Magnesium in PDB 6sd0: Structure of Beta-Galactosidase From Thermotoga Maritima.
Enzymatic activity of Structure of Beta-Galactosidase From Thermotoga Maritima.
All present enzymatic activity of Structure of Beta-Galactosidase From Thermotoga Maritima.:
3.2.1.23;
Protein crystallography data
The structure of Structure of Beta-Galactosidase From Thermotoga Maritima., PDB code: 6sd0
was solved by
E.Jimenez-Ortega,
M.Ramirez-Escudero,
J.Sanz-Aparicio,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
3.70
|
Space group
|
I 4
|
Cell size a, b, c (Å), α, β, γ (°)
|
167.852,
167.852,
519.990,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
24.1 /
28.6
|
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Structure of Beta-Galactosidase From Thermotoga Maritima.
(pdb code 6sd0). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Structure of Beta-Galactosidase From Thermotoga Maritima., PDB code: 6sd0:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6sd0
Go back to
Magnesium Binding Sites List in 6sd0
Magnesium binding site 1 out
of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg1101
b:39.6
occ:1.00
|
O
|
A:ALA511
|
2.3
|
0.7
|
1.0
|
O
|
A:GLY575
|
2.3
|
0.2
|
1.0
|
OE1
|
A:GLU584
|
2.4
|
0.6
|
1.0
|
OE1
|
A:GLU586
|
2.7
|
0.1
|
1.0
|
O
|
A:GLY513
|
2.8
|
0.9
|
1.0
|
C
|
A:GLY575
|
3.4
|
0.2
|
1.0
|
CD
|
A:GLU584
|
3.4
|
0.3
|
1.0
|
C
|
A:ALA511
|
3.5
|
0.4
|
1.0
|
N
|
A:GLY513
|
3.6
|
0.2
|
1.0
|
C
|
A:GLY513
|
3.8
|
0.9
|
1.0
|
CD
|
A:GLU586
|
3.8
|
0.6
|
1.0
|
N
|
A:GLY575
|
3.8
|
0.2
|
1.0
|
OE2
|
A:GLU584
|
3.9
|
0.9
|
1.0
|
CA
|
A:GLY513
|
4.0
|
0.2
|
1.0
|
OD1
|
A:ASP542
|
4.0
|
0.2
|
1.0
|
C
|
A:MET512
|
4.1
|
0.1
|
1.0
|
CA
|
A:GLY575
|
4.1
|
0.6
|
1.0
|
OE2
|
A:GLU586
|
4.3
|
0.4
|
1.0
|
N
|
A:MET512
|
4.3
|
0.5
|
1.0
|
CA
|
A:MET512
|
4.3
|
0.8
|
1.0
|
CB
|
A:ALA511
|
4.4
|
0.2
|
1.0
|
N
|
A:VAL576
|
4.4
|
0.3
|
1.0
|
C
|
A:ASN574
|
4.4
|
0.8
|
1.0
|
CA
|
A:ALA511
|
4.5
|
0.5
|
1.0
|
OD2
|
A:ASP542
|
4.6
|
0.9
|
1.0
|
CG
|
A:GLU584
|
4.6
|
0.7
|
1.0
|
O
|
A:ILE573
|
4.7
|
0.0
|
1.0
|
CA
|
A:VAL576
|
4.7
|
1.0
|
1.0
|
CG
|
A:ASP542
|
4.7
|
0.7
|
1.0
|
O
|
A:MET512
|
4.8
|
0.6
|
1.0
|
O
|
A:ASN574
|
5.0
|
0.1
|
1.0
|
N
|
A:ASN514
|
5.0
|
0.1
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6sd0
Go back to
Magnesium Binding Sites List in 6sd0
Magnesium binding site 2 out
of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg1101
b:41.8
