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Magnesium in PDB 3t0d: E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone, PDB code: 3t0d was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.56 / 1.93
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.930, 162.710, 203.910, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 20.9

Other elements in 3t0d:

The structure of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone (pdb code 3t0d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone, PDB code: 3t0d:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3t0d

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Magnesium binding site 1 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:18.9
occ:1.00
 O A:HOH4077 2.0 13.9 1.0
ND1 A:HIS418 2.0 15.1 1.0
OE2 A:GLU416 2.1 18.4 1.0
OE1 A:GLU461 2.1 15.9 1.0
O A:HOH4013 2.1 14.8 1.0
O A:HOH4152 2.2 15.3 1.0
CE1 A:HIS418 2.9 16.7 1.0
CG A:HIS418 3.1 15.0 1.0
CD A:GLU461 3.2 22.8 1.0
CD A:GLU416 3.2 17.5 1.0
CB A:HIS418 3.6 12.9 1.0
OE1 A:GLU416 3.8 16.9 1.0
OE2 A:GLU461 4.0 20.1 1.0
OD1 A:ASN102 4.0 19.9 1.0
NE2 A:HIS418 4.1 17.1 1.0
CB A:GLU461 4.2 17.0 1.0
CD2 A:HIS418 4.2 17.1 1.0
C2 A:1492001 4.2 20.7 1.0
CG A:GLU461 4.2 15.8 1.0
CB A:ASP201 4.3 16.7 1.0
O A:ASP199 4.3 17.3 1.0
O4 A:1492001 4.3 14.7 1.0
N A:ASP201 4.3 19.5 1.0
ND2 A:ASN460 4.4 14.0 1.0
CG A:GLU416 4.4 13.9 1.0
O3 A:1492001 4.5 15.2 1.0
O A:ASN102 4.6 19.9 1.0
O2 A:1492001 4.7 18.7 1.0
CG2 A:VAL103 4.7 20.1 1.0
CA A:ASP201 4.9 18.2 1.0
C3 A:1492001 4.9 18.8 1.0

Magnesium binding site 2 out of 9 in 3t0d

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Magnesium binding site 2 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:26.6
occ:1.00
 OD2 A:ASP193 2.1 37.6 1.0
O A:ASP15 2.1 31.3 1.0
O A:ASN18 2.3 26.8 1.0
OE1 A:GLN163 2.3 25.9 1.0
O A:VAL21 2.3 31.9 1.0
CG A:ASP193 2.9 35.0 1.0
OD1 A:ASP193 3.1 29.4 1.0
C A:ASN18 3.2 25.9 1.0
CD A:GLN163 3.2 31.2 1.0
C A:ASP15 3.3 31.9 1.0
C A:VAL21 3.4 29.9 1.0
NE2 A:GLN163 3.6 22.7 1.0
N A:ASN18 3.6 27.1 1.0
CA A:ASN18 3.8 27.3 1.0
CA A:TRP16 4.0 30.4 1.0
OH A:TYR161 4.1 35.0 1.0
N A:TRP16 4.1 31.7 1.0
CB A:ASN18 4.2 26.5 1.0
CA A:VAL21 4.2 29.3 1.0
N A:PRO19 4.2 27.7 1.0
CB A:VAL21 4.2 31.0 1.0
C A:TRP16 4.3 27.1 1.0
N A:VAL21 4.3 31.2 1.0
CB A:ASP193 4.3 25.7 1.0
CA A:ASP15 4.4 33.2 1.0
CE2 A:TYR161 4.4 30.9 1.0
N A:GLU17 4.4 26.8 1.0
N A:THR22 4.4 29.7 1.0
CA A:PRO19 4.5 28.4 1.0
CG A:GLN163 4.5 22.6 1.0
CA A:THR22 4.7 30.1 1.0
CG1 A:VAL21 4.7 26.6 1.0
CZ A:TYR161 4.7 32.6 1.0
CB A:ASP15 4.8 32.8 1.0
O A:TRP16 4.8 27.4 1.0
C A:GLU17 4.8 29.1 1.0
C A:PRO19 5.0 31.8 1.0

