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Magnesium in PDB 1jz7: E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose, PDB code: 1jz7 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) 40.00 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.590, 168.530, 200.550, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.9

Other elements in 1jz7:

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with Galactose 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 in Complex with Galactose (pdb code 1jz7). 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 in Complex with Galactose, PDB code: 1jz7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 1jz7

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


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

b:11.7
occ:1.00
 O A:HOH8582 2.0 8.8 1.0
OE1 A:GLU461 2.0 11.2 1.0
ND1 A:HIS418 2.1 11.5 1.0
O A:HOH8658 2.1 10.1 1.0
OE2 A:GLU416 2.1 11.7 1.0
O A:HOH8518 2.2 10.7 1.0
CE1 A:HIS418 3.0 14.7 1.0
CD A:GLU461 3.1 15.9 1.0
CD A:GLU416 3.2 11.5 1.0
CG A:HIS418 3.2 13.1 1.0
CB A:HIS418 3.6 10.9 1.0
OE1 A:GLU416 3.7 9.6 1.0
OE2 A:GLU461 3.9 15.4 1.0
CB A:GLU461 4.1 9.2 1.0
OD1 A:ASN102 4.1 14.6 1.0
CG A:GLU461 4.1 12.1 1.0
O4 A:GAL2001 4.2 15.0 1.0
NE2 A:HIS418 4.2 13.4 1.0
CB A:ASP201 4.2 8.6 1.0
N A:ASP201 4.2 9.3 1.0
C2 A:GAL2001 4.3 25.2 1.0
O A:ASP199 4.3 12.7 1.0
ND2 A:ASN460 4.3 10.7 1.0
O3 A:GAL2001 4.4 10.7 1.0
CD2 A:HIS418 4.4 12.7 1.0
CG A:GLU416 4.4 7.9 1.0
O2 A:GAL2001 4.6 15.8 1.0
O A:ASN102 4.8 13.2 1.0
CA A:ASP201 4.8 9.4 1.0
C3 A:GAL2001 4.8 23.0 1.0
CA A:GLN200 4.9 8.3 1.0
C A:GLN200 5.0 10.3 1.0
CG2 A:VAL103 5.0 13.3 1.0

Magnesium binding site 2 out of 15 in 1jz7

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


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

b:14.4
occ:1.00
 OE1 A:GLN163 2.2 13.1 1.0
O A:ASP15 2.3 14.2 1.0
OD2 A:ASP193 2.3 14.5 1.0
O A:VAL21 2.3 14.4 1.0
O A:ASN18 2.4 15.1 1.0
OD1 A:ASP193 3.0 14.5 1.0
CG A:ASP193 3.0 14.6 1.0
CD A:GLN163 3.1 14.3 1.0
C A:ASN18 3.3 14.0 1.0
NE2 A:GLN163 3.4 12.7 1.0
C A:ASP15 3.5 16.9 1.0
C A:VAL21 3.5 13.0 1.0
N A:ASN18 3.7 20.1 1.0
CA A:ASN18 4.0 17.6 1.0
OH A:TYR161 4.0 11.9 1.0
CA A:TRP16 4.0 14.0 1.0
N A:PRO19 4.2 15.2 1.0
N A:TRP16 4.2 12.7 1.0
C A:TRP16 4.2 15.2 1.0
CA A:VAL21 4.2 11.6 1.0
CB A:ASN18 4.3 15.4 1.0
N A:VAL21 4.3 12.5 1.0
CB A:VAL21 4.3 12.0 1.0
CE2 A:TYR161 4.4 12.0 1.0
CA A:PRO19 4.4 13.2 1.0
N A:GLU17 4.4 15.6 1.0
CG A:GLN163 4.5 12.2 1.0
CB A:ASP193 4.5 12.8 1.0
N A:THR22 4.5 11.8 1.0
CA A:THR22 4.6 13.4 1.0
CA A:ASP15 4.6 14.7 1.0
CZ A:TYR161 4.7 12.5 1.0
O A:TRP16 4.8 15.2 1.0
C A:PRO19 4.8 13.0 1.0
CG1 A:VAL21 4.9 15.1 1.0
C A:GLU17 4.9 25.0 1.0

