Magnesium in PDB 6jil: Crystal Structure of D-Cycloserine Synthetase Dcsg
Enzymatic activity of Crystal Structure of D-Cycloserine Synthetase Dcsg
All present enzymatic activity of Crystal Structure of D-Cycloserine Synthetase Dcsg:
6.3.3.5;
Protein crystallography data
The structure of Crystal Structure of D-Cycloserine Synthetase Dcsg, PDB code: 6jil
was solved by
Y.Matoba,
M.Sugiyama,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
29.76 /
2.32
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
56.450,
120.730,
102.810,
90.00,
101.01,
90.00
|
|
R / Rfree (%)
|
19.5 /
25.1
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of D-Cycloserine Synthetase Dcsg
(pdb code 6jil). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the
Crystal Structure of D-Cycloserine Synthetase Dcsg, PDB code: 6jil:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Magnesium binding site 1 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 1 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg404
b:22.3
occ:1.00
|
O2A
|
A:ADP403
|
2.2
|
18.5
|
1.0
|
|
OE2
|
A:GLU269
|
2.2
|
17.9
|
1.0
|
|
O1
|
A:TLA402
|
2.3
|
26.9
|
1.0
|
|
O
|
A:HOH501
|
2.3
|
24.2
|
1.0
|
|
O1B
|
A:ADP403
|
2.4
|
15.6
|
1.0
|
|
O
|
A:HOH527
|
2.4
|
33.0
|
1.0
|
|
CD
|
A:GLU269
|
3.3
|
18.5
|
1.0
|
|
C1
|
A:TLA402
|
3.4
|
27.9
|
1.0
|
|
NZ
|
A:LYS202
|
3.7
|
19.3
|
1.0
|
|
PA
|
A:ADP403
|
3.7
|
15.4
|
1.0
|
|
PB
|
A:ADP403
|
3.7
|
15.1
|
1.0
|
|
OD2
|
A:ASP256
|
3.8
|
23.8
|
1.0
|
|
O3'
|
A:ADP403
|
3.8
|
20.9
|
1.0
|
|
CG
|
A:GLU269
|
3.8
|
18.3
|
1.0
|
|
MG
|
A:MG405
|
3.9
|
20.4
|
1.0
|
|
O
|
A:HOH554
|
4.0
|
9.3
|
1.0
|
|
O11
|
A:TLA402
|
4.1
|
25.1
|
1.0
|
|
OE1
|
A:GLU186
|
4.1
|
19.5
|
1.0
|
|
O2B
|
A:ADP403
|
4.1
|
16.2
|
1.0
|
|
C5'
|
A:ADP403
|
4.2
|
15.7
|
1.0
|
|
NH2
|
A:ARG254
|
4.3
|
23.5
|
1.0
|
|
O3A
|
A:ADP403
|
4.3
|
18.3
|
1.0
|
|
C3'
|
A:ADP403
|
4.4
|
17.9
|
1.0
|
|
OE1
|
A:GLU269
|
4.4
|
17.8
|
1.0
|
|
C2
|
A:TLA402
|
4.4
|
28.4
|
1.0
|
|
O5'
|
A:ADP403
|
4.6
|
19.4
|
1.0
|
|
O1A
|
