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Magnesium in PDB 4duv: E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex, PDB code: 4duv was solved by R.W.Wheatley, S.Lo, L.J.Janzcewicz, M.L.Dugdale, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.41 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.570, 167.731, 201.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 20.6

Other elements in 4duv:

The structure of E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex (pdb code 4duv). 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex, PDB code: 4duv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 4duv

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:19.9
occ:1.00
 O A:HOH4999 2.0 15.5 1.0
OE2 A:GLU416 2.1 21.4 1.0
OE1 A:GLU461 2.1 15.8 1.0
O A:HOH4985 2.1 16.7 1.0
O A:HOH4966 2.2 14.7 1.0
ND1 A:HIS418 2.4 20.3 1.0
CD A:GLU416 3.2 22.8 1.0
CD A:GLU461 3.2 20.9 1.0
CE1 A:HIS418 3.3 20.0 1.0
CG A:HIS418 3.4 19.8 1.0
OE1 A:GLU416 3.6 18.4 1.0
CB A:HIS418 3.7 19.2 1.0
OE2 A:GLU461 3.9 17.8 1.0
CB A:ASP201 4.1 15.9 1.0
CB A:GLU461 4.1 12.3 1.0
O4 A:2DG2001 4.1 17.7 1.0
OD1 A:ASN102 4.1 18.8 1.0
N A:ASP201 4.1 16.7 1.0
ND2 A:ASN460 4.1 16.1 1.0
CG A:GLU461 4.2 19.1 1.0
O A:ASP199 4.3 19.9 1.0
O3 A:2DG2001 4.3 17.6 1.0
CG A:GLU416 4.4 19.0 1.0
NE2 A:HIS418 4.4 19.7 1.0
C2 A:2DG2001 4.5 15.9 1.0
CD2 A:HIS418 4.5 21.8 1.0
O A:ASN102 4.7 19.2 1.0
CA A:ASP201 4.7 19.3 1.0
O A:HOH4809 4.8 17.8 1.0
C3 A:2DG2001 4.9 18.0 1.0
C A:GLN200 4.9 20.3 1.0
CA A:GLN200 4.9 19.0 1.0

Magnesium binding site 2 out of 9 in 4duv

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:22.9
occ:1.00
 OD2 A:ASP193 2.1 21.7 1.0
O A:VAL21 2.3 24.9 1.0
O A:ASP15 2.3 24.0 1.0
OE1 A:GLN163 2.3 20.1 1.0
O A:ASN18 2.3 25.5 1.0
CG A:ASP193 2.9 26.6 1.0
OD1 A:ASP193 3.0 23.6 1.0
CD A:GLN163 3.2 26.1 1.0
C A:ASN18 3.2 24.7 1.0
NE2 A:GLN163 3.4 22.0 1.0
C A:VAL21 3.4 23.5 1.0
C A:ASP15 3.5 26.1 1.0
N A:ASN18 3.6 27.4 1.0
CA A:ASN18 3.9 27.0 1.0
OH A:TYR161 4.0 21.5 1.0
CA A:TRP16 4.1 26.5 1.0
N A:PRO19 4.1 23.6 1.0
N A:TRP16 4.2 25.7 1.0
CA A:VAL21 4.3 24.2 1.0
CB A:ASN18 4.3 25.2 1.0
C A:TRP16 4.3 23.2 1.0
CB A:ASP193 4.3 23.4 1.0
N A:VAL21 4.3 23.9 1.0
CE2 A:TYR161 4.4 16.8 1.0
CB A:VAL21 4.4 26.9 1.0
CA A:PRO19 4.4 22.7 1.0
N A:THR22 4.4 21.0 1.0
N A:GLU17 4.4 24.3 1.0
CG A:GLN163 4.5 21.6 1.0
CA A:THR22 4.6 25.4 1.0
CA A:ASP15 4.6 25.8 1.0
CZ A:TYR161 4.7 21.7 1.0
CG1 A:VAL21 4.8 23.2 1.0
C A:GLU17 4.8 25.2 1.0
O A:TRP16 4.9 24.4 1.0
C A:PRO19 4.9 22.0 1.0

