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Magnesium in PDB 1px3: E. Coli (Lacz) Beta-Galactosidase (G794A)

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (G794A), PDB code: 1px3 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) 21.70 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.700, 168.590, 200.990, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1px3:

The structure of E. Coli (Lacz) Beta-Galactosidase (G794A) also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (G794A) (pdb code 1px3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (G794A), PDB code: 1px3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 1px3

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Magnesium binding site 1 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:17.6
occ:1.00
 O A:HOH8680 2.0 11.1 1.0
O A:HOH8616 2.1 13.3 1.0
O A:HOH8756 2.1 13.1 1.0
OE2 A:GLU416 2.1 15.4 1.0
OE1 A:GLU461 2.2 18.1 1.0
ND1 A:HIS418 2.3 13.8 1.0
CE1 A:HIS418 3.1 17.7 1.0
CD A:GLU461 3.2 23.4 1.0
CD A:GLU416 3.3 17.8 1.0
CG A:HIS418 3.4 18.5 1.0
OE1 A:GLU416 3.7 14.0 1.0
CB A:HIS418 3.7 11.4 1.0
OE2 A:GLU461 4.0 19.4 1.0
OD1 A:ASN102 4.1 20.4 1.0
CB A:GLU461 4.1 9.7 1.0
CB A:ASP201 4.2 12.9 1.0
CG A:GLU461 4.2 10.7 1.0
N A:ASP201 4.2 14.8 1.0
O A:HOH8603 4.3 18.9 1.0
O A:ASP199 4.3 15.6 1.0
ND2 A:ASN460 4.3 13.3 1.0
NE2 A:HIS418 4.3 16.4 1.0
CG A:GLU416 4.4 8.6 1.0
CD2 A:HIS418 4.5 17.2 1.0
O A:ASN102 4.6 19.5 1.0
O A:HOH8891 4.6 21.5 1.0
CA A:ASP201 4.8 14.5 1.0
CA A:GLN200 4.9 10.5 1.0
C A:GLN200 4.9 15.9 1.0

Magnesium binding site 2 out of 12 in 1px3

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Magnesium binding site 2 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:17.5
occ:1.00
 O A:ASN18 2.2 17.3 1.0
O A:ASP15 2.2 19.0 1.0
OE1 A:GLN163 2.3 16.2 1.0
O A:VAL21 2.3 16.4 1.0
OD2 A:ASP193 2.4 17.9 1.0
CG A:ASP193 3.1 25.1 1.0
OD1 A:ASP193 3.1 19.4 1.0
C A:ASN18 3.1 16.8 1.0
CD A:GLN163 3.2 16.9 1.0
C A:ASP15 3.4 21.1 1.0
C A:VAL21 3.5 18.5 1.0
NE2 A:GLN163 3.5 16.6 1.0
N A:ASN18 3.6 22.2 1.0
CA A:ASN18 3.8 19.5 1.0
OH A:TYR161 4.0 13.7 1.0
CA A:TRP16 4.0 16.0 1.0
N A:PRO19 4.1 19.3 1.0
CB A:ASN18 4.1 16.8 1.0
N A:TRP16 4.1 18.2 1.0
C A:TRP16 4.2 19.2 1.0
CA A:VAL21 4.2 12.2 1.0
N A:VAL21 4.2 14.3 1.0
CB A:VAL21 4.3 17.6 1.0
CE2 A:TYR161 4.4 15.3 1.0
CA A:PRO19 4.4 14.2 1.0
N A:GLU17 4.4 17.6 1.0
CA A:ASP15 4.5 16.6 1.0
CG A:GLN163 4.5 16.3 1.0
CB A:ASP193 4.5 14.2 1.0
N A:THR22 4.5 15.2 1.0
CZ A:TYR161 4.7 13.5 1.0
CA A:THR22 4.7 20.9 1.0
O A:TRP16 4.7 19.2 1.0
C A:GLU17 4.8 27.1 1.0
C A:PRO19 4.8 16.6 1.0
CG1 A:VAL21 4.8 18.5 1.0
CB A:ASP15 4.9 17.6 1.0
CG A:ASN18 5.0 20.7 1.0

