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

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg, PDB code: 1jyw 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) 28.80 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.680, 168.600, 201.090, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 22.9

Other elements in 1jyw:

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

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg (pdb code 1jyw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg, PDB code: 1jyw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 1jyw

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Magnesium binding site 1 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:11.9
occ:1.00
OE2 A:GLU416 2.0 11.5 1.0
O A:HOH8678 2.1 8.7 1.0
O A:HOH8615 2.1 9.9 1.0
O A:HOH8753 2.1 10.6 1.0
OE1 A:GLU461 2.1 12.4 1.0
ND1 A:HIS418 2.2 11.8 1.0
CE1 A:HIS418 3.1 11.4 1.0
CD A:GLU416 3.2 12.4 1.0
CD A:GLU461 3.2 17.9 1.0
CG A:HIS418 3.3 13.0 1.0
OE1 A:GLU416 3.6 11.8 1.0
CB A:HIS418 3.6 10.4 1.0
CB A:GLU461 4.0 9.5 1.0
OE2 A:GLU461 4.0 21.0 1.0
CG A:GLU461 4.1 9.2 1.0
O A:HOH8603 4.1 12.2 1.0
OD1 A:ASN102 4.2 14.1 1.0
N A:ASP201 4.2 10.7 1.0
CB A:ASP201 4.2 9.9 1.0
ND2 A:ASN460 4.3 9.8 1.0
O A:ASP199 4.3 14.3 1.0
O4 A:1472001 4.3 11.6 1.0
NE2 A:HIS418 4.3 10.4 1.0
CG A:GLU416 4.4 9.4 1.0
CD2 A:HIS418 4.4 11.4 1.0
O3 A:1472001 4.5 14.9 1.0
O A:ASN102 4.7 12.3 1.0
CA A:ASP201 4.8 10.9 1.0
CA A:GLN200 4.9 8.7 1.0
C2 A:1472001 4.9 13.1 1.0
C A:GLN200 4.9 13.0 1.0

Magnesium binding site 2 out of 15 in 1jyw

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Magnesium binding site 2 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:14.7
occ:1.00
O A:ASP15 2.2 15.3 1.0
OE1 A:GLN163 2.3 11.9 1.0
OD2 A:ASP193 2.3 14.1 1.0
O A:ASN18 2.3 14.4 1.0
O A:VAL21 2.4 15.0 1.0
OD1 A:ASP193 3.0 16.1 1.0
CG A:ASP193 3.1 17.8 1.0
C A:ASN18 3.2 17.6 1.0
CD A:GLN163 3.2 13.1 1.0
C A:ASP15 3.4 17.1 1.0
NE2 A:GLN163 3.4 12.5 1.0
C A:VAL21 3.6 14.3 1.0
N A:ASN18 3.7 20.1 1.0
CA A:ASN18 3.9 19.0 1.0
CA A:TRP16 4.0 13.3 1.0
OH A:TYR161 4.0 12.5 1.0
N A:PRO19 4.1 18.0 1.0
N A:TRP16 4.2 14.6 1.0
CB A:ASN18 4.2 16.3 1.0
C A:TRP16 4.2 15.2 1.0
N A:VAL21 4.2 12.6 1.0
CA A:VAL21 4.2 13.8 1.0
CB A:VAL21 4.3 13.8 1.0
CA A:PRO19 4.3 16.3 1.0
CE2 A:TYR161 4.4 12.6 1.0
N A:GLU17 4.5 16.5 1.0
CB A:ASP193 4.5 12.4 1.0
N A:THR22 4.5 10.9 1.0
CG A:GLN163 4.6 14.6 1.0
CA A:ASP15 4.6 14.1 1.0
CZ A:TYR161 4.7 12.7 1.0
CA A:THR22 4.7 12.7 1.0
O A:TRP16 4.8 14.0 1.0
C A:PRO19 4.8 14.8 1.0
C A:GLU17 4.9 23.0 1.0
CG1 A:VAL21 4.9 14.6 1.0
CB A:ASP15 4.9 12.6 1.0

