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Magnesium in PDB 1jz5: E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on, PDB code: 1jz5 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) 17.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.690, 168.020, 201.040, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 23.1

Other elements in 1jz5:

The structure of E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on (pdb code 1jz5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 11 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on, PDB code: 1jz5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 11 in 1jz5

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Magnesium binding site 1 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:23.3
occ:1.00
 O A:HOH8678 2.1 15.5 1.0
OE2 A:GLU416 2.1 19.7 1.0
ND1 A:HIS418 2.1 17.9 1.0
O A:HOH8754 2.1 17.9 1.0
OE1 A:GLU461 2.2 19.8 1.0
O A:HOH8614 2.2 19.2 1.0
CE1 A:HIS418 3.0 18.9 1.0
CD A:GLU416 3.2 21.9 1.0
CG A:HIS418 3.2 19.3 1.0
CD A:GLU461 3.3 25.0 1.0
OE1 A:GLU416 3.6 19.9 1.0
CB A:HIS418 3.6 12.5 1.0
OD1 A:ASN102 4.0 22.4 1.0
CB A:GLU461 4.0 13.2 1.0
OE2 A:GLU461 4.1 24.0 1.0
CB A:ASP201 4.2 22.2 1.0
C2 A:1492001 4.2 26.2 1.0
CG A:GLU461 4.2 15.3 1.0
NE2 A:HIS418 4.3 19.0 1.0
O4 A:1492001 4.3 16.4 1.0
N A:ASP201 4.3 21.2 1.0
O A:ASP199 4.4 20.5 1.0
CD2 A:HIS418 4.4 18.8 1.0
O3 A:1492001 4.4 20.2 1.0
ND2 A:ASN460 4.4 17.0 1.0
CG A:GLU416 4.4 12.2 1.0
O A:ASN102 4.6 23.8 1.0
O2 A:1492001 4.6 19.5 1.0
CA A:ASP201 4.8 22.7 1.0
CG2 A:VAL103 4.9 24.2 1.0
C A:GLN200 4.9 19.7 1.0
CA A:GLN200 4.9 13.7 1.0
C3 A:1492001 4.9 23.1 1.0

Magnesium binding site 2 out of 11 in 1jz5

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Magnesium binding site 2 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:22.6
occ:1.00
 O A:ASN18 2.2 23.0 1.0
O A:ASP15 2.2 26.7 1.0
OE1 A:GLN163 2.2 21.9 1.0
OD2 A:ASP193 2.3 23.5 1.0
O A:VAL21 2.4 24.5 1.0
CG A:ASP193 3.0 24.0 1.0
OD1 A:ASP193 3.0 28.1 1.0
C A:ASN18 3.1 25.6 1.0
CD A:GLN163 3.2 24.5 1.0
C A:ASP15 3.4 29.6 1.0
C A:VAL21 3.5 30.3 1.0
NE2 A:GLN163 3.5 19.6 1.0
N A:ASN18 3.5 28.9 1.0
CA A:ASN18 3.9 26.6 1.0
OH A:TYR161 4.0 20.9 1.0
CA A:TRP16 4.0 18.1 1.0
N A:PRO19 4.0 23.1 1.0
N A:TRP16 4.1 21.5 1.0
CB A:ASN18 4.2 20.6 1.0
CA A:VAL21 4.2 20.2 1.0
C A:TRP16 4.2 22.8 1.0
N A:VAL21 4.3 22.5 1.0
CB A:VAL21 4.3 24.1 1.0
CA A:PRO19 4.3 18.9 1.0
CE2 A:TYR161 4.3 26.2 1.0
N A:GLU17 4.4 19.1 1.0
CB A:ASP193 4.4 18.1 1.0
N A:THR22 4.5 18.6 1.0
CG A:GLN163 4.5 18.9 1.0
CA A:ASP15 4.5 26.0 1.0
CA A:THR22 4.6 16.7 1.0
CZ A:TYR161 4.7 23.9 1.0
C A:GLU17 4.7 26.6 1.0
O A:TRP16 4.8 25.1 1.0
C A:PRO19 4.8 26.1 1.0
CG1 A:VAL21 4.9 21.6 1.0
CB A:ASP15 5.0 22.4 1.0

