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

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg, PDB code: 1jyv 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) 29.90 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.492, 167.455, 200.341, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 24

Other elements in 1jyv:

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg 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 (E537Q) in Complex with Onpg (pdb code 1jyv). 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 (E537Q) in Complex with Onpg, PDB code: 1jyv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 1jyv

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Magnesium binding site 1 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:17.7
occ:1.00
 O A:HOH8755 2.1 13.3 1.0
OE2 A:GLU416 2.1 15.7 1.0
O A:HOH8679 2.1 12.9 1.0
O A:HOH8615 2.2 11.9 1.0
ND1 A:HIS418 2.2 15.5 1.0
OE1 A:GLU461 2.2 15.4 1.0
CE1 A:HIS418 3.1 13.0 1.0
CD A:GLU416 3.2 22.7 1.0
CD A:GLU461 3.2 23.5 1.0
CG A:HIS418 3.3 19.7 1.0
OE1 A:GLU416 3.6 13.4 1.0
CB A:HIS418 3.7 15.5 1.0
CB A:GLU461 4.0 9.3 1.0
OE2 A:GLU461 4.0 16.0 1.0
OD1 A:ASN102 4.1 17.4 1.0
O A:HOH8603 4.1 15.3 1.0
CG A:GLU461 4.2 11.9 1.0
N A:ASP201 4.2 14.9 1.0
CB A:ASP201 4.2 14.7 1.0
ND2 A:ASN460 4.3 14.1 1.0
NE2 A:HIS418 4.3 14.7 1.0
O4 A:1452001 4.3 16.8 1.0
O A:ASP199 4.3 17.8 1.0
CD2 A:HIS418 4.4 15.1 1.0
CG A:GLU416 4.5 11.1 1.0
O3 A:1452001 4.5 17.5 1.0
O A:ASN102 4.6 14.7 1.0
CA A:ASP201 4.8 15.7 1.0
CA A:GLN200 4.8 10.5 1.0
CG2 A:VAL103 4.8 21.6 1.0
C A:GLN200 4.8 16.6 1.0
C2 A:1452001 4.8 14.9 1.0

Magnesium binding site 2 out of 17 in 1jyv

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Magnesium binding site 2 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:17.3
occ:1.00
 OE1 A:GLN163 2.2 15.6 1.0
O A:ASP15 2.2 14.9 1.0
OD2 A:ASP193 2.3 18.7 1.0
O A:VAL21 2.4 19.3 1.0
O A:ASN18 2.4 17.9 1.0
OD1 A:ASP193 3.0 17.4 1.0
CG A:ASP193 3.0 21.7 1.0
CD A:GLN163 3.1 13.2 1.0
C A:ASN18 3.3 19.2 1.0
NE2 A:GLN163 3.4 13.8 1.0
C A:ASP15 3.4 21.5 1.0
C A:VAL21 3.5 19.8 1.0
N A:ASN18 3.6 24.0 1.0
OH A:TYR161 3.9 16.2 1.0
CA A:TRP16 3.9 14.0 1.0
CA A:ASN18 4.0 16.3 1.0
N A:TRP16 4.1 14.5 1.0
N A:PRO19 4.2 21.2 1.0
C A:TRP16 4.2 17.6 1.0
CA A:VAL21 4.2 12.4 1.0
CB A:ASN18 4.3 17.7 1.0
CB A:VAL21 4.3 17.8 1.0
N A:VAL21 4.3 12.8 1.0
CE2 A:TYR161 4.3 16.7 1.0
N A:GLU17 4.4 15.7 1.0
CG A:GLN163 4.4 12.6 1.0
CB A:ASP193 4.5 13.8 1.0
CA A:PRO19 4.5 17.8 1.0
N A:THR22 4.5 13.3 1.0
CA A:ASP15 4.6 16.2 1.0
CZ A:TYR161 4.6 17.4 1.0
CA A:THR22 4.6 15.3 1.0
O A:TRP16 4.7 18.5 1.0
C A:GLU17 4.8 27.5 1.0
CG1 A:VAL21 4.8 17.0 1.0
C A:PRO19 4.9 17.9 1.0
CB A:ASP15 4.9 16.9 1.0

