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Magnesium in PDB 1px4: E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound, PDB code: 1px4 was solved by D.H.Juers, S.Hakda, B.W.Matthews, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.50 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.490, 168.290, 200.440, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1px4:

The structure of E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound 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 (G794A) with Iptg Bound (pdb code 1px4). 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 (G794A) with Iptg Bound, PDB code: 1px4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 1px4

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Magnesium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:15.3
occ:1.00
 O A:HOH8679 2.1 10.4 1.0
OE1 A:GLU461 2.1 14.1 1.0
O A:HOH8615 2.1 13.0 1.0
ND1 A:HIS418 2.1 13.2 1.0
O A:HOH8755 2.2 12.6 1.0
OE2 A:GLU416 2.2 11.8 1.0
CE1 A:HIS418 3.0 13.5 1.0
CD A:GLU461 3.2 19.3 1.0
CD A:GLU416 3.3 14.0 1.0
CG A:HIS418 3.3 16.2 1.0
OE1 A:GLU416 3.7 11.8 1.0
CB A:HIS418 3.7 12.4 1.0
OE2 A:GLU461 3.9 21.1 1.0
OD1 A:ASN102 4.1 18.9 1.0
CB A:GLU461 4.2 9.7 1.0
CB A:ASP201 4.2 11.4 1.0
CG A:GLU461 4.2 9.6 1.0
N A:ASP201 4.2 12.4 1.0
NE2 A:HIS418 4.3 14.4 1.0
O A:HOH8603 4.3 16.1 1.0
ND2 A:ASN460 4.3 12.4 1.0
O A:ASP199 4.4 16.8 1.0
CD2 A:HIS418 4.4 15.1 1.0
O4 A:IPT2001 4.4 14.8 1.0
CG A:GLU416 4.4 8.5 1.0
O A:HOH8891 4.4 27.1 1.0
O A:ASN102 4.7 14.5 1.0
CA A:ASP201 4.8 11.7 1.0
CA A:GLN200 4.9 10.0 1.0
C A:GLN200 4.9 14.2 1.0
C2 A:IPT2001 4.9 20.4 1.0
O3 A:IPT2001 4.9 19.9 1.0
CG2 A:VAL103 5.0 13.3 1.0

Magnesium binding site 2 out of 16 in 1px4

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Magnesium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:16.2
occ:1.00
 OE1 A:GLN163 2.2 15.1 1.0
O A:VAL21 2.2 16.6 1.0
O A:ASP15 2.2 15.2 1.0
O A:ASN18 2.3 17.7 1.0
OD2 A:ASP193 2.4 14.7 1.0
OD1 A:ASP193 3.1 21.2 1.0
CG A:ASP193 3.1 24.4 1.0
CD A:GLN163 3.1 17.0 1.0
C A:ASN18 3.2 14.9 1.0
C A:VAL21 3.4 16.8 1.0
C A:ASP15 3.4 22.3 1.0
NE2 A:GLN163 3.4 14.1 1.0
N A:ASN18 3.7 23.6 1.0
CA A:ASN18 3.9 18.2 1.0
OH A:TYR161 4.0 13.9 1.0
CA A:TRP16 4.0 16.2 1.0
N A:PRO19 4.1 17.3 1.0
N A:TRP16 4.2 14.9 1.0
CA A:VAL21 4.2 10.3 1.0
CB A:ASN18 4.2 18.4 1.0
N A:VAL21 4.2 15.7 1.0
C A:TRP16 4.3 16.1 1.0
CE2 A:TYR161 4.3 12.0 1.0
CB A:VAL21 4.4 14.1 1.0
CA A:PRO19 4.4 13.8 1.0
N A:THR22 4.4 13.8 1.0
N A:GLU17 4.5 15.1 1.0
CG A:GLN163 4.5 14.4 1.0
CA A:ASP15 4.6 15.0 1.0
CB A:ASP193 4.6 13.3 1.0
CA A:THR22 4.6 15.3 1.0
CZ A:TYR161 4.6 13.8 1.0
O A:TRP16 4.8 16.7 1.0
C A:PRO19 4.8 16.0 1.0
C A:GLU17 4.9 26.6 1.0
CG1 A:VAL21 4.9 17.8 1.0
CB A:ASP15 4.9 16.5 1.0