A:ADP403
|
4.6
|
18.2
|
1.0
|
|
OE2
|
A:GLU271
|
4.6
|
23.1
|
1.0
|
|
CD1
|
A:LEU268
|
4.7
|
15.7
|
1.0
|
|
CG
|
A:ASP256
|
4.7
|
23.4
|
1.0
|
|
C4'
|
A:ADP403
|
4.9
|
17.9
|
1.0
|
|
O3B
|
A:ADP403
|
4.9
|
14.5
|
1.0
|
|
CE
|
A:LYS202
|
5.0
|
22.6
|
1.0
|
|
CD
|
A:GLU186
|
5.0
|
20.9
|
1.0
|
|
OE2
|
A:GLU186
|
5.0
|
22.1
|
1.0
|
|
Magnesium binding site 2 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 2 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg405
b:20.4
occ:1.00
|
OE2
|
A:GLU271
|
2.2
|
23.1
|
1.0
|
|
O11
|
A:TLA402
|
2.2
|
25.1
|
1.0
|
|
OE2
|
A:GLU269
|
2.3
|
17.9
|
1.0
|
|
O
|
A:HOH526
|
2.3
|
13.5
|
1.0
|
|
O2B
|
A:ADP403
|
2.3
|
16.2
|
1.0
|
|
OE1
|
A:GLU269
|
2.3
|
17.8
|
1.0
|
|
CD
|
A:GLU269
|
2.6
|
18.5
|
1.0
|
|
O1
|
A:TLA402
|
2.9
|
26.9
|
1.0
|
|
C1
|
A:TLA402
|
2.9
|
27.9
|
1.0
|
|
CD
|
A:GLU271
|
3.1
|
22.8
|
1.0
|
|
PB
|
A:ADP403
|
3.5
|
15.1
|
1.0
|
|
O1B
|
A:ADP403
|
3.5
|
15.6
|
1.0
|
|
CG
|
A:GLU271
|
3.8
|
22.7
|
1.0
|
|
MG
|
A:MG404
|
3.9
|
22.3
|
1.0
|
|
O
|
A:HOH636
|
4.0
|
25.1
|
1.0
|
|
OE1
|
A:GLU271
|
4.0
|
24.6
|
1.0
|
|
O
|
A:HOH523
|
4.1
|
27.2
|
1.0
|
|
CG
|
A:GLU269
|
4.1
|
18.3
|
1.0
|
|
NZ
|
A:LYS92
|
4.1
|
15.1
|
1.0
|
|
CB
|
A:CYS142
|
4.2
|
20.0
|
1.0
|
|
CA
|
A:CYS142
|
4.2
|
19.3
|
1.0
|
|
C2
|
A:TLA402
|
4.3
|
28.4
|
1.0
|
|
NH2
|
A:ARG254
|
4.3
|
23.5
|
1.0
|
|
O3B
|
A:ADP403
|
4.4
|
14.5
|
1.0
|
|
O
|
A:GLY141
|
4.5
|
19.1
|
1.0
|
|
O3A
|
A:ADP403
|
4.6
|
18.3
|
1.0
|
|
O2A
|
A:ADP403
|
4.6
|
18.5
|
1.0
|
|
C3
|
A:TLA402
|
4.7
|
31.3
|
1.0
|
|
N
|
A:TYR143
|
4.7
|
18.6
|
1.0
|
|
O
|
A:HOH510
|
4.7
|
13.8
|
1.0
|
|
O2
|
A:TLA402
|
4.8
|
24.7
|
1.0
|
|
O3
|
A:TLA402
|
4.9
|
31.9
|
1.0
|
|
CB
|
A:GLU269
|
5.0
|
18.7
|
1.0
|
|
Magnesium binding site 3 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 3 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg405
b:19.4
occ:1.00
|
O2A
|
B:ADP404
|
2.2
|
16.1
|
1.0
|
|
OE2
|
B:GLU269
|
2.2
|
19.8
|
1.0
|
|
O1
|
B:TLA403
|
2.3
|
27.4
|
1.0
|
|
O1B
|
B:ADP404
|