Magnesium binding site 3 out of 12 in 1px3

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Magnesium binding site 3 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:42.2
occ:1.00
 O A:HOH9343 1.8 29.4 1.0
O A:HOH9344 1.9 41.8 1.0
O A:HOH9399 2.3 31.8 1.0
O A:HOH9192 2.3 29.6 1.0
C1 A:DMS8406 3.4 59.8 1.0
O A:DMS8406 4.0 45.9 1.0
OE2 A:GLU314 4.0 21.4 1.0
OE1 A:GLU314 4.2 17.4 1.0
S A:DMS8406 4.3 77.7 1.0
O A:HOH9421 4.3 41.0 1.0
O A:HOH9234 4.6 22.2 1.0
CD A:GLU314 4.6 19.5 1.0

Magnesium binding site 4 out of 12 in 1px3

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Magnesium binding site 4 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:14.2
occ:1.00
 O B:HOH8694 2.0 11.9 1.0
OE1 B:GLU461 2.0 14.3 1.0
O B:HOH8771 2.1 12.5 1.0
OE2 B:GLU416 2.1 13.0 1.0
ND1 B:HIS418 2.1 13.6 1.0
O B:HOH8630 2.2 11.1 1.0
CD B:GLU461 3.0 13.7 1.0
CE1 B:HIS418 3.0 12.9 1.0
CG B:HIS418 3.3 14.9 1.0
CD B:GLU416 3.3 13.1 1.0
CB B:HIS418 3.6 11.3 1.0
OE1 B:GLU416 3.7 13.7 1.0
O B:HOH9142 3.7 44.5 1.0
OE2 B:GLU461 3.8 15.4 1.0
CB B:GLU461 4.0 10.4 1.0
OD1 B:ASN102 4.0 17.2 1.0
CG B:GLU461 4.1 8.9 1.0
CB B:ASP201 4.2 15.6 1.0
O B:HOH8617 4.2 24.8 1.0
N B:ASP201 4.2 13.4 1.0
NE2 B:HIS418 4.3 12.3 1.0
ND2 B:ASN460 4.3 12.7 1.0
CD2 B:HIS418 4.4 14.0 1.0
O B:ASP199 4.4 13.4 1.0
CG B:GLU416 4.5 9.3 1.0
O B:HOH8904 4.7 20.3 1.0
O B:ASN102 4.7 18.3 1.0
CA B:ASP201 4.8 14.6 1.0
CG2 B:VAL103 4.9 17.0 1.0
C B:GLN200 4.9 14.6 1.0
CA B:GLN200 4.9 12.9 1.0

Magnesium binding site 5 out of 12 in 1px3

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Magnesium binding site 5 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:15.7
occ:1.00
 O B:ASP15 2.2 17.0 1.0
OE1 B:GLN163 2.3 16.8 1.0
OD2 B:ASP193 2.3 13.3 1.0
O B:ASN18 2.4 15.8 1.0
O B:VAL21 2.4 15.6 1.0
OD1 B:ASP193 3.0 17.4 1.0
CG B:ASP193 3.0 18.1 1.0
CD B:GLN163 3.2 13.6 1.0
C B:ASN18 3.3 16.7 1.0
C B:ASP15 3.4 15.5 1.0
NE2 B:GLN163 3.5 14.7 1.0
C B:VAL21 3.6 14.6 1.0
N B:ASN18 3.7 19.2 1.0
OH B:TYR161 3.9 17.5 1.0
CA B:ASN18 4.0 16.7 1.0
CA B:TRP16 4.0 15.8 1.0
N B:TRP16 4.2 13.8 1.0
N B:PRO19 4.2 19.1 1.0
C B:TRP16 4.3 17.6 1.0
CB B:ASN18 4.3 12.9 1.0
N B:VAL21 4.3 18.5 1.0
CA B:VAL21 4.3 14.0 1.0
CA B:PRO19 4.3 29.6 1.0
CE2 B:TYR161 4.3 14.9 1.0
CB B:VAL21 4.3 15.9 1.0
N B:GLU17 4.4 18.3 1.0
CB B:ASP193 4.5 12.1 1.0
CG B:GLN163 4.5 11.1 1.0
N B:THR22 4.5 10.7 1.0
CA B:ASP15 4.6 22.6 1.0
CA B:THR22 4.6 13.1 1.0
CZ B:TYR161 4.6 16.6 1.0
O B:TRP16 4.8 15.4 1.0
C B:PRO19 4.8 24.2 1.0
CG1 B:VAL21 4.9 19.5 1.0
C B:GLU17 4.9 18.9 1.0
CB B:ASP15 5.0 20.6 1.0