Magnesium binding site 3 out of 9 in 3t0d

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Magnesium binding site 3 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:13.1
occ:1.00
 ND1 B:HIS418 2.1 11.5 1.0
OE2 B:GLU416 2.1 11.4 1.0
OE1 B:GLU461 2.1 9.0 1.0
O B:HOH4116 2.1 10.3 1.0
O B:HOH4192 2.2 12.2 1.0
O B:HOH4052 2.3 11.4 1.0
CE1 B:HIS418 2.9 15.1 1.0
CG B:HIS418 3.2 12.6 1.0
CD B:GLU416 3.2 7.3 1.0
CD B:GLU461 3.2 13.3 1.0
CB B:HIS418 3.6 9.9 1.0
OE1 B:GLU416 3.7 7.5 1.0
OE2 B:GLU461 4.0 13.7 1.0
OD1 B:ASN102 4.0 14.2 1.0
NE2 B:HIS418 4.1 13.7 1.0
CB B:GLU461 4.1 10.1 1.0
C2 B:1492001 4.2 9.3 1.0
CG B:GLU461 4.2 10.6 1.0
O4 B:1492001 4.2 10.6 1.0
CD2 B:HIS418 4.2 11.6 1.0
CB B:ASP201 4.3 10.6 1.0
O B:ASP199 4.3 11.6 1.0
N B:ASP201 4.3 9.3 1.0
CG B:GLU416 4.4 7.6 1.0
ND2 B:ASN460 4.4 9.0 1.0
O3 B:1492001 4.5 11.8 1.0
O B:ASN102 4.7 16.7 1.0
O2 B:1492001 4.7 9.9 1.0
CG2 B:VAL103 4.8 15.9 1.0
C3 B:1492001 4.9 13.4 1.0
CA B:ASP201 4.9 10.0 1.0

Magnesium binding site 4 out of 9 in 3t0d

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Magnesium binding site 4 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:14.8
occ:1.00
 OD2 B:ASP193 2.1 17.5 1.0
O B:ASP15 2.1 15.5 1.0
O B:ASN18 2.3 15.2 1.0
OE1 B:GLN163 2.3 17.0 1.0
O B:VAL21 2.3 18.2 1.0
CG B:ASP193 2.9 14.3 1.0
OD1 B:ASP193 3.0 16.9 1.0
CD B:GLN163 3.2 19.7 1.0
C B:ASN18 3.2 16.2 1.0
C B:ASP15 3.3 13.4 1.0
C B:VAL21 3.5 18.5 1.0
NE2 B:GLN163 3.5 16.3 1.0
N B:ASN18 3.7 17.6 1.0
CA B:ASN18 3.9 17.0 1.0
CA B:TRP16 3.9 17.5 1.0
N B:TRP16 4.0 14.5 1.0
OH B:TYR161 4.1 14.7 1.0
N B:PRO19 4.2 17.1 1.0
C B:TRP16 4.2 16.0 1.0
CA B:VAL21 4.2 19.2 1.0
CB B:VAL21 4.3 19.1 1.0
CB B:ASN18 4.3 14.3 1.0
N B:VAL21 4.3 19.2 1.0
CB B:ASP193 4.3 11.9 1.0
CE2 B:TYR161 4.4 17.4 1.0
CA B:PRO19 4.4 18.0 1.0
N B:GLU17 4.4 16.5 1.0
CA B:ASP15 4.4 15.4 1.0
N B:THR22 4.5 15.6 1.0
CG B:GLN163 4.5 14.8 1.0
CA B:THR22 4.7 17.1 1.0
CZ B:TYR161 4.7 16.5 1.0
O B:TRP16 4.8 16.1 1.0
CG1 B:VAL21 4.8 21.8 1.0
C B:GLU17 4.9 17.3 1.0
CB B:ASP15 4.9 14.2 1.0
C B:PRO19 5.0 20.9 1.0

Magnesium binding site 5 out of 9 in 3t0d

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Magnesium binding site 5 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3004

b:46.0
occ:1.00
 O B:HOH4301 2.2 23.4 1.0
OE1 B:GLN718 2.3 37.7 1.0
O B:HOH4699 2.3 24.6 1.0
O B:HOH5111 2.5 38.0 1.0
O B:HOH5112 2.6 37.2 1.0
O B:HOH4639 2.9 29.0 1.0
CD B:GLN718 3.3 25.1 1.0
NE2 B:GLN718 3.6 25.9 1.0
O B:THR911 4.1 12.1 1.0
NE2 B:HIS622 4.2 10.6 1.0
O B:HOH4907 4.2 26.6 1.0
O B:HOH4317 4.3 36.0 1.0
O B:HOH4458 4.3 26.3 1.0
O B:HOH4118 4.5 19.2 1.0
O B:GLN719 4.6 15.0 1.0
CG B:GLN718 4.6 20.8 1.0
O B:HOH4291 4.8 16.7 1.0
N B:GLN719 4.8 14.1 1.0
CE1 B:HIS622 4.8 14.9 1.0
O B:HOH4982 5.0 31.4 1.0
C B:THR911 5.0 13.1 1.0

