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Magnesium in PDB 1jz8: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose, PDB code: 1jz8 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) 18.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.390, 168.710, 200.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 20.8

Other elements in 1jz8:

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose (pdb code 1jz8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose, PDB code: 1jz8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 1jz8

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Magnesium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:9.2
occ:1.00
 OE2 A:GLU416 2.0 7.5 1.0
O A:HOH8680 2.0 7.5 1.0
OE1 A:GLU461 2.1 8.8 1.0
ND1 A:HIS418 2.1 8.5 1.0
O A:HOH8757 2.1 7.9 1.0
O A:HOH8616 2.1 8.3 1.0
CE1 A:HIS418 3.0 8.4 1.0
CD A:GLU461 3.1 13.3 1.0
CD A:GLU416 3.2 7.7 1.0
CG A:HIS418 3.2 12.6 1.0
OE1 A:GLU416 3.6 8.8 1.0
CB A:HIS418 3.6 8.2 1.0
CB A:GLU461 3.9 6.8 1.0
OE2 A:GLU461 4.0 11.9 1.0
CG A:GLU461 4.1 7.8 1.0
OD1 A:ASN102 4.1 12.8 1.0
O A:HOH8603 4.2 10.4 1.0
ND2 A:ASN460 4.2 9.4 1.0
N A:ASP201 4.2 8.2 1.0
CB A:ASP201 4.2 8.7 1.0
NE2 A:HIS418 4.3 8.1 1.0
O3 A:LAK2001 4.3 14.9 1.0
O4 A:LAK2001 4.3 15.8 1.0
O A:ASP199 4.3 10.2 1.0
CD2 A:HIS418 4.4 10.5 1.0
CG A:GLU416 4.4 7.2 1.0
O A:ASN102 4.7 10.5 1.0
CA A:ASP201 4.8 8.8 1.0
C2 A:LAK2001 4.9 14.3 1.0
CA A:GLN200 4.9 7.1 1.0
C A:GLN200 4.9 9.3 1.0
CG2 A:VAL103 4.9 12.7 1.0

Magnesium binding site 2 out of 16 in 1jz8

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Magnesium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:11.9
occ:1.00
 O A:ASP15 2.2 13.2 1.0
O A:VAL21 2.3 12.7 1.0
OD2 A:ASP193 2.4 11.3 1.0
O A:ASN18 2.4 12.4 1.0
OE1 A:GLN163 2.4 10.1 1.0
OD1 A:ASP193 3.0 11.7 1.0
CG A:ASP193 3.1 13.5 1.0
C A:ASN18 3.2 11.0 1.0
CD A:GLN163 3.3 13.6 1.0
C A:ASP15 3.4 15.2 1.0
NE2 A:GLN163 3.5 11.4 1.0
C A:VAL21 3.5 10.9 1.0
N A:ASN18 3.7 15.8 1.0
CA A:ASN18 3.9 14.0 1.0
CA A:TRP16 4.0 10.6 1.0
OH A:TYR161 4.0 9.6 1.0
N A:TRP16 4.1 10.7 1.0
N A:PRO19 4.2 11.6 1.0
CB A:ASN18 4.2 14.6 1.0
CA A:VAL21 4.2 11.3 1.0
N A:VAL21 4.2 10.0 1.0
C A:TRP16 4.2 11.2 1.0
CA A:PRO19 4.4 10.4 1.0
CE2 A:TYR161 4.4 9.3 1.0
CB A:VAL21 4.4 10.0 1.0
N A:GLU17 4.4 12.1 1.0
CB A:ASP193 4.5 9.7 1.0
N A:THR22 4.5 9.4 1.0
CG A:GLN163 4.6 11.4 1.0
CA A:THR22 4.6 10.1 1.0
CA A:ASP15 4.6 10.9 1.0
CZ A:TYR161 4.7 9.8 1.0
O A:TRP16 4.8 12.4 1.0
C A:PRO19 4.8 13.4 1.0
C A:GLU17 4.9 20.3 1.0
CG1 A:VAL21 4.9 12.9 1.0
CB A:ASP15 5.0 13.5 1.0