Magnesium binding site 6 out of 12 in 1px3

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Magnesium binding site 6 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:15.0
occ:1.00
 O C:HOH8782 2.0 13.1 1.0
O C:HOH8705 2.1 15.4 1.0
OE2 C:GLU416 2.1 13.8 1.0
OE1 C:GLU461 2.1 14.1 1.0
O C:HOH8641 2.2 12.4 1.0
ND1 C:HIS418 2.3 16.4 1.0
CD C:GLU461 3.1 19.1 1.0
CE1 C:HIS418 3.2 15.7 1.0
CD C:GLU416 3.2 18.1 1.0
CG C:HIS418 3.4 12.1 1.0
OE1 C:GLU416 3.6 14.2 1.0
CB C:HIS418 3.6 9.1 1.0
OE2 C:GLU461 3.9 18.0 1.0
N C:ASP201 4.1 14.1 1.0
CB C:GLU461 4.1 9.2 1.0
OD1 C:ASN102 4.1 16.6 1.0
CB C:ASP201 4.2 12.3 1.0
CG C:GLU461 4.2 11.2 1.0
O C:ASP199 4.3 12.0 1.0
ND2 C:ASN460 4.3 11.3 1.0
O C:HOH8628 4.3 20.5 1.0
NE2 C:HIS418 4.3 14.1 1.0
CG C:GLU416 4.5 8.6 1.0
CD2 C:HIS418 4.5 13.8 1.0
O C:HOH8918 4.6 26.2 1.0
O C:ASN102 4.7 17.4 1.0
CA C:ASP201 4.7 13.4 1.0
C C:GLN200 4.8 21.5 1.0
CA C:GLN200 4.9 14.2 1.0
CG2 C:VAL103 4.9 17.9 1.0

Magnesium binding site 7 out of 12 in 1px3

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Magnesium binding site 7 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:14.0
occ:1.00
 O C:VAL21 2.2 12.5 1.0
O C:ASP15 2.2 13.5 1.0
OE1 C:GLN163 2.4 13.5 1.0
O C:ASN18 2.4 14.5 1.0
OD2 C:ASP193 2.5 17.9 1.0
OD1 C:ASP193 3.2 20.0 1.0
CG C:ASP193 3.2 22.3 1.0
CD C:GLN163 3.3 14.2 1.0
C C:ASN18 3.3 16.4 1.0
C C:VAL21 3.3 13.9 1.0
C C:ASP15 3.4 14.3 1.0
NE2 C:GLN163 3.6 11.6 1.0
N C:ASN18 3.7 21.9 1.0
CA C:ASN18 4.0 17.1 1.0
OH C:TYR161 4.0 14.6 1.0
CA C:VAL21 4.1 12.4 1.0
CA C:TRP16 4.1 12.2 1.0
N C:PRO19 4.2 16.3 1.0
N C:TRP16 4.2 12.7 1.0
N C:VAL21 4.2 11.9 1.0
CB C:VAL21 4.2 15.5 1.0
CB C:ASN18 4.3 18.4 1.0
N C:THR22 4.3 11.4 1.0
C C:TRP16 4.3 12.4 1.0
CE2 C:TYR161 4.4 12.4 1.0
CA C:PRO19 4.4 16.5 1.0
N C:GLU17 4.5 18.4 1.0
CG C:GLN163 4.5 11.4 1.0
CA C:THR22 4.6 11.5 1.0
CA C:ASP15 4.6 16.2 1.0
CB C:ASP193 4.6 12.1 1.0
CZ C:TYR161 4.7 14.8 1.0
CG1 C:VAL21 4.7 17.9 1.0
O C:TRP16 4.8 16.8 1.0
C C:PRO19 4.9 19.1 1.0
C C:GLU17 4.9 24.6 1.0
CB C:ASP15 5.0 18.4 1.0