Magnesium binding site 3 out of 16 in 1px4

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Magnesium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:30.2
occ:1.00
 O A:HOH9364 1.8 28.0 1.0
O A:HOH9215 2.1 25.5 1.0
O A:HOH9420 2.1 29.6 1.0
O A:HOH9365 2.2 39.7 1.0
C1 A:DMS8406 3.6 52.5 1.0
O A:DMS8406 3.7 83.8 1.0
O A:HOH9358 3.8 43.3 1.0
OE2 A:GLU314 4.1 19.6 1.0
OE1 A:GLU314 4.1 15.6 1.0
S A:DMS8406 4.2 66.3 1.0
O A:HOH9261 4.3 23.1 1.0
O A:HOH9445 4.3 24.2 1.0
CD A:GLU314 4.6 22.2 1.0
O A:HOH9253 5.0 24.3 1.0
O A:HOH9240 5.0 33.2 1.0

Magnesium binding site 4 out of 16 in 1px4

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Magnesium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3105

b:97.4
occ:0.50
 O A:HOH9176 2.1 23.4 0.5
O A:HOH9036 2.2 27.2 1.0
O A:ASN597 2.3 17.9 1.0
O A:HOH8821 2.6 35.7 1.0
C A:ASN597 3.4 24.0 1.0
O A:HOH9504 3.6 52.0 1.0
N A:ASN597 3.8 18.1 1.0
OE2 A:GLU797 4.0 59.5 1.0
CA A:ASN597 4.2 15.3 1.0
OD1 A:ASN597 4.2 17.5 1.0
N A:ASP598 4.5 18.1 1.0
OE1 A:GLU797 4.5 0.0 1.0
CG A:ASN597 4.5 78.8 1.0
CD A:GLU797 4.5 63.7 1.0
OD1 A:ASP598 4.6 23.1 1.0
O A:HOH9506 4.6 56.4 1.0
CA A:ASP598 4.6 19.8 1.0
O A:HOH9336 4.7 42.0 1.0
ND2 A:ASN597 4.8 17.9 1.0
NH2 A:ARG800 4.9 0.0 1.0
C A:PRO596 4.9 21.9 1.0
NH1 A:ARG800 4.9 47.7 1.0

Magnesium binding site 5 out of 16 in 1px4

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Magnesium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:12.1
occ:1.00
 OE1 B:GLU461 2.0 12.3 1.0
O B:HOH8693 2.0 11.6 1.0
O B:HOH8770 2.0 11.1 1.0
OE2 B:GLU416 2.1 12.9 1.0
ND1 B:HIS418 2.1 13.4 1.0
O B:HOH8629 2.2 11.0 1.0
CD B:GLU461 3.0 18.0 1.0
CE1 B:HIS418 3.1 11.3 1.0
CG B:HIS418 3.2 14.6 1.0
CD B:GLU416 3.3 12.6 1.0
CB B:HIS418 3.6 12.2 1.0
OE1 B:GLU416 3.7 13.6 1.0
OE2 B:GLU461 3.8 22.5 1.0
CB B:GLU461 4.0 11.2 1.0
OD1 B:ASN102 4.0 14.3 1.0
CG B:GLU461 4.1 11.6 1.0
O B:HOH8616 4.1 16.2 1.0
CB B:ASP201 4.2 13.4 1.0
N B:ASP201 4.3 10.8 1.0
NE2 B:HIS418 4.3 11.9 1.0
O4 B:IPT2001 4.4 14.2 1.0
O B:ASP199 4.4 13.6 1.0
CD2 B:HIS418 4.4 14.1 1.0
ND2 B:ASN460 4.4 13.1 1.0
CG B:GLU416 4.4 9.7 1.0
O B:HOH8907 4.6 25.2 1.0
O3 B:IPT2001 4.7 18.8 1.0
O B:ASN102 4.7 16.4 1.0
C2 B:IPT2001 4.8 16.2 1.0
CA B:ASP201 4.8 13.9 1.0
CA B:GLN200 4.9 10.4 1.0
CG2 B:VAL103 4.9 16.1 1.0

