|
D:TPP600
|
3.7
|
26.4
|
1.0
|
|
OD2
|
D:ASP463
|
3.8
|
25.5
|
1.0
|
|
N
|
D:THR492
|
4.0
|
31.0
|
1.0
|
|
N
|
D:GLY494
|
4.0
|
27.2
|
1.0
|
|
CA
|
D:THR492
|
4.1
|
29.9
|
1.0
|
|
O1B
|
D:TPP600
|
4.1
|
27.9
|
1.0
|
|
N
|
D:ASP463
|
4.1
|
27.9
|
1.0
|
|
ND2
|
D:ASN490
|
4.3
|
28.4
|
1.0
|
|
N
|
D:ASN493
|
4.3
|
28.4
|
1.0
|
|
N
|
D:ASN490
|
4.3
|
31.9
|
1.0
|
|
N
|
D:GLY464
|
4.3
|
27.9
|
1.0
|
|
CB
|
D:ASN490
|
4.4
|
31.9
|
1.0
|
|
O2B
|
D:TPP600
|
4.4
|
28.2
|
1.0
|
|
CB
|
D:THR492
|
4.5
|
30.2
|
1.0
|
|
CA
|
D:ASN493
|
4.5
|
27.5
|
1.0
|
|
O
|
D:VAL488
|
4.6
|
31.4
|
1.0
|
|
CB
|
D:ASP463
|
4.6
|
27.2
|
1.0
|
|
O2A
|
D:TPP600
|
4.6
|
27.8
|
1.0
|
|
CA
|
D:GLY494
|
4.7
|
27.1
|
1.0
|
|
CA
|
D:ASN490
|
4.7
|
31.7
|
1.0
|
|
C
|
D:ASN490
|
4.7
|
31.9
|
1.0
|
|
CA
|
D:ASP463
|
4.8
|
27.5
|
1.0
|
|
N
|
D:ASP491
|
4.8
|
32.0
|
1.0
|
|
C
|
D:ASN493
|
4.8
|
27.2
|
1.0
|
|
CE2
|
D:TYR561
|
4.9
|
44.5
|
1.0
|
|
CA
|
D:GLY462
|
4.9
|
27.6
|
1.0
|
|
C
|
D:GLY462
|
4.9
|
27.8
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 5 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Mg601
b:17.4
occ:1.00
|
O
|
E:HOH2110
|
2.0
|
25.3
|
1.0
|
|
OD1
|
E:ASN490
|
2.0
|
34.1
|
1.0
|
|
O
|
E:THR492
|
2.1
|
28.4
|
1.0
|
|
O3B
|
E:TPP600
|
2.2
|
28.5
|
1.0
|
|
O1A
|
E:TPP600
|
2.2
|
26.9
|
1.0
|
|
OD1
|
E:ASP463
|
2.3
|
26.9
|
1.0
|
|
CG
|
E:ASN490
|
3.3
|
33.8
|
1.0
|
|
PB
|
E:TPP600
|
3.3
|
31.1
|
1.0
|
|
CG
|
E:ASP463
|
3.3
|
27.7
|
1.0
|
|
C
|
E:THR492
|
3.4
|
29.4
|
1.0
|
|
PA
|
E:TPP600
|
3.4
|
27.2
|
1.0
|
|
O3A
|
E:TPP600
|
3.6
|
30.7
|
1.0
|
|
OD2
|
E:ASP463
|
3.8
|
28.0
|
1.0
|
|
O7
|
E:TPP600
|
3.9
|
28.2
|
1.0
|
|
N
|
E:THR492
|
4.0
|
31.0
|
1.0
|
|
N
|
E:GLY494
|
4.0
|
28.4
|
1.0
|
|
ND2
|
E:ASN490
|
4.0
|
34.8
|
1.0
|
|
O1B
|
E:TPP600
|
4.1
|
31.2
|
1.0
|
|
N
|
E:ASP463
|
4.1
|
29.1
|
1.0
|
|
N
|
E:ASN490
|
4.1
|
32.4
|
1.0
|
|
CA
|
E:THR492
|
4.2
|
30.2
|
1.0
|
|
N
|
E:GLY464
|
4.3
|
29.1
|
1.0
|
|
CB
|
E:ASN490
|
4.4
|
32.4
|
1.0
|
|
N
|
E:ASN493
|
4.4
|
28.6
|
1.0
|
|
O2B
|
E:TPP600
|
4.5
|
30.5
|
1.0
|
|
O
|
E:VAL488
|
4.5
|
32.5
|
1.0
|
|
CB
|
E:ASP463
|
4.5
|
28.6
|
1.0
|
|
CA
|
E:ASN490
|
4.6
|
31.9
|
1.0
|
|
CA
|
E:ASN493
|
4.6
|
28.3
|
1.0
|
|
CB
|
E:THR492
|
4.6
|
30.3
|
1.0
|
|
O2A
|
E:TPP600
|
4.7
|
28.8
|
1.0
|
|
CA
|
E:ASP463
|
4.7
|
28.9
|
1.0
|
|
CA
|
E:GLY494
|
4.7
|
28.5
|
1.0
|
|
C
|
E:ASN490
|
4.7
|
31.8
|
1.0
|
|
N
|
E:ASP491
|
4.8
|
31.8
|
1.0
|
|