Magnesium binding site 3 out of 17 in 1jyv

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Magnesium binding site 3 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:61.3
occ:1.00
 O A:HOH8864 2.2 28.5 1.0
O A:HOH9268 2.3 38.5 1.0
O A:HOH8972 2.5 43.5 1.0
OE1 A:GLN718 2.5 38.1 1.0
O A:HOH9210 2.7 46.9 1.0
CD A:GLN718 3.6 33.5 1.0
O A:HOH9427 4.0 31.9 1.0
NE2 A:GLN718 4.0 25.8 1.0
O A:THR911 4.0 17.5 1.0
NE2 A:HIS622 4.2 17.9 1.0
O A:HOH8854 4.3 28.6 1.0
O A:HOH9019 4.3 45.4 1.0
O A:GLN719 4.5 17.9 1.0
N A:GLN719 4.6 15.1 1.0
CE1 A:HIS622 4.8 17.0 1.0
CG A:GLN718 4.9 18.8 1.0
O A:HOH8681 4.9 20.4 1.0
C A:THR911 5.0 18.4 1.0

Magnesium binding site 4 out of 17 in 1jyv

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Magnesium binding site 4 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:31.2
occ:1.00
 O A:HOH9416 2.1 25.8 1.0
O A:HOH9417 2.2 30.3 1.0
O A:HOH9232 2.2 23.1 1.0
O A:HOH9490 2.3 36.6 1.0
C1 A:DMS8406 3.0 53.0 1.0
O A:DMS8406 3.6 78.6 1.0
S A:DMS8406 3.9 70.9 1.0
OE1 A:GLU314 4.2 15.7 1.0
OE2 A:GLU314 4.2 21.0 1.0
O A:HOH9281 4.3 21.6 1.0
O A:HOH9523 4.4 19.0 1.0
CD A:GLU314 4.6 22.5 1.0
O A:HOH9271 4.8 25.5 1.0
O A:HOH9256 4.9 40.7 1.0

Magnesium binding site 5 out of 17 in 1jyv

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Magnesium binding site 5 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:31.7
occ:1.00
 O A:HOH9193 2.1 7.4 0.5
O A:HOH9568 2.1 23.2 1.0
O A:HOH9081 2.2 22.6 1.0
O A:ASN597 2.2 17.0 1.0
O A:HOH9038 2.3 21.2 1.0
O A:HOH8821 2.3 22.7 1.0
C A:ASN597 3.4 23.0 1.0
N A:ASN597 3.8 15.1 1.0
NH2 A:ARG800 4.0 38.3 1.0
O A:HOH9583 4.0 42.8 1.0
OE2 A:GLU797 4.1 27.6 1.0
OD1 A:ASN597 4.1 19.3 1.0
O A:HOH9574 4.2 56.1 1.0
OD1 A:ASP598 4.2 19.1 1.0
CA A:ASN597 4.2 11.7 1.0
OE1 A:GLU797 4.3 27.6 1.0
O A:HOH9381 4.3 37.9 1.0
N A:ASP598 4.3 17.2 1.0
CA A:ASP598 4.4 17.7 1.0
CG A:ASN597 4.4 26.2 1.0
O A:HOH9041 4.5 31.6 1.0
CD A:GLU797 4.6 100.0 1.0
ND2 A:ASN597 4.8 17.9 1.0
O A:HOH9314 4.8 25.5 1.0
CG A:ASP598 4.9 17.3 1.0
C A:PRO596 4.9 25.4 1.0

