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Magnesium in PDB 3t09: E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex, PDB code: 3t09 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) 128.40 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 126.881, 151.197, 131.808, 90.00, 103.05, 90.00
R / Rfree (%) 21.5 / 25.4

Other elements in 3t09:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex (pdb code 3t09). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex, PDB code: 3t09:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 3t09

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Magnesium binding site 1 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:12.3
occ:1.00
 O A:HOH5049 2.0 12.0 1.0
O A:HOH5060 2.0 10.2 1.0
OE2 A:GLU416 2.1 12.8 1.0
OE1 A:GLU461 2.1 13.1 1.0
O A:HOH5038 2.2 13.9 1.0
ND1 A:HIS418 2.3 14.5 1.0
CD A:GLU416 3.2 13.3 1.0
CE1 A:HIS418 3.2 11.7 1.0
CD A:GLU461 3.2 16.7 1.0
CG A:HIS418 3.3 11.7 1.0
CB A:HIS418 3.6 11.8 1.0
OE1 A:GLU416 3.7 12.1 1.0
OE2 A:GLU461 3.9 19.7 1.0
OD1 A:ASN102 4.1 18.3 1.0
CB A:GLU461 4.2 13.1 1.0
CB A:ASP201 4.2 9.4 1.0
O A:ASP199 4.2 14.6 1.0
N A:ASP201 4.2 14.7 1.0
CG A:GLU461 4.2 11.8 1.0
C2 A:1492001 4.2 14.9 1.0
O4 A:1492001 4.3 13.6 1.0
NE2 A:HIS418 4.3 15.2 1.0
CD2 A:HIS418 4.4 11.0 1.0
CG A:GLU416 4.4 8.7 1.0
ND2 A:ASN460 4.4 9.7 1.0
O3 A:1492001 4.5 13.1 1.0
O A:ASN102 4.6 15.0 1.0
O2 A:1492001 4.7 12.2 1.0
CA A:ASP201 4.8 14.4 1.0
C3 A:1492001 4.9 14.2 1.0
C A:GLN200 5.0 12.9 1.0

Magnesium binding site 2 out of 11 in 3t09

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Magnesium binding site 2 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:17.0
occ:1.00
 O A:ASP15 2.1 17.9 1.0
OD2 A:ASP193 2.1 19.9 1.0
O A:ASN18 2.3 20.8 1.0
O A:VAL21 2.3 18.2 1.0
OE1 A:GLN163 2.3 18.2 1.0
CG A:ASP193 2.9 16.6 1.0
OD1 A:ASP193 3.1 19.1 1.0
CD A:GLN163 3.1 16.6 1.0
C A:ASN18 3.2 16.6 1.0
C A:ASP15 3.3 17.1 1.0
C A:VAL21 3.4 14.2 1.0
NE2 A:GLN163 3.5 12.8 1.0
N A:ASN18 3.7 19.9 1.0
CA A:ASN18 3.9 22.7 1.0
CA A:TRP16 3.9 16.6 1.0
OH A:TYR161 4.0 18.5 1.0
N A:TRP16 4.0 17.3 1.0
N A:PRO19 4.2 14.7 1.0
CB A:ASN18 4.2 23.1 1.0
C A:TRP16 4.2 17.0 1.0
CA A:VAL21 4.2 15.4 1.0
CB A:VAL21 4.3 17.8 1.0
CE2 A:TYR161 4.3 17.7 1.0
N A:VAL21 4.3 19.7 1.0
N A:GLU17 4.4 14.7 1.0
CB A:ASP193 4.4 15.6 1.0
N A:THR22 4.4 15.5 1.0
CA A:ASP15 4.4 17.1 1.0
CG A:GLN163 4.5 16.9 1.0
CA A:PRO19 4.5 17.6 1.0
CA A:THR22 4.6 14.1 1.0
CZ A:TYR161 4.6 16.5 1.0
CG1 A:VAL21 4.8 17.8 1.0
O A:TRP16 4.8 18.4 1.0
C A:GLU17 4.8 19.5 1.0
CB A:ASP15 4.9 16.0 1.0
C A:PRO19 5.0 21.3 1.0