Magnesium binding site 6 out of 16 in 1px4

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Magnesium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:15.9
occ:1.00
 O B:ASP15 2.2 18.9 1.0
OD2 B:ASP193 2.2 14.8 1.0
O B:ASN18 2.3 17.6 1.0
OE1 B:GLN163 2.3 14.8 1.0
O B:VAL21 2.4 17.6 1.0
CG B:ASP193 3.0 16.9 1.0
OD1 B:ASP193 3.0 18.1 1.0
CD B:GLN163 3.2 16.9 1.0
C B:ASN18 3.2 18.0 1.0
C B:ASP15 3.4 17.2 1.0
NE2 B:GLN163 3.5 14.9 1.0
C B:VAL21 3.5 16.3 1.0
N B:ASN18 3.6 20.4 1.0
OH B:TYR161 3.9 17.5 1.0
CA B:ASN18 3.9 15.7 1.0
CA B:TRP16 4.0 14.0 1.0
N B:PRO19 4.1 16.9 1.0
CB B:ASN18 4.2 12.4 1.0
N B:TRP16 4.2 15.5 1.0
C B:TRP16 4.2 16.6 1.0
N B:VAL21 4.3 14.7 1.0
CA B:VAL21 4.3 16.3 1.0
CB B:VAL21 4.3 18.3 1.0
CE2 B:TYR161 4.3 13.9 1.0
CA B:PRO19 4.3 25.8 1.0
N B:GLU17 4.4 17.9 1.0
CB B:ASP193 4.5 12.4 1.0
CG B:GLN163 4.5 15.1 1.0
N B:THR22 4.5 13.9 1.0
CA B:ASP15 4.6 20.3 1.0
CZ B:TYR161 4.6 14.6 1.0
CA B:THR22 4.6 12.6 1.0
C B:GLU17 4.8 23.9 1.0
O B:TRP16 4.8 14.6 1.0
C B:PRO19 4.8 29.6 1.0
CG1 B:VAL21 4.9 17.6 1.0
CB B:ASP15 5.0 16.3 1.0

Magnesium binding site 7 out of 16 in 1px4

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Magnesium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3105

b:28.9
occ:0.50
 O B:HOH9195 1.8 21.1 0.5
O B:ASN597 2.3 17.4 1.0
O B:HOH9050 2.4 24.3 1.0
O B:HOH8835 2.8 27.8 1.0
C B:ASN597 3.6 19.9 1.0
OE1 B:GLU797 3.8 0.0 1.0
N B:ASN597 3.9 16.7 1.0
OD1 B:ASP598 4.1 34.9 1.0
CA B:ASN597 4.4 15.0 1.0
OD1 B:ASN597 4.5 17.0 1.0
O B:HOH9359 4.5 50.0 1.0
N B:ASP598 4.5 14.4 1.0
CD B:GLU797 4.6 47.4 1.0
CA B:ASP598 4.6 13.8 1.0
CB B:PRO596 4.7 24.2 1.0
CG B:ASN597 4.7 23.7 1.0
OE2 B:GLU797 4.9 43.0 1.0
CG B:ASP598 4.9 22.8 1.0
C B:PRO596 5.0 23.7 1.0

