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Magnesium in PDB 1jz4: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris), PDB code: 1jz4 was solved by D.H.Juers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.500, 169.000, 200.800, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 26.7

Other elements in 1jz4:

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) also contains other interesting chemical elements:

Sodium (Na) 15 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) (pdb code 1jz4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris), PDB code: 1jz4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 1jz4

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Magnesium binding site 1 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:13.7
occ:1.00
O A:HOH8615 2.0 7.8 1.0
OE2 A:GLU416 2.0 10.0 1.0
O A:HOH8756 2.1 10.1 1.0
O A:HOH8678 2.1 5.4 1.0
ND1 A:HIS418 2.2 8.5 1.0
OE1 A:GLU461 2.2 13.8 1.0
CE1 A:HIS418 3.0 10.4 1.0
CD A:GLU416 3.1 15.2 1.0
CD A:GLU461 3.2 16.3 1.0
CG A:HIS418 3.3 14.2 1.0
OE1 A:GLU416 3.5 7.0 1.0
CB A:HIS418 3.7 17.2 1.0
OD1 A:ASN102 3.8 17.8 1.0
OE2 A:GLU461 4.0 13.1 1.0
CB A:GLU461 4.0 1.0 1.0
O4 A:2DG2001 4.1 16.5 1.0
CB A:ASP201 4.1 13.5 1.0
ND2 A:ASN460 4.1 9.9 1.0
N A:ASP201 4.1 18.7 1.0
CG A:GLU461 4.2 9.3 1.0
NE2 A:HIS418 4.2 7.0 1.0
O3 A:2DG2001 4.3 16.4 1.0
O A:ASP199 4.3 12.7 1.0
CD2 A:HIS418 4.4 9.6 1.0
CG A:GLU416 4.4 7.2 1.0
C2 A:2DG2001 4.6 15.1 1.0
O A:ASN102 4.6 15.3 1.0
CA A:ASP201 4.7 11.8 1.0
O A:HOH9135 4.7 18.7 1.0
CA A:GLN200 4.8 5.8 1.0
C A:GLN200 4.8 14.9 1.0
C3 A:2DG2001 4.9 18.0 1.0
CG2 A:VAL103 5.0 6.4 1.0

Magnesium binding site 2 out of 10 in 1jz4

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Magnesium binding site 2 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:14.3
occ:1.00
OE1 A:GLN163 2.2 14.6 1.0
O A:ASN18 2.2 15.0 1.0
O A:ASP15 2.3 22.9 1.0
O A:VAL21 2.3 11.0 1.0
OD2 A:ASP193 2.3 13.6 1.0
OD1 A:ASP193 3.0 14.2 1.0
CG A:ASP193 3.0 27.9 1.0
CD A:GLN163 3.0 16.2 1.0
C A:ASN18 3.1 11.8 1.0
NE2 A:GLN163 3.2 13.7 1.0
C A:VAL21 3.5 17.5 1.0
C A:ASP15 3.5 17.6 1.0
N A:ASN18 3.6 12.1 1.0
OH A:TYR161 3.9 12.0 1.0
CA A:ASN18 3.9 9.7 1.0
N A:PRO19 3.9 19.5 1.0
CA A:TRP16 4.0 10.5 1.0
C A:TRP16 4.1 12.7 1.0
N A:TRP16 4.2 7.5 1.0
CA A:PRO19 4.2 17.2 1.0
N A:VAL21 4.2 12.4 1.0
CA A:VAL21 4.3 10.9 1.0
N A:THR22 4.4 13.0 1.0
N A:GLU17 4.4 9.0 1.0
CB A:ASN18 4.4 1.0 1.0
CG A:GLN163 4.4 14.3 1.0
CE2 A:TYR161 4.4 14.5 1.0
CB A:ASP193 4.5 9.2 1.0
CA A:THR22 4.5 18.7 1.0
CB A:VAL21 4.5 18.7 1.0
O A:TRP16 4.6 10.7 1.0
CZ A:TYR161 4.7 9.9 1.0
CA A:ASP15 4.7 16.4 1.0
C A:PRO19 4.8 13.8 1.0
C A:GLU17 4.8 18.9 1.0
CG1 A:VAL21 5.0 20.2 1.0
N A:ASP193 5.0 13.3 1.0