Magnesium binding site 3 out of 11 in 3t09

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Magnesium binding site 3 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:31.4
occ:1.00
 O A:HOH5069 2.1 38.0 1.0
O A:HOH5050 2.2 19.1 1.0
O A:HOH5068 2.2 35.3 1.0
O A:HOH5063 2.2 30.4 1.0
OE1 A:GLN718 2.3 30.9 1.0
O A:HOH4592 2.3 33.6 1.0
CD A:GLN718 3.2 22.2 1.0
NE2 A:GLN718 3.6 21.2 1.0
O A:THR911 3.9 16.8 1.0
C1 A:DMS8023 4.0 52.6 1.0
NE2 A:HIS622 4.2 21.1 1.0
O A:HOH4403 4.3 29.1 1.0
O A:HOH5070 4.4 34.8 1.0
O A:HOH4245 4.5 22.6 1.0
O A:GLN719 4.5 17.8 1.0
N A:GLN719 4.6 14.9 1.0
CG A:GLN718 4.6 22.1 1.0
O A:HOH4076 4.7 17.4 1.0
CE1 A:HIS622 4.7 23.7 1.0
C A:THR911 4.8 13.9 1.0
CA A:THR911 4.9 15.1 1.0
CB A:THR911 5.0 18.3 1.0

Magnesium binding site 4 out of 11 in 3t09

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Magnesium binding site 4 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:39.1
occ:1.00
 O A:HOH5071 1.9 28.4 1.0
O A:HOH5072 1.9 43.2 1.0
O A:HOH5073 2.1 42.4 1.0
O A:HOH4615 2.2 24.4 1.0
O A:HOH5058 2.3 31.5 1.0
O A:HOH4887 3.9 45.0 1.0
O A:HOH4782 4.2 27.5 1.0
OE2 A:GLU314 4.3 22.6 1.0
O A:HOH4664 4.3 20.7 1.0
OE1 A:GLU314 4.3 20.3 1.0
C2 A:DMS8006 4.6 33.1 1.0
O A:DMS8006 4.7 41.9 1.0
CD A:GLU314 4.8 22.3 1.0

Magnesium binding site 5 out of 11 in 3t09

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Magnesium binding site 5 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:18.5
occ:1.00
 O B:HOH5014 2.0 18.6 1.0
OE2 B:GLU416 2.1 17.3 1.0
OE1 B:GLU461 2.1 14.5 1.0
O B:HOH5000 2.1 17.5 1.0
O B:HOH5008 2.2 13.7 1.0
ND1 B:HIS418 2.3 14.3 1.0
CE1 B:HIS418 3.2 10.9 1.0
CD B:GLU416 3.2 15.7 1.0
CD B:GLU461 3.2 11.1 1.0
CG B:HIS418 3.3 16.1 1.0
CB B:HIS418 3.6 13.7 1.0
OE1 B:GLU416 3.7 12.9 1.0
OE2 B:GLU461 4.0 16.6 1.0
CB B:GLU461 4.1 12.9 1.0
OD1 B:ASN102 4.2 18.9 1.0
C2 B:1492001 4.2 14.3 1.0
O4 B:1492001 4.2 13.4 1.0
CG B:GLU461 4.2 14.6 1.0
O B:ASP199 4.2 15.3 1.0
N B:ASP201 4.2 14.4 1.0
CB B:ASP201 4.2 12.6 1.0
NE2 B:HIS418 4.3 12.5 1.0
ND2 B:ASN460 4.3 11.3 1.0
CD2 B:HIS418 4.4 15.5 1.0
CG B:GLU416 4.4 16.9 1.0
O3 B:1492001 4.4 19.1 1.0
O B:ASN102 4.7 17.9 1.0
O2 B:1492001 4.7 14.5 1.0
CA B:ASP201 4.8 14.6 1.0
C3 B:1492001 4.8 13.9 1.0
C B:GLN200 4.9 14.9 1.0
CA B:GLN200 5.0 13.2 1.0