occ:1.00
|
O
|
B:GLY513
|
1.9
|
0.7
|
1.0
|
OE1
|
B:GLU584
|
2.0
|
0.5
|
1.0
|
OE1
|
B:GLU586
|
2.4
|
0.6
|
1.0
|
O
|
B:ALA511
|
2.7
|
91.5
|
1.0
|
CD
|
B:GLU586
|
3.0
|
0.9
|
1.0
|
C
|
B:GLY513
|
3.0
|
0.1
|
1.0
|
O
|
B:GLY575
|
3.1
|
0.7
|
1.0
|
OE2
|
B:GLU586
|
3.1
|
0.7
|
1.0
|
CD
|
B:GLU584
|
3.2
|
0.6
|
1.0
|
N
|
B:GLY513
|
3.6
|
0.8
|
1.0
|
CA
|
B:GLY513
|
3.7
|
0.1
|
1.0
|
OE2
|
B:GLU584
|
3.8
|
0.3
|
1.0
|
C
|
B:ALA511
|
3.8
|
0.5
|
1.0
|
N
|
B:ASN514
|
4.1
|
0.1
|
1.0
|
CE1
|
B:TYR883
|
4.2
|
0.7
|
1.0
|
C
|
B:MET512
|
4.2
|
0.4
|
1.0
|
C
|
B:GLY575
|
4.2
|
0.6
|
1.0
|
CG
|
B:GLU584
|
4.3
|
0.2
|
1.0
|
CG
|
B:GLU586
|
4.3
|
0.8
|
1.0
|
CB
|
B:GLU584
|
4.5
|
0.7
|
1.0
|
CD1
|
B:TYR883
|
4.5
|
0.6
|
1.0
|
CA
|
B:ASN514
|
4.6
|
0.7
|
1.0
|
O
|
B:MET512
|
4.6
|
1.0
|
1.0
|
N
|
B:MET512
|
4.7
|
0.8
|
1.0
|
CB
|
B:ALA511
|
4.7
|
0.8
|
1.0
|
CA
|
B:ALA511
|
4.7
|
0.5
|
1.0
|
N
|
B:SER515
|
4.8
|
0.9
|
1.0
|
CA
|
B:MET512
|
4.8
|
0.7
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6sd0
Go back to
Magnesium Binding Sites List in 6sd0
Magnesium binding site 3 out
of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Mg1101
b:41.0
occ:1.00
|
OE1
|
C:GLU584
|
1.8
|
0.8
|
1.0
|
O
|
C:GLY513
|
2.4
|
0.1
|
1.0
|
OE1
|
C:GLU586
|
2.6
|
0.9
|
1.0
|
O
|
C:GLY575
|
2.7
|
0.5
|
1.0
|
O
|
C:ALA511
|
2.8
|
0.7
|
1.0
|
CD
|
C:GLU584
|
3.0
|
0.5
|
1.0
|
CD
|
C:GLU586
|
3.3
|
0.8
|
1.0
|
C
|
C:GLY513
|
3.4
|
0.9
|
1.0
|
OE2
|
C:GLU586
|
3.6
|
0.3
|
1.0
|
N
|
C:GLY513
|
3.7
|
0.0
|
1.0
|
OE2
|
C:GLU584
|
3.7
|
0.9
|
1.0
|
CA
|
C:GLY513
|
3.8
|
0.5
|
1.0
|
C
|
C:GLY575
|
3.8
|
0.8
|
1.0
|
CG
|
C:GLU584
|
4.0
|
0.9
|
1.0
|
C
|
C:ALA511
|
4.1
|
0.8
|
1.0
|
CE1
|
C:TYR883
|
4.2
|
0.7
|
1.0
|
CB
|
C:GLU584
|
4.3
|
0.8
|
1.0
|
C
|
C:MET512
|
4.4
|
0.2
|
1.0
|
CD1
|
C:TYR883
|
4.4
|
0.9
|
1.0
|
N
|
C:GLY575
|
4.5
|
0.0
|
1.0
|
N
|
C:ASN514
|
4.5
|
0.1
|
1.0
|
CG
|
C:GLU586
|
4.6
|
0.7
|
1.0
|
CA
|
C:GLY575
|
4.7
|
0.5
|
1.0
|
N
|
C:VAL576
|
4.7
|
0.9
|
1.0
|
CA
|
C:VAL576
|
4.7
|
0.7
|
1.0
|
OD1
|
C:ASP542
|
4.8
|
0.0
|
1.0
|
OD2
|
C:ASP542
|
4.8
|
0.5
|
1.0
|
CB
|
C:ALA511
|
4.8
|
0.5
|
1.0
|
N
|
C:MET512
|
4.9
|
0.5
|
1.0
|
CA
|
C:MET512
|
4.9
|
0.6
|
1.0
|
CA
|
C:ALA511
|
5.0
|
0.0
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6sd0
Go back to
Magnesium Binding Sites List in 6sd0
Magnesium binding site 4 out
of 4 in the Structure of Beta-Galactosidase From Thermotoga Maritima.