Magnesium binding site 8 out of 16 in 1px4

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Magnesium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:14.0
occ:1.00
 OE2 C:GLU416 2.0 12.2 1.0
O C:HOH8781 2.1 12.8 1.0
OE1 C:GLU461 2.1 11.3 1.0
O C:HOH8639 2.1 11.4 1.0
O C:HOH8703 2.2 12.2 1.0
ND1 C:HIS418 2.2 13.9 1.0
CE1 C:HIS418 3.1 15.5 1.0
CD C:GLU461 3.1 15.0 1.0
CD C:GLU416 3.2 15.0 1.0
CG C:HIS418 3.3 11.0 1.0
OE1 C:GLU416 3.5 14.6 1.0
CB C:HIS418 3.6 10.2 1.0
OE2 C:GLU461 3.9 21.3 1.0
OD1 C:ASN102 4.1 15.9 1.0
CB C:GLU461 4.1 9.2 1.0
O C:HOH8626 4.1 16.8 1.0
CG C:GLU461 4.1 9.8 1.0
N C:ASP201 4.1 11.7 1.0
CB C:ASP201 4.2 14.9 1.0
NE2 C:HIS418 4.3 15.0 1.0
ND2 C:ASN460 4.3 12.2 1.0
O C:ASP199 4.3 11.8 1.0
CD2 C:HIS418 4.4 12.6 1.0
CG C:GLU416 4.4 9.9 1.0
O C:HOH8918 4.5 28.3 1.0
O4 C:IPT2001 4.5 14.3 1.0
CA C:ASP201 4.8 12.6 1.0
O C:ASN102 4.8 15.8 1.0
C C:GLN200 4.8 16.9 1.0
C2 C:IPT2001 4.9 28.8 1.0
O3 C:IPT2001 4.9 17.1 1.0
CA C:GLN200 4.9 13.8 1.0
CG2 C:VAL103 5.0 17.0 1.0

Magnesium binding site 9 out of 16 in 1px4

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Magnesium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:14.7
occ:1.00
 O C:VAL21 2.3 14.1 1.0
O C:ASP15 2.3 14.7 1.0
O C:ASN18 2.3 13.1 1.0
OD2 C:ASP193 2.3 16.5 1.0
OE1 C:GLN163 2.5 12.9 1.0
CG C:ASP193 3.1 17.4 1.0
OD1 C:ASP193 3.1 17.3 1.0
C C:ASN18 3.2 18.5 1.0
CD C:GLN163 3.3 13.9 1.0
C C:VAL21 3.4 12.6 1.0
C C:ASP15 3.5 15.8 1.0
NE2 C:GLN163 3.6 14.0 1.0
N C:ASN18 3.7 21.0 1.0
CA C:ASN18 4.0 17.6 1.0
OH C:TYR161 4.0 16.0 1.0
CA C:TRP16 4.1 13.7 1.0
N C:PRO19 4.1 21.4 1.0
CA C:VAL21 4.2 14.0 1.0
CB C:ASN18 4.2 15.0 1.0
N C:VAL21 4.2 12.1 1.0
N C:TRP16 4.2 12.7 1.0
CB C:VAL21 4.3 18.0 1.0
C C:TRP16 4.3 17.5 1.0
CE2 C:TYR161 4.4 11.9 1.0
CA C:PRO19 4.4 16.8 1.0
N C:THR22 4.4 11.0 1.0
N C:GLU17 4.5 16.3 1.0
CB C:ASP193 4.5 10.4 1.0
CA C:THR22 4.5 12.1 1.0
CA C:ASP15 4.6 16.4 1.0
CG C:GLN163 4.6 12.4 1.0
CZ C:TYR161 4.7 16.4 1.0
CG1 C:VAL21 4.8 18.6 1.0
C C:PRO19 4.8 13.5 1.0
O C:TRP16 4.8 17.4 1.0
C C:GLU17 4.9 29.1 1.0
CB C:ASP15 4.9 16.8 1.0

Magnesium binding site 10 out of 16 in 1px4

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Magnesium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (G794A) with Iptg Bound


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 (G794A) with Iptg Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3004

b:53.4
occ:1.00
 O C:HOH9444 2.3 40.6 1.0
CG C:GLN49 3.8 52.3 1.0
OE2 C:GLU41 4.3 20.8 1.0
O C:HOH9280 4.4 23.6 1.0
CD C:GLN49 4.5 86.0 1.0
O C:HOH9472 4.7 42.9 1.0
O C:HOH9368 4.7 19.4 1.0
O C:HOH8623 4.9 38.7 1.0
NE2 C:GLN49 4.9 0.0 1.0
O C:HOH9395 4.9 28.6 1.0

Reference:

D.H.Juers, S.Hakda, B.W.Matthews, R.E.Huber. Structural Basis For the Altered Activity of GLY794 Variants of Escherichia Coli Beta-Galactosidase Biochemistry V. 42 13505 2003.
ISSN: ISSN 0006-2960
PubMed: 14621996
DOI: 10.1021/BI035506J
Page generated: Tue Aug 13 10:57:14 2024

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