Magnesium binding site 3 out of 15 in 1jyw

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Magnesium binding site 3 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:33.8
occ:1.00
O A:HOH9426 1.9 30.2 1.0
O A:HOH9502 2.0 31.6 1.0
O A:HOH9240 2.3 25.7 1.0
O A:DMS8406 3.1 0.0 1.0
O A:HOH9417 3.8 55.2 1.0
OE2 A:GLU314 4.3 22.4 1.0
OE1 A:GLU314 4.3 16.7 1.0
S A:DMS8406 4.4 73.3 1.0
O A:HOH9289 4.4 23.3 1.0
O A:HOH9536 4.4 28.5 1.0
CD A:GLU314 4.8 17.0 1.0
C1 A:DMS8406 4.9 59.4 1.0

Magnesium binding site 4 out of 15 in 1jyw

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Magnesium binding site 4 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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 Pnpg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3105

b:21.6
occ:0.50
O A:HOH9200 1.8 17.0 0.5
O A:HOH9576 2.0 39.5 1.0
O A:HOH9080 2.1 36.4 1.0
O A:ASN597 2.2 17.0 1.0
O A:HOH9037 2.4 24.7 1.0
O A:HOH8819 2.8 24.3 1.0
C A:ASN597 3.4 19.5 1.0
N A:ASN597 3.9 15.8 1.0
OE2 A:GLU797 4.1 39.7 1.0
OE1 A:GLU797 4.2 45.4 1.0
CA A:ASN597 4.3 13.8 1.0
O A:HOH9322 4.3 37.3 1.0
OD1 A:ASN597 4.4 14.2 1.0
N A:ASP598 4.4 14.1 1.0
OD1 A:ASP598 4.4 19.1 1.0
CA A:ASP598 4.5 14.2 1.0
CD A:GLU797 4.5 0.0 1.0
CG A:ASN597 4.6 22.6 1.0
O A:HOH9040 4.8 25.4 1.0
O A:HOH9389 4.8 37.5 1.0
O A:HOH9618 4.8 39.5 1.0
ND2 A:ASN597 4.9 13.9 1.0
C A:PRO596 4.9 21.8 1.0
O A:HOH8922 5.0 35.2 1.0
CG A:ASP598 5.0 16.3 1.0

Magnesium binding site 5 out of 15 in 1jyw

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Magnesium binding site 5 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:11.0
occ:1.00
OE1 B:GLU461 2.0 12.2 1.0
OE2 B:GLU416 2.0 10.6 1.0
O B:HOH8701 2.1 9.5 1.0
O B:HOH8637 2.1 9.7 1.0
O B:HOH8776 2.1 10.6 1.0
ND1 B:HIS418 2.2 9.7 1.0
CD B:GLU461 3.0 13.9 1.0
CE1 B:HIS418 3.1 10.2 1.0
CD B:GLU416 3.2 12.3 1.0
CG B:HIS418 3.3 9.2 1.0
OE1 B:GLU416 3.6 10.7 1.0
CB B:HIS418 3.7 9.3 1.0
CB B:GLU461 3.9 8.5 1.0
OE2 B:GLU461 3.9 18.7 1.0
CG B:GLU461 4.0 8.4 1.0
O B:HOH8624 4.1 11.1 1.0
OD1 B:ASN102 4.1 12.3 1.0
N B:ASP201 4.2 9.7 1.0
CB B:ASP201 4.2 9.2 1.0
ND2 B:ASN460 4.3 10.1 1.0
O B:ASP199 4.3 11.1 1.0
NE2 B:HIS418 4.3 9.5 1.0
O4 B:1472001 4.4 10.7 1.0
CG B:GLU416 4.4 8.6 1.0
CD2 B:HIS418 4.4 10.6 1.0
O3 B:1472001 4.5 11.2 1.0
C2 B:1472001 4.7 9.9 1.0
O B:ASN102 4.8 13.3 1.0
CA B:GLN200 4.8 8.6 1.0
CA B:ASP201 4.8 10.5 1.0
C B:GLN200 4.9 11.7 1.0

Magnesium binding site 6 out of 15 in 1jyw

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Magnesium binding site 6 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:14.7
occ:1.00
O B:ASN18 2.2 14.7 1.0
OE1 B:GLN163 2.3 13.6 1.0
O B:VAL21 2.3 13.4 1.0
O B:ASP15 2.3 13.7 1.0
OD2 B:ASP193 2.3 11.9 1.0
OD1 B:ASP193 3.0 15.4 1.0
CG B:ASP193 3.1 12.8 1.0
C B:ASN18 3.2 13.6 1.0
CD B:GLN163 3.2 16.3 1.0
C B:VAL21 3.5 14.8 1.0
NE2 B:GLN163 3.5 13.0 1.0
C B:ASP15 3.5 14.3 1.0
N B:ASN18 3.7 18.6 1.0
CA B:ASN18 3.9 16.4 1.0
OH B:TYR161 4.0 13.8 1.0
N B:PRO19 4.1 14.9 1.0
CA B:TRP16 4.1 11.8 1.0
CB B:ASN18 4.2 13.9 1.0
CA B:VAL21 4.2 17.4 1.0
N B:VAL21 4.2 14.9 1.0
N B:TRP16 4.3 14.0 1.0
CA B:PRO19 4.3 21.8 1.0
C B:TRP16 4.3 12.6 1.0
CB B:VAL21 4.4 12.8 1.0
CE2 B:TYR161 4.4 11.7 1.0
N B:GLU17 4.4 14.4 1.0
N B:THR22 4.5 11.2 1.0
CG B:GLN163 4.5 12.8 1.0
CB B:ASP193 4.5 9.7 1.0
CA B:THR22 4.6 10.9 1.0
CZ B:TYR161 4.7 11.3 1.0
CA B:ASP15 4.7 20.4 1.0
C B:PRO19 4.7 18.4 1.0
CG1 B:VAL21 4.8 16.9 1.0
C B:GLU17 4.9 19.4 1.0
O B:TRP16 4.9 12.8 1.0

Magnesium binding site 7 out of 15 in 1jyw

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Magnesium binding site 7 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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 Pnpg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3105

b:18.7
occ:0.50
O B:HOH9214 1.9 16.7 0.5
O B:HOH9100 2.1 17.9 0.5
O B:HOH9598 2.1 18.9 0.5
O B:HOH9058 2.1 21.7 1.0
O B:ASN597 2.2 13.1 1.0
O B:HOH8841 2.4 23.3 1.0
C B:ASN597 3.4 13.6 1.0
N B:ASN597 3.8 13.3 1.0
O B:HOH9486 3.9 47.7 1.0
OE1 B:GLU797 4.1 0.0 1.0
OD1 B:ASN597 4.1 13.2 1.0
CA B:ASN597 4.3 11.5 1.0
O B:HOH9411 4.4 36.1 1.0
CG B:ASN597 4.4 12.8 1.0
N B:ASP598 4.4 11.6 1.0
OE2 B:GLU797 4.4 35.2 1.0
CA B:ASP598 4.5 10.1 1.0
CD B:GLU797 4.5 34.2 1.0
OD1 B:ASP598 4.6 19.5 1.0
ND2 B:ASN597 4.7 15.0 1.0
O B:HOH9476 4.7 29.3 1.0
O B:HOH9344 4.7 38.8 1.0
O B:HOH9374 4.7 36.1 1.0
C B:PRO596 5.0 16.6 1.0