Magnesium binding site 6 out of 11 in 3t09

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Magnesium binding site 6 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:21.1
occ:1.00
 O B:ASP15 2.1 20.8 1.0
OD2 B:ASP193 2.1 25.4 1.0
O B:ASN18 2.3 23.5 1.0
O B:VAL21 2.3 22.2 1.0
OE1 B:GLN163 2.3 21.6 1.0
CG B:ASP193 2.9 22.9 1.0
OD1 B:ASP193 3.0 25.1 1.0
C B:ASN18 3.2 21.9 1.0
CD B:GLN163 3.2 21.7 1.0
C B:ASP15 3.3 24.7 1.0
C B:VAL21 3.5 22.9 1.0
NE2 B:GLN163 3.6 18.8 1.0
N B:ASN18 3.7 23.4 1.0
CA B:TRP16 3.9 26.1 1.0
CA B:ASN18 3.9 24.9 1.0
OH B:TYR161 4.0 20.8 1.0
N B:TRP16 4.0 24.8 1.0
N B:PRO19 4.2 21.4 1.0
C B:TRP16 4.2 24.0 1.0
CB B:ASN18 4.3 25.9 1.0
CA B:VAL21 4.3 25.9 1.0
CE2 B:TYR161 4.3 20.5 1.0
CB B:ASP193 4.3 18.1 1.0
CA B:PRO19 4.4 20.7 1.0
N B:GLU17 4.4 23.0 1.0
CB B:VAL21 4.4 22.2 1.0
N B:VAL21 4.4 24.3 1.0
CA B:ASP15 4.4 27.1 1.0
N B:THR22 4.4 20.4 1.0
CG B:GLN163 4.6 19.2 1.0
CZ B:TYR161 4.6 18.0 1.0
CA B:THR22 4.6 19.8 1.0
O B:TRP16 4.8 19.4 1.0
CG1 B:VAL21 4.8 30.3 1.0
C B:GLU17 4.9 25.6 1.0
CB B:ASP15 4.9 28.8 1.0
C B:PRO19 4.9 22.0 1.0

Magnesium binding site 7 out of 11 in 3t09

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Magnesium binding site 7 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:27.8
occ:0.50
 O B:HOH4441 2.2 38.9 1.0
OE1 B:GLN718 2.3 31.7 1.0
O B:HOH4278 2.3 20.6 1.0
O B:HOH4676 2.4 37.3 1.0
O B:HOH4385 2.5 34.8 1.0
O B:HOH4618 2.9 39.7 1.0
CD B:GLN718 3.3 28.7 1.0
NE2 B:GLN718 3.6 22.2 1.0
O B:HOH4425 4.0 24.6 1.0
O B:THR911 4.1 18.1 1.0
NE2 B:HIS622 4.2 17.8 1.0
O B:HOH4294 4.3 26.6 1.0
O B:HOH4814 4.3 42.8 1.0
O B:HOH4098 4.4 20.8 1.0
O B:DMS8021 4.5 52.4 1.0
O B:GLN719 4.5 17.4 1.0
C1 B:DMS8021 4.6 52.1 1.0
N B:GLN719 4.6 14.7 1.0
CG B:GLN718 4.6 17.5 1.0
O B:HOH4268 4.8 20.6 1.0
CE1 B:HIS622 4.8 25.5 1.0
C B:THR911 5.0 16.1 1.0

Magnesium binding site 8 out of 11 in 3t09

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Magnesium binding site 8 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:11.9
occ:1.00
 O C:HOH5049 2.0 12.9 1.0
OE2 C:GLU416 2.1 8.2 1.0
OE1 C:GLU461 2.1 13.9 1.0
O C:HOH5033 2.1 17.9 1.0
O C:HOH5017 2.1 14.9 1.0
ND1 C:HIS418 2.3 15.6 1.0
CE1 C:HIS418 3.2 20.1 1.0
CD C:GLU416 3.2 12.8 1.0
CD C:GLU461 3.2 13.2 1.0
CG C:HIS418 3.3 16.0 1.0
CB C:HIS418 3.6 15.7 1.0
OE1 C:GLU416 3.7 13.7 1.0
OE2 C:GLU461 4.0 17.8 1.0
CB C:GLU461 4.2 16.4 1.0
OD1 C:ASN102 4.2 14.7 1.0
C2 C:1492001 4.2 10.0 1.0
N C:ASP201 4.2 16.7 1.0
CG C:GLU461 4.2 14.7 1.0
O4 C:1492001 4.2 14.0 1.0
CB C:ASP201 4.2 11.7 1.0
O C:ASP199 4.3 15.2 1.0
NE2 C:HIS418 4.3 20.6 1.0
CG C:GLU416 4.4 9.1 1.0
CD2 C:HIS418 4.4 18.9 1.0
O3 C:1492001 4.4 14.6 1.0
ND2 C:ASN460 4.4 18.1 1.0
O C:DMS8025 4.5 40.0 1.0
O2 C:1492001 4.7 13.2 1.0
O C:ASN102 4.7 17.5 1.0
CA C:ASP201 4.8 18.5 1.0
C3 C:1492001 4.8 12.3 1.0
C C:GLN200 4.9 16.9 1.0
CA C:GLN200 5.0 17.2 1.0