Magnesium binding site 3 out of 9 in 4duv

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:23.8
occ:1.00
 OE2 B:GLU416 2.1 19.4 1.0
OE1 B:GLU461 2.1 18.4 1.0
O B:HOH4937 2.1 22.4 1.0
O B:HOH4908 2.2 19.9 1.0
O B:HOH4176 2.2 19.0 1.0
ND1 B:HIS418 2.4 18.2 1.0
CD B:GLU461 3.1 21.2 1.0
CD B:GLU416 3.2 23.3 1.0
CE1 B:HIS418 3.2 19.2 1.0
CG B:HIS418 3.4 19.8 1.0
OE1 B:GLU416 3.6 16.7 1.0
CB B:HIS418 3.8 20.3 1.0
OE2 B:GLU461 3.8 17.6 1.0
O4 B:2DG2001 4.0 14.7 1.0
CB B:ASP201 4.1 20.0 1.0
CB B:GLU461 4.1 21.9 1.0
OD1 B:ASN102 4.1 17.7 1.0
ND2 B:ASN460 4.1 18.3 1.0
CG B:GLU461 4.1 22.9 1.0
N B:ASP201 4.2 20.7 1.0
O B:ASP199 4.3 20.1 1.0
O3 B:2DG2001 4.4 17.4 1.0
NE2 B:HIS418 4.4 22.3 1.0
CG B:GLU416 4.4 16.5 1.0
C2 B:2DG2001 4.5 13.8 1.0
O B:HOH4028 4.5 17.5 1.0
CD2 B:HIS418 4.5 18.8 1.0
CA B:ASP201 4.7 17.9 1.0
O B:ASN102 4.7 20.8 1.0
C3 B:2DG2001 4.9 19.3 1.0
C B:GLN200 5.0 23.4 1.0
CA B:GLN200 5.0 23.7 1.0

Magnesium binding site 4 out of 9 in 4duv

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:26.6
occ:1.00
 OD2 B:ASP193 2.1 28.1 1.0
O B:ASN18 2.3 25.2 1.0
O B:ASP15 2.3 29.3 1.0
O B:VAL21 2.3 24.1 1.0
OE1 B:GLN163 2.3 29.2 1.0
CG B:ASP193 2.9 26.4 1.0
OD1 B:ASP193 3.0 25.2 1.0
CD B:GLN163 3.2 30.7 1.0
C B:ASN18 3.2 25.7 1.0
C B:VAL21 3.5 27.0 1.0
C B:ASP15 3.5 28.9 1.0
NE2 B:GLN163 3.5 25.5 1.0
N B:ASN18 3.6 28.4 1.0
CA B:ASN18 3.9 27.0 1.0
OH B:TYR161 3.9 28.1 1.0
CA B:TRP16 4.0 26.2 1.0
N B:PRO19 4.1 27.1 1.0
N B:TRP16 4.2 25.1 1.0
C B:TRP16 4.2 24.4 1.0
CA B:VAL21 4.3 26.1 1.0
CB B:ASP193 4.3 23.9 1.0
CB B:ASN18 4.3 25.0 1.0
CA B:PRO19 4.4 28.9 1.0
N B:GLU17 4.4 27.7 1.0
CE2 B:TYR161 4.4 17.9 1.0
N B:VAL21 4.4 30.0 1.0
N B:THR22 4.4 25.2 1.0
CB B:VAL21 4.5 27.0 1.0
CG B:GLN163 4.5 24.2 1.0
CA B:THR22 4.6 27.6 1.0
CA B:ASP15 4.6 30.8 1.0
CZ B:TYR161 4.6 25.9 1.0
O B:TRP16 4.8 26.5 1.0
C B:GLU17 4.8 28.4 1.0
C B:PRO19 4.9 30.0 1.0
CG1 B:VAL21 5.0 24.9 1.0