Magnesium binding site 6 out of 17 in 1jyv

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Magnesium binding site 6 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:15.2
occ:1.00
 OE2 B:GLU416 2.0 14.7 1.0
OE1 B:GLU461 2.0 14.5 1.0
O B:HOH8634 2.0 12.1 1.0
O B:HOH8698 2.1 11.8 1.0
O B:HOH8774 2.1 13.0 1.0
ND1 B:HIS418 2.3 13.1 1.0
CD B:GLU461 3.0 13.7 1.0
CD B:GLU416 3.1 16.2 1.0
CE1 B:HIS418 3.2 14.4 1.0
CG B:HIS418 3.3 15.3 1.0
OE1 B:GLU416 3.5 14.0 1.0
CB B:HIS418 3.7 13.6 1.0
OE2 B:GLU461 3.9 19.1 1.0
CB B:GLU461 4.0 12.1 1.0
CG B:GLU461 4.0 12.4 1.0
O B:HOH8621 4.0 16.6 1.0
OD1 B:ASN102 4.2 14.9 1.0
N B:ASP201 4.2 13.4 1.0
CB B:ASP201 4.2 13.0 1.0
ND2 B:ASN460 4.2 12.6 1.0
O B:ASP199 4.3 15.1 1.0
CG B:GLU416 4.4 11.1 1.0
O3 B:1452001 4.4 14.7 1.0
O4 B:1452001 4.4 16.0 1.0
NE2 B:HIS418 4.4 13.4 1.0
CD2 B:HIS418 4.4 12.5 1.0
O B:ASN102 4.8 14.8 1.0
C2 B:1452001 4.8 12.7 1.0
CA B:ASP201 4.8 14.0 1.0
CA B:GLN200 4.9 9.4 1.0
C B:GLN200 5.0 21.1 1.0
CG2 B:VAL103 5.0 29.1 1.0

Magnesium binding site 7 out of 17 in 1jyv

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Magnesium binding site 7 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:17.3
occ:1.00
 O B:ASN18 2.3 20.2 1.0
O B:ASP15 2.3 15.3 1.0
O B:VAL21 2.3 19.1 1.0
OD2 B:ASP193 2.3 16.8 1.0
OE1 B:GLN163 2.3 18.0 1.0
OD1 B:ASP193 3.1 17.6 1.0
CG B:ASP193 3.1 16.1 1.0
C B:ASN18 3.2 15.1 1.0
CD B:GLN163 3.2 17.8 1.0
C B:VAL21 3.5 17.9 1.0
C B:ASP15 3.5 21.9 1.0
NE2 B:GLN163 3.5 13.7 1.0
N B:ASN18 3.7 22.3 1.0
CA B:ASN18 3.9 19.1 1.0
OH B:TYR161 4.0 18.0 1.0
CA B:TRP16 4.0 14.3 1.0
N B:PRO19 4.1 17.6 1.0
CB B:ASN18 4.2 15.9 1.0
CA B:VAL21 4.2 15.2 1.0
N B:TRP16 4.2 16.9 1.0
CB B:VAL21 4.3 16.9 1.0
N B:VAL21 4.3 19.8 1.0
C B:TRP16 4.3 21.0 1.0
CA B:PRO19 4.4 20.9 1.0
CE2 B:TYR161 4.4 14.1 1.0
N B:GLU17 4.4 16.4 1.0
N B:THR22 4.5 15.7 1.0
CG B:GLN163 4.5 13.6 1.0
CB B:ASP193 4.5 11.8 1.0
CA B:THR22 4.6 15.3 1.0
CA B:ASP15 4.6 20.2 1.0
CZ B:TYR161 4.7 24.1 1.0
C B:PRO19 4.8 20.8 1.0
CG1 B:VAL21 4.8 21.0 1.0
C B:GLU17 4.9 25.4 1.0
O B:TRP16 5.0 16.8 1.0

Magnesium binding site 8 out of 17 in 1jyv

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Magnesium binding site 8 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:48.9
occ:1.00
 O B:HOH8881 2.3 24.7 1.0
O B:HOH9221 2.4 33.3 1.0
O B:HOH9045 2.4 48.8 1.0
OE1 B:GLN718 2.4 38.2 1.0
O B:HOH8988 2.5 40.7 1.0
O B:HOH9281 2.6 40.2 1.0
CD B:GLN718 3.5 25.4 1.0
NE2 B:GLN718 3.8 25.0 1.0
O B:HOH8897 3.8 38.0 1.0
O B:THR911 3.9 18.5 1.0
NE2 B:HIS622 4.2 15.9 1.0
O B:HOH8871 4.4 25.8 1.0
O B:HOH9028 4.4 34.5 1.0
O B:GLN719 4.5 16.6 1.0
N B:GLN719 4.5 17.1 1.0
O B:HOH8857 4.7 44.0 1.0
O B:HOH9538 4.8 45.8 1.0
CE1 B:HIS622 4.8 15.7 1.0
CG B:GLN718 4.8 16.8 1.0
O B:HOH8700 4.9 18.8 1.0
C B:THR911 4.9 17.2 1.0