Magnesium binding site 9 out of 11 in 3t09

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Magnesium binding site 9 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


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 (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:16.6
occ:1.00
 OD2 C:ASP193 2.1 15.6 1.0
O C:ASP15 2.1 21.0 1.0
O C:ASN18 2.3 23.2 1.0
O C:VAL21 2.3 18.9 1.0
OE1 C:GLN163 2.3 16.1 1.0
CG C:ASP193 2.9 16.9 1.0
OD1 C:ASP193 3.1 22.1 1.0
CD C:GLN163 3.2 14.2 1.0
C C:ASN18 3.2 22.8 1.0
C C:ASP15 3.3 18.6 1.0
C C:VAL21 3.5 22.1 1.0
NE2 C:GLN163 3.5 14.3 1.0
N C:ASN18 3.7 21.9 1.0
CA C:TRP16 3.9 19.2 1.0
CA C:ASN18 3.9 22.2 1.0
OH C:TYR161 4.0 18.4 1.0
N C:TRP16 4.0 17.3 1.0
N C:PRO19 4.2 23.5 1.0
C C:TRP16 4.2 17.6 1.0
CA C:VAL21 4.3 18.6 1.0
CB C:ASN18 4.3 20.8 1.0
CE2 C:TYR161 4.4 16.4 1.0
CB C:ASP193 4.4 16.3 1.0
N C:VAL21 4.4 22.1 1.0
N C:GLU17 4.4 20.3 1.0
CB C:VAL21 4.4 22.9 1.0
CA C:ASP15 4.4 20.6 1.0
N C:THR22 4.5 21.2 1.0
CA C:PRO19 4.5 24.3 1.0
CG C:GLN163 4.6 19.9 1.0
CA C:THR22 4.6 19.2 1.0
CZ C:TYR161 4.7 18.3 1.0
O C:TRP16 4.8 20.1 1.0
C C:GLU17 4.9 25.4 1.0
CB C:ASP15 4.9 20.0 1.0
CG1 C:VAL21 5.0 19.4 1.0
C C:PRO19 5.0 23.9 1.0

Magnesium binding site 10 out of 11 in 3t09

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Magnesium binding site 10 out of 11 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E. Coli (Lacz) Beta-Galactosidase (S796A) Galactonolactone Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:14.7
occ:1.00
 O D:HOH5063 2.0 14.7 1.0
O D:HOH5073 2.0 10.6 1.0
OE2 D:GLU416 2.1 9.9 1.0
OE1 D:GLU461 2.1 14.5 1.0
O D:HOH5054 2.2 13.8 1.0
ND1 D:HIS418 2.3 18.0 1.0
CE1 D:HIS418 3.1 16.2 1.0
CD D:GLU416 3.1 13.5 1.0
CD D:GLU461 3.2 17.3 1.0
CG D:HIS418 3.3 11.6 1.0
OE1 D:GLU416 3.6 12.2 1.0
CB D:HIS418 3.7 10.2 1.0
OE2 D:GLU461 3.9 19.2 1.0
OD1 D:ASN102 4.1 16.6 1.0
C2 D:1492001 4.1 11.1 1.0
CB D:GLU461 4.2 13.3 1.0
CB D:ASP201 4.2 9.2 1.0
O4 D:1492001 4.2 13.1 1.0
N D:ASP201 4.2 14.8 1.0
CG D:GLU461 4.2 15.4 1.0
O D:ASP199 4.3 14.6 1.0
NE2 D:HIS418 4.3 16.7 1.0
O3 D:1492001 4.4 14.7 1.0
ND2 D:ASN460 4.4 13.0 1.0
CG D:GLU416 4.4 10.7 1.0
CD2 D:HIS418 4.4 13.1 1.0
O2 D:1492001 4.6 14.8 1.0
O D:ASN102 4.7 17.1 1.0
C3 D:1492001 4.8 12.2 1.0
CA D:ASP201 4.8 13.0 1.0
C D:GLN200 4.9 15.7 1.0
CA D:GLN200 4.9 9.0 1.0
C1 D:1492001 5.0 14.7 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 11:12:43 2024

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