2.3
|
14.1
|
1.0
|
|
O
|
B:HOH512
|
2.3
|
11.9
|
1.0
|
|
O
|
B:HOH504
|
2.4
|
23.8
|
1.0
|
|
CD
|
B:GLU269
|
3.3
|
20.1
|
1.0
|
|
C1
|
B:TLA403
|
3.4
|
31.2
|
1.0
|
|
OD2
|
B:ASP256
|
3.6
|
22.9
|
1.0
|
|
NZ
|
B:LYS202
|
3.7
|
20.2
|
1.0
|
|
PA
|
B:ADP404
|
3.7
|
13.4
|
1.0
|
|
PB
|
B:ADP404
|
3.7
|
13.6
|
1.0
|
|
CG
|
B:GLU269
|
3.8
|
15.7
|
1.0
|
|
O3'
|
B:ADP404
|
3.9
|
13.7
|
1.0
|
|
O
|
B:HOH580
|
4.0
|
24.3
|
1.0
|
|
NH2
|
B:ARG254
|
4.0
|
22.7
|
1.0
|
|
O11
|
B:TLA403
|
4.0
|
26.9
|
1.0
|
|
MG
|
B:MG406
|
4.1
|
24.5
|
1.0
|
|
C5'
|
B:ADP404
|
4.2
|
13.8
|
1.0
|
|
O2B
|
B:ADP404
|
4.3
|
15.9
|
1.0
|
|
O3A
|
B:ADP404
|
4.3
|
16.6
|
1.0
|
|
OE1
|
B:GLU269
|
4.4
|
21.6
|
1.0
|
|
CD1
|
B:LEU268
|
4.4
|
15.1
|
1.0
|
|
C3'
|
B:ADP404
|
4.4
|
14.4
|
1.0
|
|
OE2
|
B:GLU186
|
4.4
|
22.4
|
1.0
|
|
CE
|
B:LYS202
|
4.5
|
19.1
|
1.0
|
|
O5'
|
B:ADP404
|
4.6
|
15.7
|
1.0
|
|
C2
|
B:TLA403
|
4.6
|
33.3
|
1.0
|
|
O1A
|
B:ADP404
|
4.6
|
19.4
|
1.0
|
|
OE1
|
B:GLU186
|
4.7
|
23.9
|
1.0
|
|
CG
|
B:ASP256
|
4.8
|
21.9
|
1.0
|
|
O3B
|
B:ADP404
|
4.9
|
15.5
|
1.0
|
|
C4'
|
B:ADP404
|
4.9
|
13.4
|
1.0
|
|
CB
|
B:GLU269
|
4.9
|
13.8
|
1.0
|
|
OE2
|
B:GLU271
|
5.0
|
21.6
|
1.0
|
|
Magnesium binding site 4 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 4 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg406
b:24.5
occ:1.00
|
O11
|
B:TLA403
|
2.3
|
26.9
|
1.0
|
|
OE1
|
B:GLU269
|
2.3
|
21.6
|
1.0
|
|
OE2
|
B:GLU269
|
2.3
|
19.8
|
1.0
|
|
OE2
|
B:GLU271
|
2.3
|
21.6
|
1.0
|
|
O
|
B:HOH521
|
2.4
|
23.7
|
1.0
|
|
O2B
|
B:ADP404
|
2.5
|
15.9
|
1.0
|
|
CD
|
B:GLU269
|
2.6
|
20.1
|
1.0
|
|
C1
|
B:TLA403
|
3.2
|
31.2
|
1.0
|
|
CD
|
B:GLU271
|
3.3
|
23.0
|
1.0
|
|
O1
|
B:TLA403
|
3.4
|
27.4
|
1.0
|
|
PB
|
B:ADP404
|
3.6
|
13.6
|
1.0
|
|
O
|
B:HOH501
|
3.6
|
17.8
|
1.0
|
|
O1B
|
B:ADP404
|
3.6
|
14.1
|
1.0
|
|
CG
|
B:GLU271
|
3.7
|
22.7
|
1.0
|
|
NZ
|
B:LYS92
|
3.9
|
12.8
|
1.0
|
|
MG
|
B:MG405
|
4.1
|
19.4
|
1.0
|
|
CG
|
B:GLU269
|
4.2
|
15.7
|
1.0
|
|
CB
|
B:CYS142
|
4.2
|
16.0
|
1.0