Magnesium binding site 3 out of 10 in 1jz4

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Magnesium binding site 3 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:37.0
occ:1.00
O A:HOH9396 1.8 27.9 1.0
O A:HOH9473 2.0 25.9 1.0
O A:HOH9397 2.1 32.0 1.0
O A:HOH9225 2.1 27.3 1.0
O A:HOH9269 3.8 35.8 1.0
O A:HOH9503 3.9 21.6 1.0
OE1 A:GLU314 4.1 16.6 1.0
OE2 A:GLU314 4.4 27.2 1.0
C1 A:DMS8406 4.6 0.0 1.0
O A:DMS8406 4.7 53.9 1.0
CD A:GLU314 4.7 11.4 1.0
O A:HOH9246 4.9 22.5 1.0

Magnesium binding site 4 out of 10 in 1jz4

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Magnesium binding site 4 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:11.5
occ:1.00
OE1 B:GLU461 1.9 12.2 1.0
O B:HOH8694 2.0 7.3 1.0
OE2 B:GLU416 2.0 11.1 1.0
ND1 B:HIS418 2.1 7.3 1.0
O B:HOH8631 2.1 8.0 1.0
O B:HOH8771 2.2 9.3 1.0
CD B:GLU461 2.9 12.6 1.0
CE1 B:HIS418 3.0 7.4 1.0
CD B:GLU416 3.2 11.0 1.0
CG B:HIS418 3.3 13.2 1.0
OE1 B:GLU416 3.6 10.4 1.0
CB B:HIS418 3.7 12.2 1.0
OE2 B:GLU461 3.8 11.8 1.0
OD1 B:ASN102 4.0 10.4 1.0
CG B:GLU461 4.0 4.5 1.0
CB B:GLU461 4.0 8.0 1.0
O4 B:2DG2001 4.1 13.8 1.0
CB B:ASP201 4.1 16.6 1.0
O3 B:2DG2001 4.2 14.0 1.0
NE2 B:HIS418 4.2 5.3 1.0
ND2 B:ASN460 4.2 8.8 1.0
N B:ASP201 4.3 13.8 1.0
CG B:GLU416 4.3 8.3 1.0
O B:ASP199 4.3 13.0 1.0
CD2 B:HIS418 4.4 7.9 1.0
C2 B:2DG2001 4.6 18.6 1.0
O B:HOH9157 4.6 14.7 1.0
CG2 B:VAL103 4.8 16.6 1.0
O B:ASN102 4.8 10.7 1.0
CA B:ASP201 4.9 17.3 1.0
C3 B:2DG2001 4.9 17.2 1.0

Magnesium binding site 5 out of 10 in 1jz4

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Magnesium binding site 5 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:14.1
occ:1.00
OE1 B:GLN163 2.1 14.3 1.0
OD2 B:ASP193 2.3 8.1 1.0
O B:ASN18 2.4 8.8 1.0
O B:VAL21 2.4 17.0 1.0
O B:ASP15 2.4 18.6 1.0
OD1 B:ASP193 2.7 13.0 1.0
CG B:ASP193 2.9 8.2 1.0
CD B:GLN163 3.0 1.0 1.0
C B:ASN18 3.2 16.3 1.0
NE2 B:GLN163 3.3 8.9 1.0
C B:VAL21 3.6 10.2 1.0
C B:ASP15 3.6 17.2 1.0
N B:ASN18 3.7 19.2 1.0
CA B:ASN18 4.0 9.7 1.0
OH B:TYR161 4.0 14.8 1.0
N B:PRO19 4.1 12.3 1.0
CA B:TRP16 4.1 18.8 1.0
CB B:ASN18 4.2 11.4 1.0
CA B:PRO19 4.2 23.1 1.0
C B:TRP16 4.3 15.9 1.0
N B:TRP16 4.3 21.3 1.0
CB B:ASP193 4.3 3.8 1.0
CA B:VAL21 4.4 12.3 1.0
N B:VAL21 4.4 12.7 1.0
N B:GLU17 4.4 14.8 1.0
CE2 B:TYR161 4.4 13.7 1.0
CB B:VAL21 4.4 16.9 1.0
CG B:GLN163 4.4 3.9 1.0
N B:THR22 4.5 12.3 1.0
CA B:THR22 4.6 12.8 1.0
CZ B:TYR161 4.7 16.2 1.0
CA B:ASP15 4.7 20.3 1.0
C B:PRO19 4.8 21.2 1.0
O B:TRP16 4.8 15.0 1.0
C B:GLU17 4.9 21.1 1.0
CG1 B:VAL21 4.9 12.5 1.0