Magnesium binding site 3 out of 15 in 1jz7

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


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

b:30.4
occ:1.00
 O A:HOH9292 1.9 24.9 1.0
O A:HOH9131 2.1 22.4 1.0
O A:HOH9366 2.1 37.9 1.0
O A:HOH9495 2.2 54.3 1.0
O A:HOH9293 2.4 43.1 1.0
O A:DMS8406 3.2 72.6 1.0
OE2 A:GLU314 4.0 18.5 1.0
OE1 A:GLU314 4.1 15.9 1.0
C2 A:DMS8406 4.2 36.0 1.0
S A:DMS8406 4.2 67.8 1.0
O A:HOH9173 4.3 23.6 1.0
O A:HOH9523 4.4 58.0 1.0
O A:HOH9400 4.4 24.2 1.0
CD A:GLU314 4.6 16.3 1.0

Magnesium binding site 4 out of 15 in 1jz7

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


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

b:24.3
occ:0.50
 O A:HOH9091 1.8 17.3 0.5
O A:HOH8983 2.3 35.0 1.0
O A:HOH9440 2.3 43.8 1.0
O A:ASN597 2.4 16.9 1.0
O A:HOH8941 2.4 24.3 1.0
O A:HOH8725 2.9 32.2 1.0
C A:ASN597 3.6 20.1 1.0
OE2 A:GLU797 3.9 0.0 1.0
N A:ASN597 3.9 16.9 1.0
O A:HOH9494 4.2 42.0 1.0
CA A:ASN597 4.4 14.6 1.0
OD1 A:ASN597 4.4 14.7 1.0
CD A:GLU797 4.4 35.6 1.0
OD1 A:ASP598 4.5 19.2 1.0
OE1 A:GLU797 4.5 0.0 1.0
N A:ASP598 4.5 13.2 1.0
CA A:ASP598 4.5 13.0 1.0
CG A:ASN597 4.6 18.5 1.0
O A:HOH9205 4.7 30.1 1.0
O A:HOH9262 4.8 49.5 1.0
ND2 A:ASN597 4.9 14.9 1.0
NH1 A:ARG800 4.9 0.0 1.0
C A:PRO596 5.0 19.4 1.0

Magnesium binding site 5 out of 15 in 1jz7

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


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

b:10.7
occ:1.00
 OE1 B:GLU461 2.0 10.9 1.0
OE2 B:GLU416 2.0 9.6 1.0
O B:HOH8769 2.1 10.8 1.0
O B:HOH8694 2.1 10.0 1.0
O B:HOH8630 2.1 10.3 1.0
ND1 B:HIS418 2.2 12.6 1.0
CD B:GLU461 3.0 14.4 1.0
CE1 B:HIS418 3.1 11.2 1.0
CD B:GLU416 3.2 10.9 1.0
CG B:HIS418 3.3 13.9 1.0
OE1 B:GLU416 3.6 10.6 1.0
CB B:HIS418 3.7 9.9 1.0
OE2 B:GLU461 3.8 16.3 1.0
OD1 B:ASN102 4.0 13.7 1.0
CB B:GLU461 4.1 9.6 1.0
CG B:GLU461 4.1 10.7 1.0
C2 B:GAL2001 4.2 20.6 1.0
O4 B:GAL2001 4.2 13.2 1.0
CB B:ASP201 4.2 9.7 1.0
N B:ASP201 4.3 8.9 1.0
O B:ASP199 4.3 11.1 1.0
O3 B:GAL2001 4.3 11.7 1.0
NE2 B:HIS418 4.3 11.9 1.0
CG B:GLU416 4.4 8.0 1.0
ND2 B:ASN460 4.4 11.1 1.0
CD2 B:HIS418 4.5 15.1 1.0
O2 B:GAL2001 4.6 13.4 1.0
O B:ASN102 4.7 12.7 1.0
C3 B:GAL2001 4.7 31.6 1.0
CA B:ASP201 4.9 10.4 1.0
CA B:GLN200 4.9 8.4 1.0
C B:GLN200 4.9 13.0 1.0

Magnesium binding site 6 out of 15 in 1jz7

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


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

b:14.0
occ:1.00
 O B:ASN18 2.3 14.4 1.0
OD2 B:ASP193 2.3 11.6 1.0
O B:VAL21 2.3 13.4 1.0
O B:ASP15 2.3 14.3 1.0
OE1 B:GLN163 2.3 13.3 1.0
OD1 B:ASP193 3.0 13.3 1.0
CG B:ASP193 3.0 13.1 1.0
CD B:GLN163 3.2 12.9 1.0
C B:ASN18 3.2 13.5 1.0
NE2 B:GLN163 3.5 12.8 1.0
C B:VAL21 3.5 16.4 1.0
C B:ASP15 3.5 15.2 1.0
N B:ASN18 3.7 17.5 1.0
CA B:ASN18 4.0 14.3 1.0
OH B:TYR161 4.0 12.8 1.0
CA B:TRP16 4.0 11.3 1.0
N B:PRO19 4.1 13.2 1.0
CA B:VAL21 4.2 13.3 1.0
N B:TRP16 4.3 13.2 1.0
N B:VAL21 4.3 12.8 1.0
CB B:ASN18 4.3 11.4 1.0
C B:TRP16 4.3 11.9 1.0
CE2 B:TYR161 4.3 11.2 1.0
CA B:PRO19 4.3 17.1 1.0
CB B:VAL21 4.4 12.5 1.0
N B:GLU17 4.4 15.0 1.0
N B:THR22 4.4 11.1 1.0
CB B:ASP193 4.5 9.6 1.0
CA B:THR22 4.5 12.7 1.0
CG B:GLN163 4.5 9.6 1.0
CZ B:TYR161 4.6 11.8 1.0
CA B:ASP15 4.7 15.2 1.0
C B:PRO19 4.8 17.1 1.0
O B:TRP16 4.9 12.7 1.0
C B:GLU17 4.9 19.7 1.0
CG1 B:VAL21 4.9 17.2 1.0

Magnesium binding site 7 out of 15 in 1jz7

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


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

b:21.2
occ:0.50
 O B:HOH9095 1.9 58.5 1.0
O B:HOH9207 2.0 25.5 0.5
O B:ASN597 2.0 14.8 1.0
O B:HOH9595 2.2 56.5 1.0
O B:HOH9052 2.2 23.1 1.0
O B:HOH8835 2.3 22.6 1.0
C B:ASN597 3.2 13.9 1.0
N B:ASN597 3.6 13.2 1.0
OD1 B:ASN597 4.0 14.7 1.0
CA B:ASN597 4.0 12.6 1.0
N B:ASP598 4.2 13.2 1.0
CG B:ASN597 4.3 18.9 1.0
OE1 B:GLU797 4.3 51.9 1.0
CA B:ASP598 4.4 11.7 1.0
OD1 B:ASP598 4.4 22.9 1.0
O B:HOH9394 4.5 36.9 1.0
ND2 B:ASN597 4.5 18.1 1.0
CD B:GLU797 4.7 51.9 1.0
OE2 B:GLU797 4.7 41.2 1.0
C B:PRO596 4.8 16.1 1.0
CB B:ASN597 4.8 12.1 1.0
O B:HOH9361 4.9 54.3 1.0
O B:HOH9469 5.0 41.2 1.0
CA B:PRO596 5.0 18.0 1.0
N B:ARG599 5.0 11.8 1.0