Magnesium binding site 8 out of 15 in 1jyw

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Magnesium binding site 8 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:10.9
occ:1.00
OE1 C:GLU461 2.1 11.2 1.0
OE2 C:GLU416 2.1 11.4 1.0
O C:HOH8708 2.1 9.5 1.0
O C:HOH8785 2.1 10.3 1.0
O C:HOH8644 2.1 10.2 1.0
ND1 C:HIS418 2.2 11.3 1.0
CD C:GLU461 3.1 16.3 1.0
CE1 C:HIS418 3.1 11.9 1.0
CD C:GLU416 3.2 14.0 1.0
CG C:HIS418 3.3 10.3 1.0
OE1 C:GLU416 3.6 11.5 1.0
CB C:HIS418 3.7 8.9 1.0
CB C:GLU461 4.0 8.1 1.0
OE2 C:GLU461 4.0 18.2 1.0
CG C:GLU461 4.1 10.4 1.0
OD1 C:ASN102 4.1 14.2 1.0
O C:HOH8631 4.2 10.7 1.0
N C:ASP201 4.2 9.7 1.0
ND2 C:ASN460 4.2 12.2 1.0
CB C:ASP201 4.3 10.8 1.0
O C:ASP199 4.3 11.1 1.0
NE2 C:HIS418 4.4 9.7 1.0
O4 C:1472001 4.4 12.2 1.0
CD2 C:HIS418 4.4 11.6 1.0
CG C:GLU416 4.5 8.3 1.0
O3 C:1472001 4.5 12.1 1.0
C2 C:1472001 4.7 12.5 1.0
O C:ASN102 4.8 12.3 1.0
CA C:ASP201 4.8 10.7 1.0
CA C:GLN200 4.9 10.6 1.0
C C:GLN200 4.9 14.0 1.0

Magnesium binding site 9 out of 15 in 1jyw

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Magnesium binding site 9 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:13.5
occ:1.00
O C:VAL21 2.3 12.2 1.0
O C:ASP15 2.3 12.8 1.0
O C:ASN18 2.3 14.8 1.0
OD2 C:ASP193 2.3 13.9 1.0
OE1 C:GLN163 2.4 12.3 1.0
OD1 C:ASP193 3.1 14.1 1.0
CG C:ASP193 3.1 14.2 1.0
CD C:GLN163 3.2 12.0 1.0
C C:ASN18 3.3 16.5 1.0
C C:VAL21 3.4 11.1 1.0
C C:ASP15 3.5 11.0 1.0
NE2 C:GLN163 3.5 11.6 1.0
N C:ASN18 3.7 17.5 1.0
CA C:ASN18 4.0 14.2 1.0
OH C:TYR161 4.0 12.8 1.0
CA C:TRP16 4.0 11.7 1.0
N C:PRO19 4.2 16.1 1.0
CA C:VAL21 4.2 12.2 1.0
N C:TRP16 4.2 10.2 1.0
N C:VAL21 4.2 12.2 1.0
CB C:VAL21 4.3 12.2 1.0
CB C:ASN18 4.3 14.1 1.0
C C:TRP16 4.3 16.2 1.0
CA C:PRO19 4.3 13.2 1.0
CE2 C:TYR161 4.4 10.2 1.0
N C:THR22 4.4 10.4 1.0
N C:GLU17 4.5 14.6 1.0
CB C:ASP193 4.5 11.0 1.0
CA C:THR22 4.5 13.1 1.0
CG C:GLN163 4.6 10.5 1.0
CA C:ASP15 4.6 15.0 1.0
CZ C:TYR161 4.7 11.8 1.0
C C:PRO19 4.8 14.6 1.0
CG1 C:VAL21 4.8 15.3 1.0
O C:TRP16 4.8 15.4 1.0
C C:GLU17 4.9 22.6 1.0
CB C:ASP15 5.0 15.1 1.0

Magnesium binding site 10 out of 15 in 1jyw

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Magnesium binding site 10 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Pnpg


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

b:20.2
occ:0.50
O C:HOH9535 1.6 21.3 0.5
O C:HOH9560 1.9 41.5 1.0
O C:HOH9502 2.1 29.7 1.0
O C:GLU181 4.3 17.5 1.0
O C:HOH9445 4.3 30.1 1.0
O C:ALA179 4.4 20.8 1.0
N C:GLU181 4.5 16.3 1.0
CD C:ARG178 4.5 55.8 1.0
CG C:ARG178 4.7 77.2 1.0
NH1 C:ARG178 4.8 73.6 1.0
CB C:GLU181 5.0 14.5 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 06:12:01 2020

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