|
|
O
|
B:HOH616
|
4.2
|
18.3
|
1.0
|
|
CA
|
B:CYS142
|
4.3
|
16.7
|
1.0
|
|
NH2
|
B:ARG254
|
4.3
|
22.7
|
1.0
|
|
OE1
|
B:GLU271
|
4.4
|
24.7
|
1.0
|
|
C2
|
B:TLA403
|
4.5
|
33.3
|
1.0
|
|
O
|
B:GLY141
|
4.5
|
16.7
|
1.0
|
|
O3A
|
B:ADP404
|
4.6
|
16.6
|
1.0
|
|
O
|
B:HOH540
|
4.7
|
27.7
|
1.0
|
|
O3B
|
B:ADP404
|
4.7
|
15.5
|
1.0
|
|
O2A
|
B:ADP404
|
4.8
|
16.1
|
1.0
|
|
O2
|
B:TLA403
|
4.8
|
34.5
|
1.0
|
|
C3
|
B:TLA403
|
4.9
|
34.9
|
1.0
|
|
CE
|
B:LYS92
|
4.9
|
10.8
|
1.0
|
|
N
|
B:TYR143
|
4.9
|
14.5
|
1.0
|
|
O3
|
B:TLA403
|
4.9
|
34.0
|
1.0
|
|
O
|
B:HOH556
|
4.9
|
18.1
|
1.0
|
|
CB
|
B:GLU269
|
5.0
|
13.8
|
1.0
|
|
Magnesium binding site 5 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 5 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg405
b:29.4
occ:1.00
|
O2A
|
C:ADP404
|
2.2
|
24.6
|
1.0
|
|
O1
|
C:TLA403
|
2.3
|
34.0
|
1.0
|
|
O3B
|
C:ADP404
|
2.3
|
22.0
|
1.0
|
|
O
|
C:HOH501
|
2.4
|
22.4
|
1.0
|
|
OE2
|
C:GLU269
|
2.4
|
20.8
|
1.0
|
|
O
|
C:HOH570
|
2.5
|
63.1
|
1.0
|
|
C1
|
C:TLA403
|
3.3
|
36.3
|
1.0
|
|
NZ
|
C:LYS202
|
3.4
|
20.4
|
1.0
|
|
O3'
|
C:ADP404
|
3.4
|
22.7
|
1.0
|
|
O
|
C:HOH548
|
3.5
|
19.0
|
1.0
|
|
CD
|
C:GLU269
|
3.6
|
19.6
|
1.0
|
|
PA
|
C:ADP404
|
3.6
|
21.6
|
1.0
|
|
PB
|
C:ADP404
|
3.7
|
21.2
|
1.0
|
|
C5'
|
C:ADP404
|
3.8
|
20.4
|
1.0
|
|
O11
|
C:TLA403
|
3.9
|
33.5
|
1.0
|
|
C3'
|
C:ADP404
|
4.1
|
23.2
|
1.0
|
|
OE1
|
C:GLU186
|
4.2
|
29.7
|
1.0
|
|
MG
|
C:MG406
|
4.2
|
28.7
|
1.0
|
|
O1B
|
C:ADP404
|
4.2
|
19.4
|
1.0
|
|
O5'
|
C:ADP404
|
4.3
|
21.9
|
1.0
|
|
CG
|
C:GLU269
|
4.3
|
21.6
|
1.0
|
|
O3A
|
C:ADP404
|
4.3
|
25.2
|
1.0
|
|
OD2
|
C:ASP256
|
4.4
|
25.3
|
1.0
|
|
C4'
|
C:ADP404
|
4.4
|
23.5
|
1.0
|
|
C2
|
C:TLA403
|
4.4
|
37.9
|
1.0
|
|
OE2
|
C:GLU186
|
4.5
|
32.1
|
1.0
|
|
CE
|
C:LYS202
|
4.6
|
22.5
|
1.0
|
|
OE1
|
C:GLU269
|
4.6
|
20.3
|
1.0
|
|
NH2
|
C:ARG254
|
4.7
|
25.1
|
1.0
|
|
O1A
|
C:ADP404
|
4.7
|
27.0
|
1.0
|
|
CD
|
C:LYS202
|
4.7
|
21.3
|
1.0
|
|
CD1
|
C:LEU268
|
4.7
|
15.9
|
1.0
|
|
CD
|
C:GLU186
|