Magnesium binding site 3 out of 16 in 1jz8

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Magnesium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:25.7
occ:1.00
 O A:HOH9450 1.9 21.8 1.0
O A:HOH9530 1.9 26.8 1.0
O A:HOH9451 2.1 42.6 1.0
O A:HOH9251 2.1 23.5 1.0
C2 A:DMS8406 3.0 45.5 1.0
O A:HOH9441 3.7 42.8 1.0
C1 A:DMS8406 3.9 72.8 1.0
OE1 A:GLU314 4.2 14.9 1.0
O A:HOH9307 4.2 19.9 1.0
OE2 A:GLU314 4.2 18.7 1.0
S A:DMS8406 4.3 69.6 1.0
O A:HOH9568 4.4 19.3 1.0
CD A:GLU314 4.7 14.8 1.0

Magnesium binding site 4 out of 16 in 1jz8

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Magnesium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3105

b:45.1
occ:1.00
 O A:HOH9207 2.1 33.9 1.0
O A:HOH9090 2.2 28.7 1.0
O A:ASN597 2.3 12.2 1.0
O A:HOH9047 2.4 19.9 1.0
O A:HOH9613 2.4 37.4 1.0
O A:HOH8823 2.8 18.9 1.0
C A:ASN597 3.5 15.0 1.0
OE2 A:GLU797 3.9 78.2 1.0
N A:ASN597 3.9 12.0 1.0
O A:HOH9674 4.3 47.0 1.0
O A:HOH9341 4.3 29.2 1.0
OD1 A:ASN597 4.3 13.1 1.0
CA A:ASN597 4.4 10.6 1.0
OE1 A:GLU797 4.4 53.6 1.0
CD A:GLU797 4.4 40.4 1.0
O A:HOH9628 4.5 30.1 1.0
O A:HOH9620 4.5 52.0 1.0
NH1 A:ARG800 4.5 57.1 1.0
N A:ASP598 4.5 9.9 1.0
CA A:ASP598 4.5 10.3 1.0
OD1 A:ASP598 4.6 15.0 1.0
CG A:ASN597 4.6 17.4 1.0
O A:HOH9408 4.6 33.3 1.0
ND2 A:ASN597 4.9 13.1 1.0
O A:HOH9050 5.0 24.5 1.0

Magnesium binding site 5 out of 16 in 1jz8

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Magnesium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:8.4
occ:1.00
 OE2 B:GLU416 2.0 8.9 1.0
OE1 B:GLU461 2.0 9.2 1.0
O B:HOH8809 2.1 7.9 1.0
O B:HOH8885 2.1 7.5 1.0
ND1 B:HIS418 2.1 7.5 1.0
O B:HOH8745 2.2 8.1 1.0
CD B:GLU461 3.0 10.3 1.0
CE1 B:HIS418 3.1 7.5 1.0
CD B:GLU416 3.2 9.2 1.0
CG B:HIS418 3.3 9.0 1.0
OE1 B:GLU416 3.6 8.6 1.0
CB B:HIS418 3.7 8.2 1.0
OE2 B:GLU461 3.9 10.5 1.0
CB B:GLU461 3.9 8.5 1.0
CG B:GLU461 4.0 7.7 1.0
OD1 B:ASN102 4.1 11.8 1.0
O B:HOH8732 4.1 9.0 1.0
ND2 B:ASN460 4.2 7.7 1.0
NE2 B:HIS418 4.3 7.8 1.0
N B:ASP201 4.3 7.7 1.0
CB B:ASP201 4.3 8.4 1.0
O B:ASP199 4.3 9.2 1.0
O3 B:LAK2001 4.3 12.0 1.0
CG B:GLU416 4.4 6.7 1.0
O4 B:LAK2001 4.4 15.4 1.0
CD2 B:HIS418 4.4 8.9 1.0
C2 B:LAK2001 4.7 13.6 1.0
O B:ASN102 4.8 10.3 1.0
CA B:GLN200 4.9 7.8 1.0
CA B:ASP201 4.9 6.6 1.0
CG2 B:VAL103 5.0 9.7 1.0
C B:GLN200 5.0 9.5 1.0

