Atomistry » Magnesium » PDB 6s5d-6sh6 » 6sd0
Atomistry »
  Magnesium »
    PDB 6s5d-6sh6 »
      6sd0 »

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

Last articles

Cl in 4AX6
Cl in 4AWU
Cl in 4AX8
Cl in 4AW1
Cl in 4AWK
Cl in 4AVG
Cl in 4AWE
Cl in 4AW7
Cl in 4AW0
Cl in 4AUX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy