Magnesium in PDB 6ojr: Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
Enzymatic activity of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
All present enzymatic activity of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda:
1.13.11.43;
Protein crystallography data
The structure of Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr
was solved by
E.Kuatsjah,
M.M.Verstraete,
M.J.Kobylarz,
A.K.N.Liu,
M.E.P.Murphy,
L.D.Eltis,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.27 /
2.30
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
181.364,
181.364,
94.983,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
18.2 /
20.5
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
(pdb code 6ojr). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the
Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda, PDB code: 6ojr:
Jump to Magnesium binding site number:
1;
2;
3;
Magnesium binding site 1 out
of 3 in 6ojr
Go back to
Magnesium Binding Sites List in 6ojr
Magnesium binding site 1 out
of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg504
b:43.6
occ:1.00
|
OD2
|
A:ASP372
|
2.3
|
44.4
|
1.0
|
OG1
|
A:THR390
|
2.7
|
30.7
|
1.0
|
HE3
|
A:LYS375
|
2.8
|
53.7
|
1.0
|
HH22
|
A:ARG347
|
2.8
|
53.4
|
1.0
|
HB2
|
A:TRP405
|
2.9
|
35.8
|
1.0
|
HB2
|
A:ASP372
|
3.0
|
54.0
|
1.0
|
HB3
|
A:ASP372
|
3.1
|
54.0
|
1.0
|
CG
|
A:ASP372
|
3.1
|
49.0
|
1.0
|
HG21
|
A:THR390
|
3.2
|
39.5
|
1.0
|
CB
|
A:ASP372
|
3.3
|
45.0
|
1.0
|
HG1
|
A:THR390
|
3.3
|
36.8
|
1.0
|
HG3
|
A:LYS375
|
3.3
|
57.6
|
1.0
|
HE2
|
A:LYS375
|
3.4
|
53.7
|
1.0
|
NH2
|
A:ARG347
|
3.5
|
44.5
|
1.0
|
CE
|
A:LYS375
|
3.5
|
44.7
|
1.0
|
HH21
|
A:ARG347
|
3.5
|
53.4
|
1.0
|
HG23
|
A:THR390
|
3.6
|
39.5
|
1.0
|
CG2
|
A:THR390
|
3.7
|
32.9
|
1.0
|
CB
|
A:THR390
|
3.8
|
33.6
|
1.0
|
CB
|
A:TRP405
|
3.8
|
29.9
|
1.0
|
HG2
|
A:LYS375
|
3.8
|
57.6
|
1.0
|
HD1
|
A:TRP405
|
3.9
|
41.4
|
1.0
|
CG
|
A:LYS375
|
3.9
|
48.0
|
1.0
|
HA
|
A:TRP405
|
4.1
|
38.3
|
1.0
|
CG
|
A:TRP405
|
4.2
|
35.3
|
1.0
|
CD1
|
A:TRP405
|
4.2
|
34.5
|
1.0
|
HB
|
A:THR390
|
4.2
|
40.3
|
1.0
|
CD
|
A:LYS375
|
4.3
|
42.9
|
1.0
|
OD1
|
A:ASP372
|
4.3
|
49.4
|
1.0
|
HG
|
A:SER403
|
4.4
|
39.9
|
1.0
|
CA
|
A:TRP405
|
4.5
|
31.9
|
1.0
|
HB3
|
A:TRP405
|
4.5
|