Magnesium binding site 6 out of 10 in 1jz4

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Magnesium binding site 6 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:12.2
occ:1.00
OE2 C:GLU416 2.0 10.8 1.0
OE1 C:GLU461 2.0 7.8 1.0
O C:HOH8634 2.1 6.4 1.0
ND1 C:HIS418 2.2 13.5 1.0
O C:HOH8698 2.2 6.7 1.0
O C:HOH8775 2.2 5.8 1.0
CD C:GLU461 3.0 14.4 1.0
CE1 C:HIS418 3.1 14.7 1.0
CD C:GLU416 3.1 11.2 1.0
CG C:HIS418 3.3 3.4 1.0
OE1 C:GLU416 3.6 13.9 1.0
CB C:HIS418 3.7 7.8 1.0
OE2 C:GLU461 3.8 7.2 1.0
CB C:GLU461 4.0 5.1 1.0
O4 C:2DG2001 4.0 15.8 1.0
CG C:GLU461 4.0 8.8 1.0
OD1 C:ASN102 4.1 15.8 1.0
ND2 C:ASN460 4.1 6.4 1.0
N C:ASP201 4.2 14.6 1.0
NE2 C:HIS418 4.3 12.4 1.0
CG C:GLU416 4.3 2.8 1.0
CD2 C:HIS418 4.4 8.0 1.0
O C:ASP199 4.4 10.9 1.0
CB C:ASP201 4.4 8.2 1.0
O3 C:2DG2001 4.5 14.1 1.0
C2 C:2DG2001 4.5 13.8 1.0
O C:HOH9150 4.6 11.5 1.0
CA C:ASP201 4.8 9.2 1.0
CG2 C:VAL103 4.8 17.1 1.0
O C:ASN102 4.9 12.1 1.0
C3 C:2DG2001 4.9 7.7 1.0
C C:GLN200 5.0 22.8 1.0
CA C:GLN200 5.0 13.9 1.0

Magnesium binding site 7 out of 10 in 1jz4

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Magnesium binding site 7 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:12.0
occ:1.00
O C:VAL21 2.3 6.4 1.0
O C:ASN18 2.3 6.8 1.0
O C:ASP15 2.4 13.4 1.0
OE1 C:GLN163 2.5 8.9 1.0
OD2 C:ASP193 2.5 7.8 1.0
OD1 C:ASP193 3.0 9.6 1.0
C C:ASN18 3.1 18.3 1.0
CG C:ASP193 3.1 18.3 1.0
CD C:GLN163 3.3 11.8 1.0
C C:VAL21 3.3 14.6 1.0
NE2 C:GLN163 3.6 6.6 1.0
C C:ASP15 3.6 11.4 1.0
N C:ASN18 3.7 19.1 1.0
CA C:ASN18 3.9 21.1 1.0
OH C:TYR161 4.0 11.3 1.0
N C:PRO19 4.0 15.1 1.0
CA C:VAL21 4.1 14.4 1.0
CA C:TRP16 4.1 18.7 1.0
CB C:VAL21 4.2 18.2 1.0
N C:VAL21 4.2 13.8 1.0
CB C:ASN18 4.2 11.6 1.0
N C:TRP16 4.3 11.8 1.0
CA C:PRO19 4.3 14.6 1.0
C C:TRP16 4.3 20.8 1.0
N C:THR22 4.4 6.3 1.0
N C:GLU17 4.5 16.2 1.0
CG1 C:VAL21 4.5 16.2 1.0
CE2 C:TYR161 4.5 17.5 1.0
CA C:THR22 4.5 7.6 1.0
CB C:ASP193 4.6 10.8 1.0
CG C:GLN163 4.7 5.9 1.0
CA C:ASP15 4.7 15.0 1.0
CZ C:TYR161 4.7 9.5 1.0
C C:PRO19 4.8 17.6 1.0
C C:GLU17 4.8 18.8 1.0
O C:TRP16 4.9 15.0 1.0
N C:GLY20 5.0 14.3 1.0

Magnesium binding site 8 out of 10 in 1jz4

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Magnesium binding site 8 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:15.2
occ:1.00
O D:HOH8818 1.9 9.2 1.0
OE1 D:GLU461 2.1 9.8 1.0
O D:HOH8754 2.1 8.1 1.0
ND1 D:HIS418 2.2 11.2 1.0
O D:HOH8894 2.2 10.0 1.0
OE2 D:GLU416 2.3 18.4 1.0
CE1 D:HIS418 3.0 12.2 1.0
CD D:GLU461 3.1 18.6 1.0
CG D:HIS418 3.4 8.3 1.0
CD D:GLU416 3.4 12.8 1.0
CB D:ASP201 3.8 14.0 1.0
OE2 D:GLU461 3.8 14.2 1.0
OE1 D:GLU416 3.9 12.9 1.0
CB D:HIS418 3.9 10.7 1.0
OD1 D:ASN102 3.9 13.3 1.0
O4 D:2DG2001 3.9 9.9 1.0
N D:ASP201 4.1 14.4 1.0
ND2 D:ASN460 4.2 8.4 1.0
O3 D:2DG2001 4.2 15.5 1.0
CG D:GLU461 4.2 10.5 1.0
NE2 D:HIS418 4.2 13.7 1.0
CB D:GLU461 4.3 9.2 1.0
C2 D:2DG2001 4.3 9.0 1.0
O D:ASP199 4.4 11.0 1.0
CD2 D:HIS418 4.4 8.5 1.0
CA D:ASP201 4.6 10.4 1.0
O D:HOH9268 4.6 18.9 1.0
CG D:GLU416 4.6 1.9 1.0
C3 D:2DG2001 4.6 15.6 1.0
CG2 D:VAL103 4.7 7.0 1.0
O D:ASN102 4.7 12.3 1.0
O D:HOH9651 4.8 25.1 1.0
C4 D:2DG2001 4.9 16.0 1.0
CG D:ASP201 4.9 14.6 1.0
C D:GLN200 5.0 17.4 1.0

Magnesium binding site 9 out of 10 in 1jz4

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Magnesium binding site 9 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:19.7
occ:1.00
O D:ASN18 2.1 14.1 1.0
O D:VAL21 2.3 8.6 1.0
O D:ASP15 2.3 22.2 1.0
OE1 D:GLN163 2.4 13.3 1.0
OD2 D:ASP193 2.4 16.7 1.0
OD1 D:ASP193 2.9 10.8 1.0
C D:ASN18 2.9 14.3 1.0
CG D:ASP193 3.0 19.2 1.0
CD D:GLN163 3.2 18.6 1.0
C D:VAL21 3.4 15.2 1.0
NE2 D:GLN163 3.5 11.1 1.0
C D:ASP15 3.5 18.8 1.0
N D:ASN18 3.6 16.9 1.0
CA D:ASN18 3.8 15.2 1.0
N D:PRO19 3.8 15.0 1.0
CA D:PRO19 4.1 9.0 1.0
CA D:TRP16 4.1 19.6 1.0
CA D:VAL21 4.2 7.9 1.0
CB D:ASN18 4.2 16.7 1.0
N D:VAL21 4.2 17.2 1.0
OH D:TYR161 4.2 14.2 1.0
N D:TRP16 4.2 8.9 1.0
CB D:VAL21 4.3 19.1 1.0
C D:TRP16 4.3 11.5 1.0
N D:THR22 4.4 19.0 1.0
CB D:ASP193 4.4 9.6 1.0
N D:GLU17 4.5 12.8 1.0
CG D:GLN163 4.6 9.5 1.0
CE2 D:TYR161 4.6 9.7 1.0
CA D:THR22 4.6 14.5 1.0
C D:PRO19 4.6 15.0 1.0
CA D:ASP15 4.7 8.4 1.0
C D:GLU17 4.8 26.1 1.0
CG1 D:VAL21 4.9 4.4 1.0
CZ D:TYR161 4.9 21.5 1.0
O D:TRP16 4.9 14.0 1.0
N D:GLY20 4.9 19.6 1.0
CG2 D:THR22 5.0 5.7 1.0
CG D:ASN18 5.0 28.3 1.0

Magnesium binding site 10 out of 10 in 1jz4

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Magnesium binding site 10 out of 10 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris)


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-Trapped 2-Deoxy-Galactosyl-Enzyme Intermediate (Low Bis-Tris) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3005

b:43.5
occ:1.00
NE2 A:GLN135 4.1 0.0 1.0
CB A:GLN135 4.1 18.1 1.0
O A:HOH9493 4.3 31.1 1.0
CD A:GLN135 4.4 0.0 1.0
CG A:GLN135 4.5 69.8 1.0
OE1 A:GLU136 4.6 67.8 1.0
O A:HOH9371 4.8 30.2 1.0

Reference:

D.H.Juers, T.D.Heightman, A.Vasella, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews. A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Mon Dec 14 06:12:14 2020

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