Magnesium binding site 8 out of 15 in 1jz7

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


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

b:10.8
occ:1.00
 OE2 C:GLU416 2.0 10.8 1.0
O C:HOH8784 2.0 9.9 1.0
OE1 C:GLU461 2.0 11.0 1.0
O C:HOH8708 2.1 9.9 1.0
O C:HOH8644 2.2 11.2 1.0
ND1 C:HIS418 2.2 11.7 1.0
CD C:GLU461 3.1 11.1 1.0
CE1 C:HIS418 3.1 13.7 1.0
CD C:GLU416 3.2 9.8 1.0
CG C:HIS418 3.3 9.3 1.0
OE1 C:GLU416 3.6 9.8 1.0
CB C:HIS418 3.6 10.0 1.0
OE2 C:GLU461 3.8 15.3 1.0
OD1 C:ASN102 4.0 14.8 1.0
CB C:GLU461 4.1 7.8 1.0
CG C:GLU461 4.1 8.4 1.0
N C:ASP201 4.2 9.4 1.0
O4 C:GAL2001 4.3 14.5 1.0
O C:ASP199 4.3 10.9 1.0
C2 C:GAL2001 4.3 17.0 1.0
CB C:ASP201 4.3 12.2 1.0
ND2 C:ASN460 4.3 11.2 1.0
NE2 C:HIS418 4.3 11.9 1.0
O3 C:GAL2001 4.4 11.9 1.0
CG C:GLU416 4.4 8.1 1.0
CD2 C:HIS418 4.4 12.0 1.0
O2 C:GAL2001 4.5 13.9 1.0
O C:ASN102 4.7 13.5 1.0
CA C:ASP201 4.8 13.0 1.0
C3 C:GAL2001 4.9 22.5 1.0
CA C:GLN200 4.9 9.5 1.0
C C:GLN200 4.9 13.6 1.0

Magnesium binding site 9 out of 15 in 1jz7

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


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

b:13.4
occ:1.00
 O C:VAL21 2.2 14.2 1.0
O C:ASN18 2.3 12.6 1.0
O C:ASP15 2.3 13.4 1.0
OD2 C:ASP193 2.4 13.1 1.0
OE1 C:GLN163 2.4 13.3 1.0
OD1 C:ASP193 3.1 13.4 1.0
CG C:ASP193 3.1 15.2 1.0
C C:ASN18 3.2 14.8 1.0
CD C:GLN163 3.3 12.3 1.0
C C:VAL21 3.3 13.3 1.0
C C:ASP15 3.5 13.7 1.0
NE2 C:GLN163 3.6 10.0 1.0
N C:ASN18 3.8 17.2 1.0
OH C:TYR161 4.0 13.6 1.0
CA C:ASN18 4.0 12.1 1.0
CA C:TRP16 4.1 11.0 1.0
N C:PRO19 4.1 15.2 1.0
CA C:VAL21 4.2 11.5 1.0
N C:TRP16 4.2 11.1 1.0
CB C:ASN18 4.2 13.2 1.0
N C:VAL21 4.2 11.6 1.0
CB C:VAL21 4.3 14.2 1.0
CA C:PRO19 4.3 15.2 1.0
C C:TRP16 4.3 15.0 1.0
N C:THR22 4.4 10.7 1.0
CE2 C:TYR161 4.4 11.2 1.0
CA C:THR22 4.5 10.7 1.0
N C:GLU17 4.5 13.1 1.0
CG C:GLN163 4.5 11.1 1.0
CB C:ASP193 4.5 9.8 1.0
CA C:ASP15 4.6 14.8 1.0
CZ C:TYR161 4.7 14.8 1.0
C C:PRO19 4.8 14.6 1.0
CG1 C:VAL21 4.9 16.0 1.0
O C:TRP16 4.9 16.2 1.0
C C:GLU17 4.9 24.6 1.0

Magnesium binding site 10 out of 15 in 1jz7

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


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 in Complex with Galactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3006

b:23.6
occ:1.00
 O C:HOH9506 1.9 27.9 1.0
O C:HOH9479 2.0 29.8 1.0
O C:HOH9449 2.1 19.5 1.0
CD C:ARG178 4.0 52.8 1.0
O C:HOH9497 4.1 42.8 1.0
O C:ALA179 4.2 19.4 1.0
O C:GLU181 4.2 17.6 1.0
O C:HOH9406 4.3 24.6 1.0
CG C:ARG178 4.4 42.7 1.0
N C:GLU181 4.6 16.1 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 07:00:28 2024

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