Magnesium in PDB 6s6z: 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;

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Beta-Galactosidase From Thermotoga Maritima (pdb code 6s6z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Structure of Beta-Galactosidase From Thermotoga Maritima, PDB code: 6s6z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 6s6z

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Magnesium binding site 1 out of 8 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:Mg3001

b:19.3
occ:1.00
 OE1 A:GLU586 2.2 46.9 1.0
O A:ALA511 2.2 34.0 1.0
OE1 A:GLU584 2.3 46.5 1.0
O A:GLY575 2.3 31.0 1.0
O A:HOH3236 2.4 37.2 1.0
O A:GLY513 2.5 31.7 1.0
CD A:GLU586 3.2 53.1 1.0
C A:ALA511 3.5 31.4 1.0
OE2 A:GLU586 3.6 47.6 1.0
C A:GLY575 3.6 33.5 1.0
C A:GLY513 3.6 38.0 1.0
CD A:GLU584 3.6 53.1 1.0
N A:GLY513 3.7 39.1 1.0
CA A:GLY513 4.1 37.1 1.0
CB A:ALA511 4.1 36.1 1.0
C A:MET512 4.2 39.5 1.0
CA A:ALA511 4.3 32.1 1.0
N A:MET512 4.4 33.3 1.0
OE2 A:GLU584 4.4 55.3 1.0
N A:GLY575 4.4 31.3 1.0
N A:VAL576 4.5 32.5 1.0
CG A:GLU586 4.5 44.7 1.0
CA A:MET512 4.5 36.9 1.0
CG A:GLU584 4.6 46.8 1.0
CA A:GLY575 4.6 32.9 1.0
O A:HOH3195 4.7 40.6 1.0
CA A:VAL576 4.7 34.4 1.0
N A:ASN514 4.7 36.2 1.0
C A:ASN574 4.8 38.7 1.0
OD1 A:ASP542 4.9 51.2 1.0
CE1 A:TYR883 4.9 48.1 1.0
CB A:GLU584 4.9 44.6 1.0
O A:MET512 4.9 39.1 1.0
O A:ASN574 5.0 42.8 1.0
O A:HOH3103 5.0 35.9 1.0

Magnesium binding site 2 out of 8 in 6s6z

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Magnesium binding site 2 out of 8 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
D:Mg3001

b:19.3
occ:1.00
 OE1 D:GLU586 2.2 46.9 1.0
O D:ALA511 2.2 34.0 1.0
OE1 D:GLU584 2.3 46.5 1.0
O D:GLY575 2.3 31.0 1.0
O D:HOH3236 2.4 37.2 1.0
O D:GLY513 2.5 31.7 1.0
CD D:GLU586 3.2 53.1 1.0
C D:ALA511 3.5 31.4 1.0
OE2 D:GLU586 3.6 47.6 1.0
C D:GLY575 3.6 33.5 1.0
C D:GLY513 3.6 38.0 1.0
CD D:GLU584 3.6 53.1 1.0
N D:GLY513 3.7 39.1 1.0
CA D:GLY513 4.1 37.1 1.0
CB D:ALA511 4.1 36.1 1.0
C D:MET512 4.2 39.5 1.0
CA D:ALA511 4.3 32.1 1.0
N D:MET512 4.4 33.3 1.0
OE2 D:GLU584 4.4 55.3 1.0
N D:GLY575 4.4 31.3 1.0
N D:VAL576 4.5 32.5 1.0
CG D:GLU586 4.5 44.7 1.0
CA D:MET512 4.5 36.9 1.0
CG D:GLU584 4.6 46.8 1.0
CA D:GLY575 4.6 32.9 1.0
O D:HOH3195 4.7 40.6 1.0
CA D:VAL576 4.7 34.4 1.0
N D:ASN514 4.7 36.2 1.0
C D:ASN574 4.8 38.7 1.0
OD1 D:ASP542 4.9 51.2 1.0
CE1 D:TYR883 4.9 48.1 1.0
CB D:GLU584 4.9 44.6 1.0
O D:MET512 4.9 39.1 1.0
O D:ASN574 5.0 42.8 1.0
O D:HOH3103 5.0 35.9 1.0