4.8
|
30.5
|
1.0
|
|
O2B
|
C:ADP404
|
4.9
|
21.5
|
1.0
|
|
C3
|
C:TLA403
|
5.0
|
40.8
|
1.0
|
|
Magnesium binding site 6 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 6 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg406
b:28.7
occ:1.00
|
OE1
|
C:GLU269
|
2.2
|
20.3
|
1.0
|
|
OE2
|
C:GLU271
|
2.2
|
32.5
|
1.0
|
|
O11
|
C:TLA403
|
2.3
|
33.5
|
1.0
|
|
OE2
|
C:GLU269
|
2.4
|
20.8
|
1.0
|
|
O1B
|
C:ADP404
|
2.4
|
19.4
|
1.0
|
|
O
|
C:HOH562
|
2.4
|
17.2
|
1.0
|
|
CD
|
C:GLU269
|
2.6
|
19.6
|
1.0
|
|
C1
|
C:TLA403
|
2.9
|
36.3
|
1.0
|
|
O1
|
C:TLA403
|
2.9
|
34.0
|
1.0
|
|
CD
|
C:GLU271
|
3.1
|
32.1
|
1.0
|
|
PB
|
C:ADP404
|
3.6
|
21.2
|
1.0
|
|
O3B
|
C:ADP404
|
3.6
|
22.0
|
1.0
|
|
CG
|
C:GLU271
|
3.6
|
30.7
|
1.0
|
|
NH2
|
C:ARG254
|
4.0
|
25.1
|
1.0
|
|
CG
|
C:GLU269
|
4.0
|
21.6
|
1.0
|
|
OE1
|
C:GLU271
|
4.1
|
33.4
|
1.0
|
|
C2
|
C:TLA403
|
4.1
|
37.9
|
1.0
|
|
O
|
C:HOH538
|
4.1
|
15.6
|
1.0
|
|
MG
|
C:MG405
|
4.2
|
29.4
|
1.0
|
|
CB
|
C:CYS142
|
4.3
|
20.1
|
1.0
|
|
CA
|
C:CYS142
|
4.4
|
20.4
|
1.0
|
|
C3
|
C:TLA403
|
4.4
|
40.8
|
1.0
|
|
O2B
|
C:ADP404
|
4.5
|
21.5
|
1.0
|
|
O2A
|
C:ADP404
|
4.5
|
24.6
|
1.0
|
|
O3
|
C:TLA403
|
4.5
|
39.6
|
1.0
|
|
O2
|
C:TLA403
|
4.5
|
35.9
|
1.0
|
|
NZ
|
C:LYS92
|
4.7
|
18.4
|
1.0
|
|
N
|
C:TYR143
|
4.7
|
19.9
|
1.0
|
|
O3A
|
C:ADP404
|
4.7
|
25.2
|
1.0
|
|
O
|
C:HOH504
|
4.7
|
24.0
|
1.0
|
|
O
|
C:GLY141
|
4.8
|
23.5
|
1.0
|
|
CE
|
C:LYS92
|
4.9
|
17.7
|
1.0
|
|
CB
|
C:GLU269
|
5.0
|
21.4
|
1.0
|
|
Magnesium binding site 7 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 7 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg404
b:22.3
occ:1.00
|
OE2
|
D:GLU269
|
2.2
|
26.3
|
1.0
|
|
O
|
D:HOH502
|
2.2
|
16.5
|
1.0
|
|
O11
|
D:TLA402
|
2.3
|
33.6
|
1.0
|
|
O3B
|
D:ADP403
|
2.3
|
16.7
|
1.0
|
|
O2A
|
D:ADP403
|
2.3
|
18.1
|
1.0
|
|
O
|
D:HOH505
|
2.4
|
14.3
|
1.0
|
|
C1
|
D:TLA402
|
3.1
|
40.3
|
1.0
|
|
O1
|
D:TLA402
|
3.2
|
37.0
|
1.0
|
|
CD
|
D:GLU269
|
3.4
|
26.4
|
1.0
|
|
NZ
|
D:LYS202
|
3.5
|
17.5
|
1.0