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Structure of Beta-Galactosidase From Thermotoga Maritima. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg1101
b:41.2
occ:1.00
|
O
|
D:ALA511
|
2.4
|
0.0
|
1.0
|
O
|
D:GLY513
|
2.4
|
0.7
|
1.0
|
OE1
|
D:GLU584
|
2.5
|
0.3
|
1.0
|
O
|
D:GLY575
|
2.8
|
0.3
|
1.0
|
N
|
D:GLY513
|
2.9
|
1.0
|
1.0
|
OE1
|
D:GLU586
|
3.1
|
0.4
|
1.0
|
C
|
D:GLY513
|
3.2
|
0.7
|
1.0
|
CA
|
D:GLY513
|
3.3
|
0.8
|
1.0
|
C
|
D:ALA511
|
3.5
|
0.6
|
1.0
|
CD
|
D:GLU584
|
3.5
|
0.3
|
1.0
|
C
|
D:MET512
|
3.7
|
1.0
|
1.0
|
OE2
|
D:GLU584
|
3.9
|
0.1
|
1.0
|
C
|
D:GLY575
|
3.9
|
0.8
|
1.0
|
CD
|
D:GLU586
|
4.0
|
0.9
|
1.0
|
CA
|
D:MET512
|
4.1
|
0.8
|
1.0
|
OE2
|
D:GLU586
|
4.1
|
0.5
|
1.0
|
N
|
D:MET512
|
4.2
|
0.4
|
1.0
|
N
|
D:GLY575
|
4.2
|
0.9
|
1.0
|
OD1
|
D:ASP542
|
4.4
|
0.4
|
1.0
|
N
|
D:ASN514
|
4.5
|
0.1
|
1.0
|
O
|
D:MET512
|
4.6
|
0.9
|
1.0
|
CE1
|
D:TYR883
|
4.6
|
0.7
|
1.0
|
CA
|
D:ALA511
|
4.6
|
0.8
|
1.0
|
C
|
D:ASN574
|
4.6
|
0.6
|
1.0
|
CA
|
D:GLY575
|
4.7
|
0.3
|
1.0
|
CB
|
D:ALA511
|
4.7
|
0.1
|
1.0
|
CD1
|
D:TYR883
|
4.7
|
0.9
|
1.0
|
CG
|
D:GLU584
|
4.9
|
0.2
|
1.0
|
O
|
D:ILE573
|
4.9
|
0.2
|
1.0
|
N
|
D:VAL576
|
5.0
|
0.5
|
1.0
|
|
Reference:
S.Miguez Amil,
E.Jimenez-Ortega,
M.Ramirez-Escudero,
D.Talens-Perales,
J.Marin-Navarro,
J.Polaina,
J.Sanz-Aparicio,
R.Fernandez-Leiro.
The Cryo-Em Structure Ofthermotoga Maritimabeta-Galactosidase: Quaternary Structure Guides Protein Engineering. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31874027
DOI: 10.1021/ACSCHEMBIO.9B00752
Page generated: Tue Oct 1 17:53:23 2024
|