Magnesium binding site 3 out of 8 in 6s6z

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Magnesium binding site 3 out of 8 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
B:Mg3001

b:19.3
occ:1.00
 OE1 B:GLU586 2.2 46.9 1.0
O B:ALA511 2.2 34.0 1.0
OE1 B:GLU584 2.3 46.5 1.0
O B:GLY575 2.3 31.0 1.0
O B:HOH3236 2.4 37.2 1.0
O B:GLY513 2.5 31.7 1.0
CD B:GLU586 3.2 53.1 1.0
C B:ALA511 3.5 31.4 1.0
OE2 B:GLU586 3.6 47.6 1.0
C B:GLY575 3.6 33.5 1.0
C B:GLY513 3.6 38.0 1.0
CD B:GLU584 3.6 53.1 1.0
N B:GLY513 3.7 39.1 1.0
CA B:GLY513 4.1 37.1 1.0
CB B:ALA511 4.1 36.1 1.0
C B:MET512 4.2 39.5 1.0
CA B:ALA511 4.3 32.1 1.0
N B:MET512 4.4 33.3 1.0
OE2 B:GLU584 4.4 55.3 1.0
N B:GLY575 4.4 31.3 1.0
N B:VAL576 4.5 32.5 1.0
CG B:GLU586 4.5 44.7 1.0
CA B:MET512 4.5 36.9 1.0
CG B:GLU584 4.6 46.8 1.0
CA B:GLY575 4.6 32.9 1.0
O B:HOH3195 4.7 40.6 1.0
CA B:VAL576 4.7 34.4 1.0
N B:ASN514 4.7 36.2 1.0
C B:ASN574 4.8 38.7 1.0
OD1 B:ASP542 4.9 51.2 1.0
CE1 B:TYR883 4.9 48.1 1.0
CB B:GLU584 4.9 44.6 1.0
O B:MET512 4.9 39.1 1.0
O B:ASN574 5.0 42.8 1.0
O B:HOH3103 5.0 35.9 1.0

Magnesium binding site 4 out of 8 in 6s6z

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Magnesium binding site 4 out of 8 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
H:Mg3001

b:19.3
occ:1.00
 OE1 H:GLU586 2.2 46.9 1.0
O H:ALA511 2.2 34.0 1.0
OE1 H:GLU584 2.3 46.5 1.0
O H:GLY575 2.3 31.0 1.0
O H:HOH3236 2.4 37.2 1.0
O H:GLY513 2.5 31.7 1.0
CD H:GLU586 3.2 53.1 1.0
C H:ALA511 3.5 31.4 1.0
OE2 H:GLU586 3.6 47.6 1.0
C H:GLY575 3.6 33.5 1.0
C H:GLY513 3.6 38.0 1.0
CD H:GLU584 3.6 53.1 1.0
N H:GLY513 3.7 39.1 1.0
CA H:GLY513 4.1 37.1 1.0
CB H:ALA511 4.1 36.1 1.0
C H:MET512 4.2 39.5 1.0
CA H:ALA511 4.3 32.1 1.0
N H:MET512 4.4 33.3 1.0
OE2 H:GLU584 4.4 55.3 1.0
N H:GLY575 4.4 31.3 1.0
N H:VAL576 4.5 32.5 1.0
CG H:GLU586 4.5 44.7 1.0
CA H:MET512 4.5 36.9 1.0
CG H:GLU584 4.6 46.8 1.0
CA H:GLY575 4.6 32.9 1.0
O H:HOH3195 4.7 40.6 1.0
CA H:VAL576 4.7 34.4 1.0
N H:ASN514 4.7 36.2 1.0
C H:ASN574 4.8 38.7 1.0
OD1 H:ASP542 4.9 51.2 1.0
CE1 H:TYR883 4.9 48.1 1.0
CB H:GLU584 4.9 44.6 1.0
O H:MET512 4.9 39.1 1.0
O H:ASN574 5.0 42.8 1.0
O H:HOH3103 5.0 35.9 1.0