Magnesium binding site 9 out of 17 in 1jyv

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Magnesium binding site 9 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:28.0
occ:1.00
 O B:HOH9094 2.1 30.5 1.0
O B:HOH9202 2.1 9.9 0.5
O B:ASN597 2.1 19.5 1.0
O B:HOH9539 2.2 32.5 1.0
O B:HOH8838 2.3 23.6 1.0
O B:HOH9049 2.3 21.5 1.0
C B:ASN597 3.3 26.4 1.0
N B:ASN597 3.8 18.4 1.0
NH2 B:ARG800 4.0 37.7 1.0
OD1 B:ASN597 4.0 19.6 1.0
OE2 B:GLU797 4.1 25.6 1.0
OD1 B:ASP598 4.1 18.4 1.0
CA B:ASN597 4.2 15.2 1.0
O B:HOH9387 4.3 31.3 1.0
N B:ASP598 4.3 17.3 1.0
O B:HOH9552 4.3 32.0 1.0
CA B:ASP598 4.3 15.4 1.0
OE1 B:GLU797 4.4 27.1 1.0
O B:HOH9544 4.5 48.5 1.0
CG B:ASN597 4.5 29.0 1.0
O B:HOH9052 4.5 32.4 1.0
CD B:GLU797 4.6 38.3 1.0
O B:HOH9325 4.8 31.1 1.0
CG B:ASP598 4.8 21.9 1.0
O B:HOH9350 4.9 56.5 1.0
ND2 B:ASN597 4.9 22.3 1.0
CB B:PRO596 4.9 20.2 1.0
C B:PRO596 4.9 19.7 1.0
N B:ARG599 5.0 16.6 1.0

Magnesium binding site 10 out of 17 in 1jyv

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Magnesium binding site 10 out of 17 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Onpg


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

b:15.1
occ:1.00
 OE2 C:GLU416 2.0 14.2 1.0
O C:HOH8879 2.1 13.1 1.0
OE1 C:GLU461 2.1 14.2 1.0
O C:HOH8737 2.1 12.8 1.0
O C:HOH8801 2.2 13.3 1.0
ND1 C:HIS418 2.2 15.1 1.0
CD C:GLU461 3.1 16.1 1.0
CE1 C:HIS418 3.1 14.2 1.0
CD C:GLU416 3.2 22.2 1.0
CG C:HIS418 3.3 16.2 1.0
OE1 C:GLU416 3.6 16.1 1.0
CB C:HIS418 3.6 12.8 1.0
CB C:GLU461 4.0 11.7 1.0
OE2 C:GLU461 4.0 17.3 1.0
CG C:GLU461 4.0 13.4 1.0
OD1 C:ASN102 4.1 17.2 1.0
O C:HOH8724 4.1 14.9 1.0
ND2 C:ASN460 4.2 15.0 1.0
N C:ASP201 4.2 13.0 1.0
CB C:ASP201 4.2 17.1 1.0
O C:ASP199 4.3 15.1 1.0
O4 C:1452001 4.3 16.2 1.0
NE2 C:HIS418 4.3 12.1 1.0
CG C:GLU416 4.4 12.5 1.0
CD2 C:HIS418 4.4 17.6 1.0
O3 C:1452001 4.5 14.9 1.0
O C:ASN102 4.7 16.6 1.0
CA C:ASP201 4.8 14.7 1.0
C2 C:1452001 4.8 15.6 1.0
CA C:GLN200 5.0 14.8 1.0
C C:GLN200 5.0 20.1 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 06:52:41 2024

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