CA
|
E:GLY462
|
4.8
|
28.6
|
1.0
|
|
C
|
E:GLY462
|
4.8
|
29.0
|
1.0
|
|
C
|
E:ASN493
|
4.9
|
28.2
|
1.0
|
|
CE2
|
E:TYR561
|
4.9
|
45.6
|
1.0
|
|
OH
|
E:TYR561
|
5.0
|
44.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 1upc
Go back to
Magnesium Binding Sites List in 1upc
Magnesium binding site 6 out
of 6 in the Carboxyethylarginine Synthase From Streptomyces Clavuligerus
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Carboxyethylarginine Synthase From Streptomyces Clavuligerus within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg601
b:15.5
occ:1.00
|
O
|
F:HOH2126
|
2.0
|
25.0
|
1.0
|
|
OD1
|
F:ASN490
|
2.1
|
33.3
|
1.0
|
|
O1A
|
F:TPP600
|
2.2
|
27.0
|
1.0
|
|
O
|
F:THR492
|
2.2
|
28.6
|
1.0
|
|
O3B
|
F:TPP600
|
2.3
|
27.8
|
1.0
|
|
OD1
|
F:ASP463
|
2.3
|
25.7
|
1.0
|
|
CG
|
F:ASN490
|
3.3
|
32.7
|
1.0
|
|
PA
|
F:TPP600
|
3.3
|
25.8
|
1.0
|
|
CG
|
F:ASP463
|
3.4
|
27.2
|
1.0
|
|
PB
|
F:TPP600
|
3.4
|
29.6
|
1.0
|
|
C
|
F:THR492
|
3.5
|
28.4
|
1.0
|
|
O3A
|
F:TPP600
|
3.6
|
27.9
|
1.0
|
|
O7
|
F:TPP600
|
3.8
|
25.9
|
1.0
|
|
OD2
|
F:ASP463
|
3.9
|
24.9
|
1.0
|
|
N
|
F:ASP463
|
4.0
|
28.0
|
1.0
|
|
ND2
|
F:ASN490
|
4.1
|
33.4
|
1.0
|
|
N
|
F:THR492
|
4.1
|
29.4
|
1.0
|
|
N
|
F:GLY494
|
4.1
|
27.9
|
1.0
|
|
N
|
F:ASN490
|
4.1
|
31.9
|
1.0
|
|
O1B
|
F:TPP600
|
4.3
|
28.4
|
1.0
|
|
CA
|
F:THR492
|
4.3
|
29.2
|
1.0
|
|
N
|
F:GLY464
|
4.3
|
28.7
|
1.0
|
|
O
|
F:VAL488
|
4.5
|
30.7
|
1.0
|
|
CB
|
F:ASN490
|
4.5
|
31.8
|
1.0
|
|
N
|
F:ASN493
|
4.5
|
27.6
|
1.0
|
|
CB
|
F:ASP463
|
4.5
|
28.0
|
1.0
|
|
O2B
|
F:TPP600
|
4.5
|
28.0
|
1.0
|
|
O2A
|
F:TPP600
|
4.6
|
24.3
|
1.0
|
|
CA
|
F:ASN490
|
4.6
|
31.3
|
1.0
|
|
CA
|
F:ASN493
|
4.7
|
27.1
|
1.0
|
|
CA
|
F:ASP463
|
4.7
|
28.2
|
1.0
|
|
CB
|
F:THR492
|
4.8
|
29.3
|
1.0
|
|
C
|
F:ASN490
|
4.8
|
30.8
|
1.0
|
|
N
|
F:ASP491
|
4.8
|
30.8
|
1.0
|
|
C
|
F:GLY462
|
4.8
|
27.5
|
1.0
|
|
CA
|
F:GLY494
|
4.8
|
27.6
|
1.0
|
|
CA
|
F:GLY462
|
4.8
|
27.7
|
1.0
|
|
C
|
F:ASN493
|
4.9
|
27.2
|
1.0
|
|
CE2
|
F:TYR561
|
4.9
|
44.4
|
1.0
|
|
OH
|
F:TYR561
|
4.9
|
42.7
|
1.0
|
|
Reference:
M.E.C.Caines,
J.M.Elkins,
K.S.Hewitson,
C.J.Schofield.
Crystal Structure and Mechanistic Implications of N2-(2-Carboxyethyl)Arginine Synthase, the First Enzyme in the Clavulanic Acid Biosynthesis Pathway J.Biol.Chem. V. 279 5685 2004.
ISSN: ISSN 0021-9258
PubMed: 14623876
DOI: 10.1074/JBC.M310803200
Page generated: Tue Aug 13 14:53:40 2024
|