Magnesium binding site 5 out of 8 in 6s6z

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Magnesium binding site 5 out of 8 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 5 of Structure of Beta-Galactosidase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg3001

b:19.3
occ:1.00
 OE1 F:GLU586 2.2 46.9 1.0
O F:ALA511 2.2 34.0 1.0
OE1 F:GLU584 2.3 46.5 1.0
O F:GLY575 2.3 31.0 1.0
O F:HOH3236 2.4 37.2 1.0
O F:GLY513 2.5 31.7 1.0
CD F:GLU586 3.2 53.1 1.0
C F:ALA511 3.5 31.4 1.0
OE2 F:GLU586 3.6 47.6 1.0
C F:GLY575 3.6 33.5 1.0
C F:GLY513 3.6 38.0 1.0
CD F:GLU584 3.6 53.1 1.0
N F:GLY513 3.7 39.1 1.0
CA F:GLY513 4.1 37.1 1.0
CB F:ALA511 4.1 36.1 1.0
C F:MET512 4.2 39.5 1.0
CA F:ALA511 4.3 32.1 1.0
N F:MET512 4.4 33.3 1.0
OE2 F:GLU584 4.4 55.3 1.0
N F:GLY575 4.4 31.3 1.0
N F:VAL576 4.5 32.5 1.0
CG F:GLU586 4.5 44.7 1.0
CA F:MET512 4.5 36.9 1.0
CG F:GLU584 4.6 46.8 1.0
CA F:GLY575 4.6 32.9 1.0
O F:HOH3195 4.7 40.6 1.0
CA F:VAL576 4.7 34.4 1.0
N F:ASN514 4.7 36.2 1.0
C F:ASN574 4.8 38.7 1.0
OD1 F:ASP542 4.9 51.2 1.0
CE1 F:TYR883 4.9 48.1 1.0
CB F:GLU584 4.9 44.6 1.0
O F:MET512 4.9 39.1 1.0
O F:ASN574 5.0 42.8 1.0
O F:HOH3103 5.0 35.9 1.0

Magnesium binding site 6 out of 8 in 6s6z

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Magnesium binding site 6 out of 8 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 6 of Structure of Beta-Galactosidase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg3001

b:19.3
occ:1.00
 OE1 G:GLU586 2.2 46.9 1.0
O G:ALA511 2.2 34.0 1.0
OE1 G:GLU584 2.3 46.5 1.0
O G:GLY575 2.3 31.0 1.0
O G:HOH3236 2.4 37.2 1.0
O G:GLY513 2.5 31.7 1.0
CD G:GLU586 3.2 53.1 1.0
C G:ALA511 3.5 31.4 1.0
OE2 G:GLU586 3.6 47.6 1.0
C G:GLY575 3.6 33.5 1.0
C G:GLY513 3.6 38.0 1.0
CD G:GLU584 3.6 53.1 1.0
N G:GLY513 3.7 39.1 1.0
CA G:GLY513 4.1 37.1 1.0
CB G:ALA511 4.1 36.1 1.0
C G:MET512 4.2 39.5 1.0
CA G:ALA511 4.3 32.1 1.0
N G:MET512 4.4 33.3 1.0
OE2 G:GLU584 4.4 55.3 1.0
N G:GLY575 4.4 31.3 1.0
N G:VAL576 4.5 32.5 1.0
CG G:GLU586 4.5 44.7 1.0
CA G:MET512 4.5 36.9 1.0
CG G:GLU584 4.6 46.8 1.0
CA G:GLY575 4.6 32.9 1.0
O G:HOH3195 4.7 40.6 1.0
CA G:VAL576 4.7 34.4 1.0
N G:ASN514 4.7 36.2 1.0
C G:ASN574 4.8 38.7 1.0
OD1 G:ASP542 4.9 51.2 1.0
CE1 G:TYR883 4.9 48.1 1.0
CB G:GLU584 4.9 44.6 1.0
O G:MET512 4.9 39.1 1.0
O G:ASN574 5.0 42.8 1.0
O G:HOH3103 5.0 35.9 1.0

