Atomistry » Magnesium » PDB 4dob-4dv6 » 4duv
Atomistry »
  Magnesium »
    PDB 4dob-4dv6 »
      4duv »

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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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

Go back to Magnesium Binding Sites List in 4duv
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.
Page generated: Thu Aug 15 19:29:44 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy