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Magnesium in PDB 1jz3: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate, PDB code: 1jz3 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) 16.00 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.560, 168.190, 200.690, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / 22.2

Other elements in 1jz3:

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

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate (pdb code 1jz3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate, PDB code: 1jz3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 1jz3

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Magnesium binding site 1 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:16.7
occ:1.00
 OE2 A:GLU416 2.1 15.1 1.0
O A:HOH8615 2.2 13.5 1.0
O A:HOH8756 2.2 12.5 1.0
ND1 A:HIS418 2.2 14.2 1.0
OE1 A:GLU461 2.2 16.5 1.0
O A:HOH8678 2.2 11.1 1.0
CE1 A:HIS418 3.0 14.2 1.0
CD A:GLU461 3.2 21.3 1.0
CD A:GLU416 3.2 18.2 1.0
CG A:HIS418 3.3 16.2 1.0
OE1 A:GLU416 3.6 13.2 1.0
CB A:HIS418 3.7 13.0 1.0
CB A:GLU461 3.9 10.1 1.0
OE2 A:GLU461 4.0 13.8 1.0
OD1 A:ASN102 4.0 17.8 1.0
ND2 A:ASN460 4.1 14.8 1.0
O4 A:2DG2001 4.2 13.9 1.0
CG A:GLU461 4.2 10.7 1.0
CB A:ASP201 4.2 13.5 1.0
N A:ASP201 4.2 14.9 1.0
NE2 A:HIS418 4.2 13.4 1.0
O A:ASP199 4.3 17.8 1.0
CD2 A:HIS418 4.4 13.5 1.0
O3 A:2DG2001 4.4 13.1 1.0
CG A:GLU416 4.4 11.5 1.0
C2 A:2DG2001 4.6 14.7 1.0
O A:HOH9152 4.7 17.0 1.0
O A:ASN102 4.7 13.7 1.0
CA A:ASP201 4.8 15.4 1.0
CA A:GLN200 4.9 8.5 1.0
C A:GLN200 4.9 13.9 1.0
CG2 A:VAL103 5.0 16.5 1.0

Magnesium binding site 2 out of 17 in 1jz3

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Magnesium binding site 2 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:17.3
occ:1.00
 OE1 A:GLN163 2.2 18.2 1.0
O A:ASP15 2.2 17.8 1.0
OD2 A:ASP193 2.3 16.5 1.0
O A:ASN18 2.5 18.2 1.0
O A:VAL21 2.5 16.4 1.0
OD1 A:ASP193 3.0 18.3 1.0
CG A:ASP193 3.0 18.9 1.0
CD A:GLN163 3.1 18.4 1.0
C A:ASN18 3.3 18.4 1.0
NE2 A:GLN163 3.4 14.2 1.0
C A:ASP15 3.4 17.3 1.0
C A:VAL21 3.6 20.1 1.0
N A:ASN18 3.6 19.9 1.0
CA A:TRP16 3.9 11.1 1.0
CA A:ASN18 3.9 18.2 1.0
OH A:TYR161 4.0 13.3 1.0
N A:TRP16 4.1 12.7 1.0
C A:TRP16 4.2 19.5 1.0
N A:PRO19 4.2 24.0 1.0
CB A:ASN18 4.2 14.6 1.0
CE2 A:TYR161 4.3 15.9 1.0
N A:VAL21 4.3 13.1 1.0
CA A:VAL21 4.3 14.0 1.0
CB A:VAL21 4.4 14.0 1.0
N A:GLU17 4.4 16.4 1.0
CA A:PRO19 4.4 17.2 1.0
CG A:GLN163 4.5 18.6 1.0
CB A:ASP193 4.5 11.5 1.0
CA A:ASP15 4.6 15.3 1.0
N A:THR22 4.6 10.0 1.0
CZ A:TYR161 4.6 17.0 1.0
CA A:THR22 4.6 14.2 1.0
O A:TRP16 4.7 19.5 1.0
C A:GLU17 4.8 29.2 1.0
C A:PRO19 4.9 17.0 1.0
CB A:ASP15 4.9 15.4 1.0
CG1 A:VAL21 5.0 21.2 1.0

Magnesium binding site 3 out of 17 in 1jz3

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Magnesium binding site 3 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:26.9
occ:0.50
 O A:HOH8865 2.0 23.3 1.0
O A:HOH9288 2.4 31.3 1.0
OE1 A:GLN718 2.4 32.0 1.0
O A:HOH9226 2.6 38.4 1.0
O A:HOH8976 2.6 42.5 1.0
O A:HOH9038 2.6 53.3 1.0
CD A:GLN718 3.3 32.6 1.0
NE2 A:GLN718 3.6 25.8 1.0
O A:THR911 3.9 16.4 1.0
NE2 A:HIS622 4.0 17.4 1.0
O A:HOH9456 4.1 28.3 1.0
O A:HOH8881 4.3 37.1 1.0
O A:HOH9021 4.4 39.3 1.0
O A:HOH8680 4.6 19.8 1.0
CE1 A:HIS622 4.6 21.0 1.0
O A:GLN719 4.6 15.5 1.0
O A:HOH8855 4.6 19.7 1.0
N A:GLN719 4.7 13.3 1.0
CG A:GLN718 4.8 17.5 1.0
C A:THR911 4.9 14.4 1.0
CB A:THR911 4.9 12.7 1.0
O A:HOH9622 5.0 38.5 1.0

Magnesium binding site 4 out of 17 in 1jz3

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Magnesium binding site 4 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:30.4
occ:1.00
 O A:HOH9446 1.9 25.3 1.0
O A:HOH9447 2.1 36.1 1.0
O A:HOH9246 2.1 20.5 1.0
O A:HOH9540 2.2 29.5 1.0
C1 A:DMS8406 3.1 33.4 1.0
O A:HOH9436 3.6 48.5 1.0
O A:DMS8406 4.0 73.6 1.0
OE2 A:GLU314 4.1 18.3 1.0
OE1 A:GLU314 4.1 17.7 1.0
S A:DMS8406 4.2 65.8 1.0
O A:HOH9302 4.3 24.7 1.0
O A:HOH9575 4.3 19.8 1.0
CD A:GLU314 4.6 24.3 1.0

Magnesium binding site 5 out of 17 in 1jz3

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Magnesium binding site 5 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:15.4
occ:1.00
 O B:HOH8699 2.0 11.5 1.0
OE2 B:GLU416 2.0 13.0 1.0
OE1 B:GLU461 2.0 12.3 1.0
O B:HOH8635 2.1 11.7 1.0
O B:HOH8776 2.2 17.3 1.0
ND1 B:HIS418 2.2 12.3 1.0
CD B:GLU461 3.0 13.0 1.0
CE1 B:HIS418 3.1 13.0 1.0
CD B:GLU416 3.2 17.0 1.0
CG B:HIS418 3.4 17.8 1.0
OE1 B:GLU416 3.6 14.8 1.0
CB B:HIS418 3.7 12.8 1.0
OE2 B:GLU461 3.9 14.7 1.0
OD1 B:ASN102 4.0 13.9 1.0
CB B:GLU461 4.0 12.7 1.0
CG B:GLU461 4.0 12.0 1.0
O4 B:2DG2001 4.1 9.7 0.9
CB B:ASP201 4.2 12.3 1.0
ND2 B:ASN460 4.2 10.1 1.0
N B:ASP201 4.3 11.7 1.0
NE2 B:HIS418 4.3 11.4 1.0
O3 B:2DG2001 4.3 12.9 0.9
O B:ASP199 4.4 13.2 1.0
CG B:GLU416 4.4 10.3 1.0
CD2 B:HIS418 4.5 12.0 1.0
C2 B:2DG2001 4.6 9.9 0.9
O B:HOH9166 4.7 15.4 1.0
O B:ASN102 4.8 16.0 1.0
CA B:ASP201 4.8 11.6 1.0
C3 B:2DG2001 4.9 12.1 0.9
CA B:GLN200 5.0 10.8 1.0

Magnesium binding site 6 out of 17 in 1jz3

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Magnesium binding site 6 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:19.1
occ:1.00
 O B:ASN18 2.3 19.8 1.0
OD2 B:ASP193 2.3 13.4 1.0
OE1 B:GLN163 2.3 17.6 1.0
O B:VAL21 2.4 17.0 1.0
O B:ASP15 2.4 16.5 1.0
CG B:ASP193 3.1 16.0 1.0
OD1 B:ASP193 3.1 17.1 1.0
C B:ASN18 3.2 14.7 1.0
CD B:GLN163 3.2 19.6 1.0
NE2 B:GLN163 3.5 17.9 1.0
C B:VAL21 3.5 20.9 1.0
C B:ASP15 3.6 25.6 1.0
N B:ASN18 3.7 20.9 1.0
CA B:ASN18 4.0 14.5 1.0
OH B:TYR161 4.0 17.0 1.0
CA B:TRP16 4.0 8.4 1.0
N B:PRO19 4.1 17.8 1.0
CB B:ASN18 4.2 13.3 1.0
N B:TRP16 4.3 13.8 1.0
C B:TRP16 4.3 17.2 1.0
N B:VAL21 4.3 18.8 1.0
CA B:VAL21 4.3 18.9 1.0
CA B:PRO19 4.4 26.3 1.0
CB B:VAL21 4.4 16.7 1.0
CE2 B:TYR161 4.4 14.2 1.0
N B:GLU17 4.4 16.0 1.0
CB B:ASP193 4.5 12.3 1.0
N B:THR22 4.5 13.4 1.0
CG B:GLN163 4.5 15.2 1.0
CA B:THR22 4.6 14.4 1.0
CZ B:TYR161 4.7 20.3 1.0
CA B:ASP15 4.7 20.9 1.0
C B:PRO19 4.8 23.7 1.0
C B:GLU17 4.9 23.2 1.0
O B:TRP16 4.9 18.7 1.0
CG1 B:VAL21 5.0 24.3 1.0

Magnesium binding site 7 out of 17 in 1jz3

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Magnesium binding site 7 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:25.1
occ:0.50
 O B:HOH9052 2.3 37.2 1.0
O B:HOH9236 2.3 29.9 1.0
O B:HOH9299 2.3 32.3 1.0
O B:HOH8884 2.3 21.6 1.0
O B:HOH8993 2.5 39.2 1.0
OE1 B:GLN718 2.5 44.8 1.0
CD B:GLN718 3.5 24.0 1.0
NE2 B:GLN718 3.8 26.7 1.0
C2 B:DMS8427 3.9 38.1 1.0
O B:HOH8900 4.0 39.0 1.0
O B:THR911 4.1 20.0 1.0
O B:HOH9035 4.3 25.2 1.0
NE2 B:HIS622 4.3 19.3 1.0
O B:DMS8427 4.4 53.8 1.0
O B:HOH9637 4.4 37.6 1.0
O B:HOH8874 4.5 21.2 1.0
O B:HOH8860 4.5 38.1 1.0
O B:GLN719 4.6 14.3 1.0
O B:HOH8701 4.6 17.2 1.0
N B:GLN719 4.8 15.1 1.0
S B:DMS8427 4.8 66.8 1.0
O B:HOH9479 4.8 57.6 1.0
C1 B:DMS8427 4.9 35.8 1.0
CG B:GLN718 4.9 11.4 1.0
O B:HOH9520 4.9 54.6 1.0

Magnesium binding site 8 out of 17 in 1jz3

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Magnesium binding site 8 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:16.0
occ:1.00
 OE2 C:GLU416 2.0 13.9 1.0
O C:HOH8776 2.0 13.8 1.0
OE1 C:GLU461 2.1 12.1 1.0
O C:HOH8635 2.1 11.8 1.0
O C:HOH8699 2.2 13.0 1.0
ND1 C:HIS418 2.3 13.5 1.0
CD C:GLU461 3.1 12.9 1.0
CD C:GLU416 3.1 23.8 1.0
CE1 C:HIS418 3.2 16.2 1.0
CG C:HIS418 3.4 12.0 1.0
OE1 C:GLU416 3.5 14.8 1.0
CB C:HIS418 3.7 14.7 1.0
OE2 C:GLU461 4.0 13.0 1.0
CB C:GLU461 4.0 11.4 1.0
OD1 C:ASN102 4.1 14.6 1.0
CG C:GLU461 4.1 13.0 1.0
ND2 C:ASN460 4.1 14.0 1.0
O4 C:2DG2001 4.2 14.5 1.0
O C:ASP199 4.2 12.7 1.0
CB C:ASP201 4.2 13.8 1.0
N C:ASP201 4.3 11.4 1.0
CG C:GLU416 4.4 9.4 1.0
NE2 C:HIS418 4.4 12.7 1.0
O3 C:2DG2001 4.5 13.8 1.0
CD2 C:HIS418 4.5 14.5 1.0
C2 C:2DG2001 4.7 10.1 1.0
O C:ASN102 4.8 14.6 1.0
O C:HOH9167 4.8 16.8 1.0
CA C:ASP201 4.8 11.8 1.0
CA C:GLN200 4.9 15.8 1.0
C C:GLN200 5.0 21.2 1.0

Magnesium binding site 9 out of 17 in 1jz3

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Magnesium binding site 9 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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

b:15.0
occ:1.00
 O C:VAL21 2.2 14.0 1.0
O C:ASN18 2.3 19.0 1.0
O C:ASP15 2.3 15.9 1.0
OE1 C:GLN163 2.3 15.4 1.0
OD2 C:ASP193 2.4 17.5 1.0
OD1 C:ASP193 3.0 18.6 1.0
CG C:ASP193 3.1 17.9 1.0
CD C:GLN163 3.2 17.6 1.0
C C:ASN18 3.2 24.7 1.0
C C:VAL21 3.4 16.6 1.0
C C:ASP15 3.5 21.2 1.0
NE2 C:GLN163 3.5 14.3 1.0
N C:ASN18 3.8 18.1 1.0
CA C:ASN18 4.0 17.6 1.0
OH C:TYR161 4.0 16.4 1.0
CA C:TRP16 4.0 16.8 1.0
N C:PRO19 4.2 22.0 1.0
CA C:VAL21 4.2 12.8 1.0
N C:TRP16 4.2 13.2 1.0
N C:VAL21 4.3 16.0 1.0
C C:TRP16 4.3 20.7 1.0
CE2 C:TYR161 4.3 9.4 1.0
CB C:VAL21 4.3 16.9 1.0
CB C:ASN18 4.3 16.8 1.0
N C:THR22 4.4 10.7 1.0
CA C:PRO19 4.4 18.6 1.0
CA C:THR22 4.5 12.5 1.0
CG C:GLN163 4.5 13.0 1.0
N C:GLU17 4.5 19.1 1.0
CB C:ASP193 4.6 13.6 1.0
CA C:ASP15 4.6 16.0 1.0
CZ C:TYR161 4.6 14.5 1.0
CG1 C:VAL21 4.8 15.7 1.0
O C:TRP16 4.8 16.6 1.0
C C:PRO19 4.9 18.3 1.0
C C:GLU17 5.0 24.3 1.0
CB C:ASP15 5.0 15.2 1.0

Magnesium binding site 10 out of 17 in 1jz3

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Magnesium binding site 10 out of 17 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-Deoxy- Galactosyl Enzyme Intermediate


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3003

b:24.6
occ:0.50
 O C:HOH8885 2.0 25.4 1.0
OE1 C:GLN718 2.2 39.1 1.0
O C:HOH9306 2.2 36.6 1.0
O C:HOH9241 2.2 35.5 1.0
O C:HOH8996 2.5 51.0 1.0
O C:HOH9057 2.6 40.9 1.0
CD C:GLN718 3.2 31.5 1.0
NE2 C:GLN718 3.5 26.2 1.0
C2 C:DMS8427 4.0 42.8 1.0
NE2 C:HIS622 4.0 19.3 1.0
O C:THR911 4.1 17.2 1.0
O C:HOH9040 4.2 41.6 1.0
O C:HOH9590 4.3 44.6 1.0
O C:HOH8901 4.4 35.7 1.0
O C:HOH8701 4.6 19.6 1.0
CG C:GLN718 4.6 17.0 1.0
O C:HOH9476 4.6 52.1 1.0
O C:GLN719 4.6 16.9 1.0
CE1 C:HIS622 4.6 21.7 1.0
N C:GLN719 4.7 20.8 1.0
O C:DMS8427 4.8 70.0 1.0
O C:HOH8875 4.8 18.0 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: Tue Aug 13 06:54:33 2024

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