Magnesium binding site 5 out of 9 in 4duv

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:53.1
occ:1.00
 O B:HOH4545 2.0 36.8 1.0
O B:HOH4279 2.1 34.2 1.0
O B:HOH4958 2.3 48.4 1.0
O B:HOH4801 2.4 38.1 1.0
O B:HOH4587 2.5 44.4 1.0
OE1 B:GLN718 2.8 41.1 1.0
CD B:GLN718 3.8 34.8 1.0
O B:THR911 3.8 22.0 1.0
NE2 B:GLN718 4.0 26.7 1.0
NE2 B:HIS622 4.2 23.3 1.0
O B:HOH4026 4.3 45.5 1.0
O B:HOH4692 4.3 45.2 1.0
O B:HOH4294 4.4 37.7 1.0
O B:HOH4102 4.4 21.6 1.0
O B:HOH4410 4.6 40.9 1.0
O B:HOH4766 4.6 46.9 1.0
C B:THR911 4.7 23.2 1.0
O B:HOH4269 4.7 34.8 1.0
CB B:THR911 4.7 20.5 1.0
CA B:THR911 4.7 22.0 1.0
O B:GLN719 4.9 27.4 1.0
CE1 B:HIS622 4.9 23.0 1.0

Magnesium binding site 6 out of 9 in 4duv

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:22.5
occ:1.00
 OE2 C:GLU416 2.1 18.1 1.0
OE1 C:GLU461 2.1 19.1 1.0
O C:HOH4931 2.2 18.7 1.0
O C:HOH4892 2.2 17.9 1.0
O C:HOH4951 2.2 18.7 1.0
ND1 C:HIS418 2.4 18.0 1.0
CD C:GLU461 3.1 20.6 1.0
CD C:GLU416 3.2 24.0 1.0
CE1 C:HIS418 3.3 21.3 1.0
CG C:HIS418 3.4 17.0 1.0
OE1 C:GLU416 3.7 24.0 1.0
CB C:HIS418 3.7 20.0 1.0
OE2 C:GLU461 3.8 22.1 1.0
CB C:GLU461 4.1 19.7 1.0
O4 C:2DG2001 4.1 17.9 1.0
ND2 C:ASN460 4.1 17.5 1.0
OD1 C:ASN102 4.1 19.0 1.0
CB C:ASP201 4.1 21.6 1.0
CG C:GLU461 4.1 18.5 1.0
N C:ASP201 4.2 22.3 1.0
O C:ASP199 4.3 22.8 1.0
O3 C:2DG2001 4.3 23.0 1.0
NE2 C:HIS418 4.4 18.7 1.0
CG C:GLU416 4.4 19.8 1.0
C2 C:2DG2001 4.5 13.8 1.0
O C:HOH4979 4.5 20.6 1.0
CD2 C:HIS418 4.5 18.7 1.0
O C:ASN102 4.7 23.2 1.0
CA C:ASP201 4.8 20.1 1.0
C3 C:2DG2001 4.9 19.2 1.0
CG2 C:VAL103 5.0 24.0 1.0
CA C:GLN200 5.0 23.8 1.0
C C:GLN200 5.0 23.4 1.0

Magnesium binding site 7 out of 9 in 4duv

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:28.2
occ:1.00
 OD2 C:ASP193 2.1 29.6 1.0
O C:ASN18 2.3 27.1 1.0
OE1 C:GLN163 2.3 30.1 1.0
O C:VAL21 2.3 28.6 1.0
O C:ASP15 2.3 32.4 1.0
CG C:ASP193 2.9 28.1 1.0
OD1 C:ASP193 3.0 28.1 1.0
CD C:GLN163 3.2 33.5 1.0
C C:ASN18 3.2 29.8 1.0
C C:VAL21 3.5 27.6 1.0
C C:ASP15 3.5 30.7 1.0
NE2 C:GLN163 3.5 25.9 1.0
N C:ASN18 3.7 33.0 1.0
CA C:ASN18 4.0 29.4 1.0
OH C:TYR161 4.0 25.3 1.0
CA C:TRP16 4.0 28.8 1.0
N C:PRO19 4.2 29.7 1.0
N C:TRP16 4.2 29.6 1.0
C C:TRP16 4.2 28.8 1.0
CA C:VAL21 4.3 27.7 1.0
CB C:ASP193 4.3 25.9 1.0
CB C:ASN18 4.4 27.6 1.0
CE2 C:TYR161 4.4 22.6 1.0
N C:VAL21 4.4 27.4 1.0
N C:GLU17 4.4 30.8 1.0
CA C:PRO19 4.4 29.8 1.0
N C:THR22 4.4 26.9 1.0
CG C:GLN163 4.5 26.0 1.0
CB C:VAL21 4.5 33.3 1.0
CA C:THR22 4.6 27.6 1.0
CA C:ASP15 4.6 31.8 1.0
CZ C:TYR161 4.7 23.2 1.0
O C:TRP16 4.8 29.8 1.0
C C:GLU17 4.9 32.4 1.0
C C:PRO19 4.9 29.8 1.0