Magnesium binding site 8 out of 12 in 1px3

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Magnesium binding site 8 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3004

b:52.9
occ:1.00
 O C:HOH9432 2.0 20.0 0.5
O C:HOH9434 2.4 37.7 1.0
CG C:GLN49 3.9 44.3 1.0
O C:HOH9276 4.3 19.6 1.0
OE2 C:GLU41 4.3 16.9 1.0
O C:HOH9466 4.5 47.5 1.0
CD C:GLN49 4.6 86.9 1.0
NE2 C:GLN49 4.7 55.9 1.0
O C:HOH9360 4.7 19.8 1.0

Magnesium binding site 9 out of 12 in 1px3

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Magnesium binding site 9 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3006

b:31.7
occ:1.00
 O C:HOH9459 1.8 36.3 1.0
O C:HOH9436 2.1 34.0 1.0
O C:HOH9411 2.1 32.1 1.0
O C:HOH9454 4.0 38.0 1.0
CD C:ARG178 4.2 51.9 1.0
O C:HOH9364 4.2 28.0 1.0
O C:ALA179 4.2 24.8 1.0
O C:GLU181 4.3 18.4 1.0
CG C:ARG178 4.6 32.9 1.0
N C:GLU181 4.6 16.7 1.0

Magnesium binding site 10 out of 12 in 1px3

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Magnesium binding site 10 out of 12 in the E. Coli (Lacz) Beta-Galactosidase (G794A)


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

b:14.7
occ:1.00
 O D:HOH8822 1.9 13.1 1.0
OE1 D:GLU461 2.0 15.3 1.0
O D:HOH8898 2.1 13.7 1.0
O D:HOH8759 2.1 12.4 1.0
ND1 D:HIS418 2.2 16.2 1.0
OE2 D:GLU416 2.2 15.4 1.0
CE1 D:HIS418 3.0 18.3 1.0
CD D:GLU461 3.1 24.2 1.0
CD D:GLU416 3.3 13.0 1.0
CG D:HIS418 3.3 12.0 1.0
OE1 D:GLU416 3.7 14.1 1.0
CB D:HIS418 3.8 11.3 1.0
OE2 D:GLU461 3.9 20.1 1.0
CB D:ASP201 4.1 14.8 1.0
CB D:GLU461 4.1 9.3 1.0
CG D:GLU461 4.1 11.9 1.0
O D:HOH8746 4.2 19.8 1.0
N D:ASP201 4.2 14.7 1.0
OD1 D:ASN102 4.2 21.1 1.0
NE2 D:HIS418 4.3 16.2 1.0
ND2 D:ASN460 4.3 12.1 1.0
O D:ASP199 4.3 13.5 1.0
CD2 D:HIS418 4.4 15.2 1.0
CG D:GLU416 4.5 9.0 1.0
O D:HOH9033 4.5 19.5 1.0
O D:ASN102 4.7 18.3 1.0
CA D:ASP201 4.7 14.8 1.0
O D:HOH9020 4.9 35.3 1.0
CA D:GLN200 4.9 13.2 1.0
C D:GLN200 4.9 14.5 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 10:57:09 2024

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