Magnesium binding site 6 out of 16 in 1jz8

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Magnesium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:11.7
occ:1.00
 OE1 B:GLN163 2.3 10.8 1.0
OD2 B:ASP193 2.3 9.7 1.0
O B:ASP15 2.3 11.2 1.0
O B:VAL21 2.3 13.3 1.0
O B:ASN18 2.3 11.1 1.0
OD1 B:ASP193 3.0 11.4 1.0
CG B:ASP193 3.0 11.7 1.0
CD B:GLN163 3.2 10.2 1.0
C B:ASN18 3.3 12.6 1.0
NE2 B:GLN163 3.5 10.6 1.0
C B:VAL21 3.5 11.3 1.0
C B:ASP15 3.5 11.7 1.0
N B:ASN18 3.7 14.3 1.0
OH B:TYR161 4.0 10.6 1.0
CA B:ASN18 4.0 12.8 1.0
CA B:TRP16 4.0 10.6 1.0
N B:PRO19 4.2 12.1 1.0
N B:TRP16 4.2 10.9 1.0
CB B:ASN18 4.2 11.9 1.0
CA B:VAL21 4.2 11.4 1.0
N B:VAL21 4.3 11.3 1.0
C B:TRP16 4.3 13.2 1.0
CB B:VAL21 4.3 11.3 1.0
CE2 B:TYR161 4.3 8.8 1.0
CA B:PRO19 4.4 14.5 1.0
N B:THR22 4.5 8.3 1.0
N B:GLU17 4.5 12.6 1.0
CB B:ASP193 4.5 6.9 1.0
CG B:GLN163 4.5 7.8 1.0
CA B:THR22 4.5 8.1 1.0
CZ B:TYR161 4.6 10.1 1.0
CA B:ASP15 4.7 14.3 1.0
O B:TRP16 4.8 11.6 1.0
C B:PRO19 4.8 13.6 1.0
C B:GLU17 4.9 14.8 1.0
CG1 B:VAL21 4.9 12.9 1.0

Magnesium binding site 7 out of 16 in 1jz8

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Magnesium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3105

b:35.0
occ:1.00
 O B:HOH9328 2.1 30.5 1.0
O B:ASN597 2.2 10.5 1.0
O B:HOH9169 2.2 19.0 1.0
O B:HOH9214 2.2 25.3 1.0
O B:HOH8951 2.5 19.6 1.0
C B:ASN597 3.4 12.6 1.0
N B:ASN597 3.9 10.7 1.0
OD1 B:ASN597 4.2 11.3 1.0
OE1 B:GLU797 4.2 73.7 1.0
CA B:ASN597 4.3 8.4 1.0
O B:HOH9528 4.3 37.8 1.0
N B:ASP598 4.4 10.1 1.0
CG B:ASN597 4.4 10.1 1.0
O B:HOH9594 4.5 21.4 1.0
CA B:ASP598 4.5 8.6 1.0
O B:HOH9461 4.5 33.1 1.0
CD B:GLU797 4.6 35.0 1.0
OE2 B:GLU797 4.6 39.6 1.0
ND2 B:ASN597 4.7 10.8 1.0
OD1 B:ASP598 4.7 15.6 1.0
O B:HOH9738 4.9 46.1 1.0
C B:PRO596 5.0 13.7 1.0