Magnesium binding site 8 out of 9 in 4duv

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:24.0
occ:1.00
 OE2 D:GLU416 2.1 19.9 1.0
OE1 D:GLU461 2.1 18.3 1.0
O D:HOH4910 2.1 14.5 1.0
O D:HOH4060 2.2 16.6 1.0
O D:HOH4200 2.3 13.0 1.0
ND1 D:HIS418 2.4 16.0 1.0
CD D:GLU461 3.1 21.3 1.0
CD D:GLU416 3.2 13.0 1.0
CE1 D:HIS418 3.3 17.6 1.0
CG D:HIS418 3.4 15.8 1.0
CB D:HIS418 3.7 15.3 1.0
OE1 D:GLU416 3.7 19.2 1.0
OE2 D:GLU461 3.8 21.9 1.0
CB D:GLU461 4.0 13.5 1.0
O4 D:2DG2001 4.1 19.3 1.0
CB D:ASP201 4.1 16.0 1.0
OD1 D:ASN102 4.1 20.1 1.0
CG D:GLU461 4.1 13.6 1.0
N D:ASP201 4.2 19.6 1.0
O D:ASP199 4.3 20.9 1.0
ND2 D:ASN460 4.3 16.1 1.0
CG D:GLU416 4.4 14.2 1.0
NE2 D:HIS418 4.4 15.1 1.0
O3 D:2DG2001 4.5 20.6 1.0
CD2 D:HIS418 4.5 15.8 1.0
O D:HOH4757 4.5 17.2 1.0
C2 D:2DG2001 4.6 16.6 1.0
O D:ASN102 4.6 19.9 1.0
CA D:ASP201 4.7 17.6 1.0
C3 D:2DG2001 5.0 22.2 1.0

Magnesium binding site 9 out of 9 in 4duv

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris 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 (G974A) 2-Deoxy-Galactosyl-Enzyme and Bis-Tris Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:24.3
occ:1.00
 OD2 D:ASP193 2.1 19.6 1.0
O D:ASN18 2.3 23.0 1.0
O D:ASP15 2.3 29.2 1.0
OE1 D:GLN163 2.3 23.2 1.0
O D:VAL21 2.3 24.1 1.0
CG D:ASP193 2.8 26.2 1.0
OD1 D:ASP193 2.9 21.2 1.0
CD D:GLN163 3.2 26.2 1.0
C D:ASN18 3.2 25.6 1.0
C D:ASP15 3.5 28.9 1.0
NE2 D:GLN163 3.5 19.0 1.0
C D:VAL21 3.5 24.4 1.0
N D:ASN18 3.7 29.8 1.0
CA D:ASN18 3.9 26.7 1.0
CA D:TRP16 4.0 27.0 1.0
OH D:TYR161 4.0 22.0 1.0
N D:PRO19 4.1 25.1 1.0
N D:TRP16 4.2 25.1 1.0
C D:TRP16 4.2 25.6 1.0
CB D:ASP193 4.3 23.3 1.0
CA D:VAL21 4.3 24.8 1.0
CB D:ASN18 4.3 24.8 1.0
CA D:PRO19 4.4 26.4 1.0
N D:VAL21 4.4 25.2 1.0
N D:GLU17 4.4 24.7 1.0
N D:THR22 4.5 23.2 1.0
CB D:VAL21 4.5 25.6 1.0
CE2 D:TYR161 4.5 25.2 1.0
CG D:GLN163 4.5 19.8 1.0
CA D:ASP15 4.6 29.6 1.0
CA D:THR22 4.6 22.9 1.0
CZ D:TYR161 4.7 26.1 1.0
O D:TRP16 4.8 27.1 1.0
C D:GLU17 4.9 28.8 1.0
C D:PRO19 4.9 25.9 1.0
CG1 D:VAL21 4.9 26.3 1.0

Reference:

R.W.Wheatley, S.Lo, L.J.Janzcewicz, M.L.Dugdale, R.E.Huber. The Glucose Acceptor Site of Lacz Beta-Galactosidase For the Synthesis of Allolactose - the Natural Inducer of the Lac Operon To Be Published.
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