Magnesium binding site 7 out of 8 in 6s6z

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Magnesium binding site 7 out of 8 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 7 of Structure of Beta-Galactosidase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg3001

b:19.3
occ:1.00
 OE1 E:GLU586 2.2 46.9 1.0
O E:ALA511 2.2 34.0 1.0
OE1 E:GLU584 2.3 46.5 1.0
O E:GLY575 2.3 31.0 1.0
O E:HOH3236 2.4 37.2 1.0
O E:GLY513 2.5 31.7 1.0
CD E:GLU586 3.2 53.1 1.0
C E:ALA511 3.5 31.4 1.0
OE2 E:GLU586 3.6 47.6 1.0
C E:GLY575 3.6 33.5 1.0
C E:GLY513 3.6 38.0 1.0
CD E:GLU584 3.6 53.1 1.0
N E:GLY513 3.7 39.1 1.0
CA E:GLY513 4.1 37.1 1.0
CB E:ALA511 4.1 36.1 1.0
C E:MET512 4.2 39.5 1.0
CA E:ALA511 4.3 32.1 1.0
N E:MET512 4.4 33.3 1.0
OE2 E:GLU584 4.4 55.3 1.0
N E:GLY575 4.4 31.3 1.0
N E:VAL576 4.5 32.5 1.0
CG E:GLU586 4.5 44.7 1.0
CA E:MET512 4.5 36.9 1.0
CG E:GLU584 4.6 46.8 1.0
CA E:GLY575 4.6 32.9 1.0
O E:HOH3195 4.7 40.6 1.0
CA E:VAL576 4.7 34.4 1.0
N E:ASN514 4.7 36.2 1.0
C E:ASN574 4.8 38.7 1.0
OD1 E:ASP542 4.9 51.2 1.0
CE1 E:TYR883 4.9 48.1 1.0
CB E:GLU584 4.9 44.6 1.0
O E:MET512 4.9 39.1 1.0
O E:ASN574 5.0 42.8 1.0
O E:HOH3103 5.0 35.9 1.0

Magnesium binding site 8 out of 8 in 6s6z

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Magnesium binding site 8 out of 8 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 8 of Structure of Beta-Galactosidase From Thermotoga Maritima within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:19.3
occ:1.00
 OE1 C:GLU586 2.2 46.9 1.0
O C:ALA511 2.2 34.0 1.0
OE1 C:GLU584 2.3 46.5 1.0
O C:GLY575 2.3 31.0 1.0
O C:HOH3236 2.4 37.2 1.0
O C:GLY513 2.5 31.7 1.0
CD C:GLU586 3.2 53.1 1.0
C C:ALA511 3.5 31.4 1.0
OE2 C:GLU586 3.6 47.6 1.0
C C:GLY575 3.6 33.5 1.0
C C:GLY513 3.6 38.0 1.0
CD C:GLU584 3.6 53.1 1.0
N C:GLY513 3.7 39.1 1.0
CA C:GLY513 4.1 37.1 1.0
CB C:ALA511 4.1 36.1 1.0
C C:MET512 4.2 39.5 1.0
CA C:ALA511 4.3 32.1 1.0
N C:MET512 4.4 33.3 1.0
OE2 C:GLU584 4.4 55.3 1.0
N C:GLY575 4.4 31.3 1.0
N C:VAL576 4.5 32.5 1.0
CG C:GLU586 4.5 44.7 1.0
CA C:MET512 4.5 36.9 1.0
CG C:GLU584 4.6 46.8 1.0
CA C:GLY575 4.6 32.9 1.0
O C:HOH3195 4.7 40.6 1.0
CA C:VAL576 4.7 34.4 1.0
N C:ASN514 4.7 36.2 1.0
C C:ASN574 4.8 38.7 1.0
OD1 C:ASP542 4.9 51.2 1.0
CE1 C:TYR883 4.9 48.1 1.0
CB C:GLU584 4.9 44.6 1.0
O C:MET512 4.9 39.1 1.0
O C:ASN574 5.0 42.8 1.0
O C:HOH3103 5.0 35.9 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. V. 15 179 2020.
ISSN: ESSN 1554-8937
PubMed: 31874027
DOI: 10.1021/ACSCHEMBIO.9B00752
Page generated: Tue Dec 15 00:03:23 2020

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