35.8
|
1.0
|
HZ1
|
A:LYS375
|
4.5
|
74.5
|
1.0
|
HG22
|
A:THR390
|
4.6
|
39.5
|
1.0
|
NZ
|
A:LYS375
|
4.6
|
62.1
|
1.0
|
HH12
|
A:ARG347
|
4.7
|
50.1
|
1.0
|
CZ
|
A:ARG347
|
4.7
|
43.9
|
1.0
|
HD2
|
A:LYS375
|
4.7
|
51.5
|
1.0
|
OD1
|
A:ASN389
|
4.7
|
31.8
|
1.0
|
CA
|
A:ASP372
|
4.8
|
45.4
|
1.0
|
N
|
A:TRP405
|
4.8
|
31.2
|
1.0
|
HA
|
A:THR390
|
4.9
|
39.4
|
1.0
|
OG
|
A:SER403
|
4.9
|
33.2
|
1.0
|
CA
|
A:THR390
|
5.0
|
32.8
|
1.0
|
HZ2
|
A:LYS375
|
5.0
|
74.5
|
1.0
|
|
Magnesium binding site 2 out
of 3 in 6ojr
Go back to
Magnesium Binding Sites List in 6ojr
Magnesium binding site 2 out
of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg505
b:36.6
occ:1.00
|
H
|
A:ILE354
|
2.3
|
30.2
|
1.0
|
OE2
|
A:GLU356
|
2.4
|
45.4
|
1.0
|
HD2
|
A:ARG353
|
2.5
|
31.8
|
1.0
|
O
|
A:HOH750
|
2.6
|
34.0
|
1.0
|
HA
|
A:ARG353
|
2.7
|
30.2
|
1.0
|
HH11
|
A:ARG353
|
2.7
|
39.3
|
1.0
|
HG12
|
A:ILE354
|
2.8
|
36.1
|
1.0
|
N
|
A:ILE354
|
3.1
|
25.2
|
1.0
|
CD
|
A:ARG353
|
3.4
|
26.5
|
1.0
|
HB3
|
A:ARG353
|
3.4
|
29.7
|
1.0
|
CD
|
A:GLU356
|
3.4
|
46.3
|
1.0
|
CA
|
A:ARG353
|
3.4
|
25.1
|
1.0
|
HG13
|
A:ILE354
|
3.5
|
36.1
|
1.0
|
HD3
|
A:ARG353
|
3.5
|
31.8
|
1.0
|
NH1
|
A:ARG353
|
3.5
|
32.8
|
1.0
|
O
|
A:HOH870
|
3.6
|
38.2
|
1.0
|
CG1
|
A:ILE354
|
3.6
|
30.1
|
1.0
|
HG3
|
A:GLU356
|
3.6
|
52.7
|
1.0
|
C
|
A:ARG353
|
3.7
|
28.9
|
1.0
|
O
|
A:HOH741
|
3.7
|
29.7
|
1.0
|
O
|
A:ILE354
|
3.8
|
29.7
|
1.0
|
CB
|
A:ARG353
|
3.8
|
24.8
|
1.0
|
HH12
|
A:ARG353
|
4.0
|
39.3
|
1.0
|
CA
|
A:ILE354
|
4.1
|
31.4
|
1.0
|
CG
|
A:GLU356
|
4.1
|
43.9
|
1.0
|
O
|
A:HOH858
|
4.2
|
38.6
|
1.0
|
CG
|
A:ARG353
|
4.2
|
27.0
|
1.0
|
HG23
|
A:ILE354
|
4.3
|
34.6
|
1.0
|
C
|
A:ILE354
|
4.3
|
30.9
|
1.0
|
NE
|
A:ARG353
|
4.3
|
39.6
|
1.0
|
OE1
|
A:GLU356
|
4.3
|
61.6
|
1.0
|
CB
|
A:ILE354
|
4.4
|
30.2
|
1.0
|
CZ
|
A:ARG353
|
4.4
|
30.6
|
1.0
|
O
|
A:PRO352
|
4.5
|
30.9
|
1.0
|
HD11
|
A:ILE354
|
4.6
|
38.6
|
1.0
|
N
|
A:ARG353
|
4.6
|
27.4
|
1.0
|
HG2
|
A:GLU356
|
4.7
|
52.7
|
1.0
|
CD1
|
A:ILE354
|
4.7
|
32.2
|
1.0
|
O
|
A:HOH846
|
4.7
|
44.0
|
1.0
|
HB2
|
A:ARG353
|
4.7
|
29.7
|
1.0
|
HG2
|
A:ARG353
|
4.8
|
32.4
|
1.0
|
O
|
A:MET284
|
4.8
|
25.4
|
1.0
|
CG2
|
A:ILE354
|
4.9
|
28.8
|
1.0
|
HA
|
A:ILE354
|
4.9
|
37.7
|
1.0
|
HG3
|