Magnesium binding site 6 out of 9 in 3t0d

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Magnesium binding site 6 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:11.3
occ:1.00
 O C:HOH4211 2.0 11.1 1.0
ND1 C:HIS418 2.1 10.1 1.0
OE2 C:GLU416 2.1 10.8 1.0
OE1 C:GLU461 2.1 12.3 1.0
O C:HOH4133 2.1 8.5 1.0
O C:HOH4069 2.3 6.7 1.0
CE1 C:HIS418 2.9 12.6 1.0
CG C:HIS418 3.2 13.7 1.0
CD C:GLU416 3.2 13.5 1.0
CD C:GLU461 3.3 15.5 1.0
CB C:HIS418 3.6 10.2 1.0
OE1 C:GLU416 3.8 10.7 1.0
OD1 C:ASN102 4.0 15.9 1.0
OE2 C:GLU461 4.1 14.1 1.0
NE2 C:HIS418 4.1 11.0 1.0
CB C:GLU461 4.1 9.8 1.0
C2 C:1492001 4.2 10.9 1.0
O4 C:1492001 4.2 13.0 1.0
CG C:GLU461 4.2 6.7 1.0
CD2 C:HIS418 4.2 8.8 1.0
O C:ASP199 4.2 11.3 1.0
CB C:ASP201 4.3 9.3 1.0
N C:ASP201 4.3 11.3 1.0
ND2 C:ASN460 4.4 9.1 1.0
CG C:GLU416 4.4 10.3 1.0
O3 C:1492001 4.5 12.4 1.0
O C:ASN102 4.7 16.3 1.0
O2 C:1492001 4.7 10.5 1.0
CA C:ASP201 4.9 10.5 1.0
CG2 C:VAL103 4.9 11.9 1.0
C3 C:1492001 4.9 13.9 1.0
C1 C:DMS8028 5.0 46.8 1.0

Magnesium binding site 7 out of 9 in 3t0d

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Magnesium binding site 7 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:16.5
occ:1.00
 OD2 C:ASP193 2.1 19.6 1.0
O C:ASP15 2.1 15.7 1.0
O C:VAL21 2.3 18.2 1.0
O C:ASN18 2.3 16.9 1.0
OE1 C:GLN163 2.3 18.4 1.0
CG C:ASP193 2.9 14.1 1.0
OD1 C:ASP193 3.1 14.4 1.0
CD C:GLN163 3.2 12.9 1.0
C C:ASN18 3.2 17.1 1.0
C C:ASP15 3.3 17.6 1.0
C C:VAL21 3.4 20.6 1.0
NE2 C:GLN163 3.5 13.3 1.0
N C:ASN18 3.7 16.2 1.0
CA C:ASN18 3.9 17.8 1.0
CA C:TRP16 4.0 16.1 1.0
OH C:TYR161 4.0 15.0 1.0
N C:TRP16 4.1 14.1 1.0
CA C:VAL21 4.2 23.4 1.0
N C:PRO19 4.2 17.6 1.0
C C:TRP16 4.2 16.7 1.0
CB C:VAL21 4.3 24.9 1.0
CB C:ASN18 4.3 15.7 1.0
N C:VAL21 4.3 24.9 1.0
CB C:ASP193 4.4 13.6 1.0
CE2 C:TYR161 4.4 17.3 1.0
N C:GLU17 4.4 16.7 1.0
CA C:ASP15 4.4 18.2 1.0
N C:THR22 4.5 18.0 1.0
CA C:PRO19 4.5 17.9 1.0
CG C:GLN163 4.5 18.2 1.0
CZ C:TYR161 4.7 16.2 1.0
CA C:THR22 4.7 17.8 1.0
CG1 C:VAL21 4.7 21.8 1.0
O C:TRP16 4.8 16.7 1.0
C C:GLU17 4.8 19.5 1.0
CB C:ASP15 4.9 15.6 1.0
C C:PRO19 5.0 21.6 1.0