Magnesium binding site 3 out of 11 in 1jz5

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Magnesium binding site 3 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:45.5
occ:1.00
 O A:HOH9434 1.8 40.7 1.0
O A:HOH9204 2.1 28.8 1.0
O A:HOH9362 2.2 36.0 1.0
O A:HOH9357 3.5 45.4 1.0
C1 A:DMS8406 3.9 37.2 1.0
O A:DMS8406 4.0 62.7 1.0
O A:HOH9466 4.3 33.8 1.0
O A:HOH9519 4.3 48.0 1.0
OE2 A:GLU314 4.3 20.2 1.0
OE1 A:GLU314 4.4 23.1 1.0
O A:HOH9249 4.5 35.6 1.0
S A:DMS8406 4.5 56.1 1.0
O A:HOH9531 4.7 39.7 1.0
CD A:GLU314 4.8 30.2 1.0
O A:HOH9226 4.8 46.9 1.0

Magnesium binding site 4 out of 11 in 1jz5

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Magnesium binding site 4 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:18.4
occ:1.00
 OE2 B:GLU416 2.0 18.7 1.0
OE1 B:GLU461 2.1 21.1 1.0
O B:HOH8691 2.1 16.1 1.0
O B:HOH8627 2.1 14.4 1.0
O B:HOH8768 2.1 21.8 1.0
ND1 B:HIS418 2.2 16.3 1.0
CD B:GLU461 3.2 17.7 1.0
CD B:GLU416 3.2 20.5 1.0
CE1 B:HIS418 3.2 17.5 1.0
CG B:HIS418 3.3 22.0 1.0
OE1 B:GLU416 3.5 16.0 1.0
CB B:HIS418 3.7 16.9 1.0
OD1 B:ASN102 4.0 20.9 1.0
OE2 B:GLU461 4.1 20.5 1.0
CG B:GLU461 4.1 11.0 1.0
CB B:GLU461 4.1 13.0 1.0
C2 B:1492001 4.2 16.7 1.0
N B:ASP201 4.2 17.4 1.0
CB B:ASP201 4.2 17.0 1.0
O4 B:1492001 4.3 18.6 1.0
O B:ASP199 4.3 17.9 1.0
O3 B:1492001 4.3 19.0 1.0
ND2 B:ASN460 4.4 14.7 1.0
NE2 B:HIS418 4.4 15.4 1.0
CG B:GLU416 4.4 12.2 1.0
CD2 B:HIS418 4.5 19.4 1.0
O2 B:1492001 4.7 17.2 1.0
O B:ASN102 4.7 19.4 1.0
CA B:ASP201 4.8 15.4 1.0
C3 B:1492001 4.9 23.6 1.0
CA B:GLN200 4.9 14.6 1.0
C B:GLN200 5.0 20.8 1.0