A:ARG353
|
4.9
|
32.4
|
1.0
|
O
|
A:ARG353
|
4.9
|
24.0
|
1.0
|
|
Magnesium binding site 3 out
of 3 in 6ojr
Go back to
Magnesium Binding Sites List in 6ojr
Magnesium binding site 3 out
of 3 in the Crystal Structure of Sphingomonas Paucimobilis TMY1009 Apo-Lsda
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 Sphingomonas Paucimobilis TMY1009 Apo-Lsda within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg506
b:46.0
occ:1.00
|
HE22
|
A:GLN469
|
1.6
|
44.9
|
1.0
|
NE2
|
A:GLN469
|
2.4
|
37.5
|
1.0
|
HE21
|
A:GLN469
|
2.7
|
44.9
|
1.0
|
O
|
A:ILE412
|
2.8
|
27.1
|
1.0
|
HG1
|
A:THR388
|
2.9
|
46.9
|
1.0
|
HB1
|
A:ALA411
|
3.0
|
41.0
|
1.0
|
OG1
|
A:THR388
|
3.1
|
39.1
|
1.0
|
O
|
A:HOH735
|
3.2
|
45.0
|
1.0
|
HG2
|
A:GLN413
|
3.3
|
36.6
|
1.0
|
CD
|
A:GLN469
|
3.5
|
37.7
|
1.0
|
C
|
A:ILE412
|
3.5
|
27.9
|
1.0
|
HB3
|
A:ALA411
|
3.5
|
41.0
|
1.0
|
H
|
A:ILE412
|
3.5
|
34.4
|
1.0
|
HA
|
A:GLN413
|
3.6
|
35.8
|
1.0
|
CB
|
A:ALA411
|
3.7
|
34.1
|
1.0
|
O
|
A:HOH616
|
3.7
|
33.9
|
1.0
|
OE1
|
A:GLN469
|
3.8
|
40.2
|
1.0
|
N
|
A:ILE412
|
3.8
|
28.7
|
1.0
|
CG
|
A:GLN413
|
4.1
|
30.5
|
1.0
|
N
|
A:GLN413
|
4.1
|
25.1
|
1.0
|
HG3
|
A:GLN413
|
4.1
|
36.6
|
1.0
|
H
|
A:THR388
|
4.2
|
42.2
|
1.0
|
CA
|
A:GLN413
|
4.3
|
29.8
|
1.0
|
CA
|
A:ILE412
|
4.3
|
29.2
|
1.0
|
HB2
|
A:ALA411
|
4.3
|
41.0
|
1.0
|
C
|
A:ALA411
|
4.4
|
28.4
|
1.0
|
O
|
A:THR388
|
4.4
|
35.1
|
1.0
|
CB
|
A:THR388
|
4.5
|
35.7
|
1.0
|
CA
|
A:ALA411
|
4.7
|
31.9
|
1.0
|
HA
|
A:ILE412
|
4.8
|
35.0
|
1.0
|
H
|
A:GLN413
|
4.8
|
30.1
|
1.0
|
HD13
|
A:LEU369
|
4.8
|
31.2
|
1.0
|
CG
|
A:GLN469
|
4.8
|
39.2
|
1.0
|
HB2
|
A:GLN469
|
4.8
|
35.1
|
1.0
|
CB
|
A:GLN413
|
4.8
|
27.9
|
1.0
|
OD2
|
A:ASP436
|
4.9
|
27.7
|
1.0
|
HG2
|
A:GLN469
|
4.9
|
47.0
|
1.0
|
HB
|
A:THR388
|
5.0
|
42.8
|
1.0
|
N
|
A:THR388
|
5.0
|
35.1
|
1.0
|
HE1
|
A:HIS438
|
5.0
|
56.4
|
1.0
|
HA
|
A:GLN469
|
5.0
|
33.1
|
1.0
|
|
Reference:
E.Kuatsjah,
M.M.Verstraete,
M.J.Kobylarz,
A.K.N.Liu,
M.E.P.Murphy,
L.D.Eltis.
Identification of Functionally Important Residues and Structural Features in A Bacterial Lignostilbene Dioxygenase. J.Biol.Chem. V. 294 12911 2019.
ISSN: ESSN 1083-351X
PubMed: 31292192
DOI: 10.1074/JBC.RA119.009428
Page generated: Tue Oct 1 13:24:19 2024
|