|
|
OD2
|
D:ASP256
|
3.6
|
27.5
|
1.0
|
|
PB
|
D:ADP403
|
3.7
|
17.0
|
1.0
|
|
O
|
D:HOH542
|
3.8
|
17.2
|
1.0
|
|
PA
|
D:ADP403
|
3.8
|
12.9
|
1.0
|
|
OE1
|
D:GLU269
|
3.9
|
31.5
|
1.0
|
|
NH2
|
D:ARG254
|
3.9
|
29.3
|
1.0
|
|
O2B
|
D:ADP403
|
4.1
|
14.9
|
1.0
|
|
O3'
|
D:ADP403
|
4.2
|
16.2
|
1.0
|
|
O3A
|
D:ADP403
|
4.4
|
18.1
|
1.0
|
|
C5'
|
D:ADP403
|
4.4
|
15.3
|
1.0
|
|
C2
|
D:TLA402
|
4.5
|
42.0
|
1.0
|
|
CG
|
D:GLU269
|
4.6
|
25.0
|
1.0
|
|
CB
|
D:GLU269
|
4.6
|
19.4
|
1.0
|
|
O1A
|
D:ADP403
|
4.7
|
18.8
|
1.0
|
|
CG
|
D:ASP256
|
4.7
|
25.4
|
1.0
|
|
OE1
|
D:GLU186
|
4.8
|
25.2
|
1.0
|
|
O5'
|
D:ADP403
|
4.8
|
17.4
|
1.0
|
|
C3'
|
D:ADP403
|
4.8
|
18.6
|
1.0
|
|
OE2
|
D:GLU271
|
4.8
|
34.1
|
1.0
|
|
O1B
|
D:ADP403
|
4.8
|
17.8
|
1.0
|
|
OE2
|
D:GLU186
|
4.8
|
26.2
|
1.0
|
|
CE
|
D:LYS202
|
4.9
|
17.0
|
1.0
|
|
Magnesium binding site 8 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 8 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg405
b:34.5
occ:1.00
|
OE1
|
D:GLU269
|
2.3
|
31.5
|
1.0
|
|
OE2
|
D:GLU271
|
2.4
|
34.1
|
1.0
|
|
O2B
|
D:ADP403
|
2.7
|
14.9
|
1.0
|
|
O1
|
D:TLA402
|
3.0
|
37.0
|
1.0
|
|
O
|
D:GLY141
|
3.2
|
24.1
|
1.0
|
|
CB
|
D:CYS142
|
3.2
|
22.8
|
1.0
|
|
O
|
D:HOH545
|
3.4
|
24.9
|
1.0
|
|
CA
|
D:CYS142
|
3.4
|
21.8
|
1.0
|
|
CD
|
D:GLU271
|
3.5
|
30.9
|
1.0
|
|
CD
|
D:GLU269
|
3.6
|
26.4
|
1.0
|
|
NZ
|
D:LYS92
|
3.7
|
16.6
|
1.0
|
|
O
|
D:HOH560
|
3.8
|
16.0
|
1.0
|
|
C
|
D:GLY141
|
4.1
|
24.2
|
1.0
|
|
N
|
D:CYS142
|
4.2
|
22.9
|
1.0
|
|
PB
|
D:ADP403
|
4.2
|
17.0
|
1.0
|
|
O3
|
D:TLA402
|
4.3
|
47.8
|
1.0
|
|
C1
|
D:TLA402
|
4.3
|
40.3
|
1.0
|
|
MG
|
D:MG406
|
4.3
|
33.3
|
1.0
|
|
OE2
|
D:GLU269
|
4.3
|
26.3
|
1.0
|
|
CG
|
D:GLU271
|
4.3
|
28.9
|
1.0
|
|
OE1
|
D:GLU271
|
4.3
|
32.6
|
1.0
|
|
C3
|
D:TLA402
|
4.4
|
44.7
|
1.0
|
|
CG
|
D:GLU269
|
4.6
|
25.0
|
1.0
|
|
O
|
D:HOH533
|
4.6
|
19.0
|
1.0
|
|
C
|
D:CYS142
|
4.6
|
21.4
|
1.0
|
|
N
|
D:TYR143
|
4.7
|
20.7
|
1.0
|
|
O3B
|
D:ADP403
|
4.8
|
16.7
|
1.0
|
|
O1B
|
D:ADP403
|