Magnesium binding site 8 out of 9 in 3t0d

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Magnesium binding site 8 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:18.5
occ:1.00
 O D:HOH4116 2.0 16.8 1.0
ND1 D:HIS418 2.1 15.8 1.0
OE2 D:GLU416 2.1 18.7 1.0
OE1 D:GLU461 2.1 14.9 1.0
O D:HOH4193 2.1 16.1 1.0
O D:HOH4052 2.3 14.1 1.0
CE1 D:HIS418 2.9 21.1 1.0
CG D:HIS418 3.2 18.5 1.0
CD D:GLU416 3.2 17.1 1.0
CD D:GLU461 3.2 18.3 1.0
CB D:HIS418 3.6 17.9 1.0
OE1 D:GLU416 3.7 15.4 1.0
OE2 D:GLU461 4.0 22.6 1.0
OD1 D:ASN102 4.1 19.5 1.0
NE2 D:HIS418 4.1 15.4 1.0
C2 D:1492001 4.1 16.0 1.0
CB D:GLU461 4.1 18.3 1.0
O4 D:1492001 4.2 19.3 1.0
CG D:GLU461 4.2 17.3 1.0
CD2 D:HIS418 4.2 15.0 1.0
CB D:ASP201 4.3 20.4 1.0
ND2 D:ASN460 4.3 13.3 1.0
N D:ASP201 4.3 19.9 1.0
O D:ASP199 4.4 18.7 1.0
O3 D:1492001 4.4 18.7 1.0
CG D:GLU416 4.4 18.6 1.0
O2 D:1492001 4.6 18.4 1.0
O D:ASN102 4.7 22.5 1.0
C3 D:1492001 4.8 20.3 1.0
CG2 D:VAL103 4.9 21.0 1.0
CA D:ASP201 4.9 17.6 1.0
C1 D:1492001 5.0 16.1 1.0

Magnesium binding site 9 out of 9 in 3t0d

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Magnesium binding site 9 out of 9 in the E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E.Coli (Lacz) Beta-Galactosidase (S796T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:24.9
occ:1.00
 OD2 D:ASP193 2.1 27.1 1.0
O D:ASP15 2.1 24.2 1.0
O D:ASN18 2.3 25.1 1.0
OE1 D:GLN163 2.3 28.2 1.0
O D:VAL21 2.3 25.5 1.0
CG D:ASP193 2.8 28.8 1.0
OD1 D:ASP193 2.9 28.1 1.0
CD D:GLN163 3.2 27.9 1.0
C D:ASN18 3.2 25.8 1.0
C D:ASP15 3.3 25.7 1.0
C D:VAL21 3.5 22.8 1.0
NE2 D:GLN163 3.6 22.3 1.0
N D:ASN18 3.7 28.2 1.0
CA D:ASN18 3.9 28.2 1.0
CA D:TRP16 3.9 26.4 1.0
OH D:TYR161 4.0 23.9 1.0
N D:TRP16 4.1 26.3 1.0
C D:TRP16 4.2 24.9 1.0
N D:PRO19 4.2 26.5 1.0
CA D:VAL21 4.2 26.0 1.0
CB D:ASN18 4.3 28.6 1.0
CB D:ASP193 4.3 23.4 1.0
CE2 D:TYR161 4.3 19.5 1.0
CB D:VAL21 4.3 27.2 1.0
N D:VAL21 4.3 27.4 1.0
N D:GLU17 4.4 26.9 1.0
CA D:PRO19 4.5 27.9 1.0
CA D:ASP15 4.5 27.2 1.0
N D:THR22 4.5 21.2 1.0
CG D:GLN163 4.5 26.2 1.0
CZ D:TYR161 4.6 23.0 1.0
CA D:THR22 4.7 21.4 1.0
O D:TRP16 4.7 26.5 1.0
CG1 D:VAL21 4.8 27.7 1.0
C D:GLU17 4.8 29.1 1.0
CB D:ASP15 4.9 23.7 1.0
C D:PRO19 4.9 27.0 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Thu Aug 15 11:12:47 2024

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