Magnesium binding site 8 out of 16 in 1jz8

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Magnesium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:8.3
occ:1.00
 OE2 C:GLU416 2.0 10.3 1.0
OE1 C:GLU461 2.0 9.1 1.0
O C:HOH8782 2.1 7.6 1.0
O C:HOH8705 2.1 8.0 1.0
O C:HOH8641 2.1 8.1 1.0
ND1 C:HIS418 2.2 9.4 1.0
CD C:GLU461 3.1 13.4 1.0
CE1 C:HIS418 3.1 9.8 1.0
CD C:GLU416 3.1 10.7 1.0
CG C:HIS418 3.3 7.8 1.0
OE1 C:GLU416 3.6 7.9 1.0
CB C:HIS418 3.6 7.0 1.0
OE2 C:GLU461 4.0 11.8 1.0
CB C:GLU461 4.0 5.0 1.0
CG C:GLU461 4.0 8.2 1.0
OD1 C:ASN102 4.1 12.0 1.0
O C:HOH8628 4.2 8.9 1.0
ND2 C:ASN460 4.2 8.5 1.0
N C:ASP201 4.2 8.1 1.0
CB C:ASP201 4.3 9.8 1.0
O C:ASP199 4.3 8.6 1.0
NE2 C:HIS418 4.3 8.5 1.0
O3 C:LAK2001 4.4 13.5 1.0
CG C:GLU416 4.4 5.3 1.0
O4 C:LAK2001 4.4 14.7 1.0
CD2 C:HIS418 4.4 8.7 1.0
O C:ASN102 4.8 10.7 1.0
C2 C:LAK2001 4.8 12.7 1.0
CA C:ASP201 4.8 8.8 1.0
CA C:GLN200 4.9 7.9 1.0
CG2 C:VAL103 4.9 12.2 1.0
C C:GLN200 4.9 9.9 1.0

Magnesium binding site 9 out of 16 in 1jz8

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Magnesium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:10.4
occ:1.00
 O C:ASN18 2.2 12.0 1.0
O C:VAL21 2.3 10.7 1.0
O C:ASP15 2.3 11.8 1.0
OE1 C:GLN163 2.4 9.3 1.0
OD2 C:ASP193 2.4 11.5 1.0
OD1 C:ASP193 3.1 11.2 1.0
CG C:ASP193 3.1 12.0 1.0
CD C:GLN163 3.2 8.6 1.0
C C:ASN18 3.3 14.3 1.0
C C:VAL21 3.4 9.6 1.0
C C:ASP15 3.5 10.6 1.0
NE2 C:GLN163 3.5 10.0 1.0
N C:ASN18 3.8 14.0 1.0
OH C:TYR161 4.0 11.4 1.0
CA C:ASN18 4.0 11.4 1.0
CA C:TRP16 4.1 11.4 1.0
N C:PRO19 4.2 14.3 1.0
CA C:VAL21 4.2 7.9 1.0
N C:TRP16 4.2 10.0 1.0
N C:VAL21 4.2 9.6 1.0
CB C:ASN18 4.2 10.4 1.0
CB C:VAL21 4.3 11.4 1.0
C C:TRP16 4.3 11.4 1.0
CE2 C:TYR161 4.3 8.5 1.0
CA C:PRO19 4.4 11.5 1.0
N C:THR22 4.4 8.7 1.0
N C:GLU17 4.5 12.5 1.0
CA C:THR22 4.5 9.2 1.0
CG C:GLN163 4.5 9.4 1.0
CB C:ASP193 4.5 8.1 1.0
CA C:ASP15 4.6 13.0 1.0
CZ C:TYR161 4.6 9.4 1.0
CG1 C:VAL21 4.9 15.1 1.0
O C:TRP16 4.9 12.4 1.0
C C:PRO19 4.9 11.6 1.0
C C:GLU17 4.9 19.3 1.0
CB C:ASP15 5.0 12.5 1.0

Magnesium binding site 10 out of 16 in 1jz8

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Magnesium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Allolactose


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 (E537Q) in Complex with Allolactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3004

b:36.3
occ:1.00
 O C:HOH9556 2.2 40.5 1.0
O C:HOH9558 2.3 23.3 1.0
O C:HOH9569 2.5 39.8 1.0
CD C:GLN49 3.7 0.0 1.0
OE1 C:GLN49 3.8 0.0 1.0
CG C:GLN49 3.8 35.7 1.0
O C:HOH9335 4.2 16.9 1.0
O C:HOH9600 4.2 37.9 1.0
OE2 C:GLU41 4.2 15.4 1.0
NE2 C:GLN49 4.3 51.4 1.0
O C:HOH9455 4.7 20.3 1.0
O C:HOH9489 4.9 18.2 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: Tue Aug 13 07:01:45 2024

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