4.9
|
17.8
|
1.0
|
|
SG
|
D:CYS142
|
4.9
|
25.0
|
1.0
|
|
CE
|
D:LYS92
|
5.0
|
15.1
|
1.0
|
|
C2
|
D:TLA402
|
5.0
|
42.0
|
1.0
|
|
Magnesium binding site 9 out
of 9 in 6jil
Go back to
Magnesium Binding Sites List in 6jil
Magnesium binding site 9 out
of 9 in the Crystal Structure of D-Cycloserine Synthetase Dcsg
 Mono view
 Stereo pair view
|
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of D-Cycloserine Synthetase Dcsg within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg406
b:33.3
occ:1.00
|
OE2
|
D:GLU274
|
2.4
|
27.0
|
1.0
|
|
O41
|
D:TLA402
|
2.4
|
43.4
|
1.0
|
|
OE1
|
D:GLU271
|
2.5
|
32.6
|
1.0
|
|
O
|
D:GLU274
|
2.9
|
21.5
|
1.0
|
|
CD
|
D:GLU274
|
3.2
|
24.2
|
1.0
|
|
CD
|
D:GLU271
|
3.2
|
30.9
|
1.0
|
|
C4
|
D:TLA402
|
3.2
|
45.9
|
1.0
|
|
C3
|
D:TLA402
|
3.3
|
44.7
|
1.0
|
|
OE1
|
D:GLU274
|
3.3
|
25.0
|
1.0
|
|
OE2
|
D:GLU271
|
3.3
|
34.1
|
1.0
|
|
NE1
|
D:TRP57
|
3.4
|
15.8
|
1.0
|
|
O3
|
D:TLA402
|
3.7
|
47.8
|
1.0
|
|
C
|
D:GLU274
|
3.8
|
22.3
|
1.0
|
|
CD1
|
D:TRP57
|
3.9
|
15.8
|
1.0
|
|
CA
|
D:PRO275
|
4.2
|
23.0
|
1.0
|
|
CE2
|
D:TRP57
|
4.2
|
13.4
|
1.0
|
|
MG
|
D:MG405
|
4.3
|
34.5
|
1.0
|
|
N
|
D:PRO275
|
4.4
|
22.5
|
1.0
|
|
O4
|
D:TLA402
|
4.4
|
44.8
|
1.0
|
|
CB
|
D:CYS142
|
4.4
|
22.8
|
1.0
|
|
CG
|
D:GLU271
|
4.4
|
28.9
|
1.0
|
|
CG
|
D:GLU274
|
4.5
|
24.1
|
1.0
|
|
N
|
D:SER276
|
4.6
|
22.4
|
1.0
|
|
C2
|
D:TLA402
|
4.6
|
42.0
|
1.0
|
|
C
|
D:PRO275
|
4.7
|
23.2
|
1.0
|
|
CB
|
D:GLU271
|
4.7
|
25.0
|
1.0
|
|
CZ2
|
D:TRP57
|
4.7
|
13.4
|
1.0
|
|
CG
|
D:TRP57
|
4.8
|
15.9
|
1.0
|
|
SG
|
D:CYS142
|
4.8
|
25.0
|
1.0
|
|
O1
|
D:TLA402
|
4.9
|
37.0
|
1.0
|
|
CA
|
D:GLU274
|
4.9
|
22.0
|
1.0
|
|
CB
|
D:GLU274
|
4.9
|
21.6
|
1.0
|
|
CD2
|
D:TRP57
|
5.0
|
13.7
|
1.0
|
|
Reference:
Y.Matoba,
N.Uda,
M.Kudo,
M.Sugiyama.
Cyclization Mechanism Catalyzed By An Atp-Grasp Enzyme Essential For D-Cycloserine Biosynthesis. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31793174
DOI: 10.1111/FEBS.15163
Page generated: Mon Dec 14 23:01:06 2020
|