Magnesium binding site 5 out of 11 in 1jz5

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Magnesium binding site 5 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:22.0
occ:1.00
 OD2 B:ASP193 2.3 18.1 1.0
O B:ASN18 2.3 20.9 1.0
O B:ASP15 2.3 23.7 1.0
OE1 B:GLN163 2.3 25.9 1.0
O B:VAL21 2.3 21.2 1.0
OD1 B:ASP193 3.0 22.8 1.0
CG B:ASP193 3.0 19.2 1.0
C B:ASN18 3.2 20.8 1.0
CD B:GLN163 3.2 18.5 1.0
NE2 B:GLN163 3.5 18.0 1.0
C B:VAL21 3.5 20.1 1.0
C B:ASP15 3.5 28.8 1.0
N B:ASN18 3.6 26.8 1.0
CA B:ASN18 3.9 19.8 1.0
CA B:TRP16 4.0 15.9 1.0
OH B:TYR161 4.0 25.1 1.0
N B:PRO19 4.1 22.5 1.0
N B:TRP16 4.2 19.3 1.0
C B:TRP16 4.2 21.0 1.0
CB B:ASN18 4.2 20.2 1.0
CA B:VAL21 4.2 24.9 1.0
N B:GLU17 4.3 21.6 1.0
N B:VAL21 4.4 22.0 1.0
CB B:VAL21 4.4 24.1 1.0
CA B:PRO19 4.4 27.1 1.0
CE2 B:TYR161 4.5 18.2 1.0
CB B:ASP193 4.5 12.4 1.0
N B:THR22 4.5 17.5 1.0
CG B:GLN163 4.5 16.1 1.0
CA B:ASP15 4.6 28.2 1.0
CA B:THR22 4.7 17.8 1.0
CZ B:TYR161 4.7 28.3 1.0
C B:GLU17 4.8 28.1 1.0
O B:TRP16 4.8 21.4 1.0
C B:PRO19 4.9 24.4 1.0
CG1 B:VAL21 5.0 23.2 1.0

Magnesium binding site 6 out of 11 in 1jz5

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Magnesium binding site 6 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:53.6
occ:1.00
 O B:HOH8877 2.2 30.9 1.0
O B:HOH9198 2.3 36.8 1.0
O B:HOH9251 2.6 34.7 1.0
O B:HOH8984 3.3 48.0 1.0
OE1 B:GLN718 3.3 72.4 1.0
O B:THR911 3.5 21.8 1.0
O B:HOH8893 3.8 29.5 1.0
O B:HOH9486 4.0 30.4 1.0
NE2 B:HIS622 4.0 20.5 1.0
O B:HOH8867 4.0 30.9 1.0
CD B:GLN718 4.1 35.7 1.0
NE2 B:GLN718 4.2 27.6 1.0
C B:THR911 4.3 18.5 1.0
CA B:THR911 4.3 15.4 1.0
CB B:THR911 4.4 20.1 1.0
O B:HOH8854 4.5 37.3 1.0
O B:HOH8693 4.5 27.9 1.0
CG2 B:THR911 4.9 21.4 1.0
CD2 B:HIS622 4.9 19.8 1.0
CE1 B:HIS622 4.9 21.6 1.0

Magnesium binding site 7 out of 11 in 1jz5

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Magnesium binding site 7 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:18.6
occ:1.00
 OE2 C:GLU416 2.0 17.9 1.0
O C:HOH8779 2.1 18.5 1.0
OE1 C:GLU461 2.2 17.3 1.0
O C:HOH8638 2.2 16.5 1.0
O C:HOH8702 2.2 15.1 1.0
ND1 C:HIS418 2.2 22.6 1.0
CD C:GLU416 3.2 22.4 1.0
CE1 C:HIS418 3.2 23.2 1.0
CD C:GLU461 3.2 22.2 1.0
CG C:HIS418 3.3 18.3 1.0
OE1 C:GLU416 3.5 14.8 1.0
CB C:HIS418 3.6 16.5 1.0
CB C:GLU461 4.1 11.0 1.0
OE2 C:GLU461 4.1 20.4 1.0
CG C:GLU461 4.2 16.4 1.0
N C:ASP201 4.2 21.2 1.0
OD1 C:ASN102 4.2 20.9 1.0
O C:ASP199 4.2 17.0 1.0
O4 C:1492001 4.2 21.1 1.0
CB C:ASP201 4.3 21.6 1.0
C2 C:1492001 4.3 18.2 1.0
ND2 C:ASN460 4.3 15.7 1.0
NE2 C:HIS418 4.4 17.6 1.0
CG C:GLU416 4.4 14.5 1.0
O3 C:1492001 4.4 18.3 1.0
CD2 C:HIS418 4.5 18.0 1.0
O2 C:1492001 4.6 20.1 1.0
O C:ASN102 4.6 19.6 1.0
CA C:ASP201 4.8 18.5 1.0
CG2 C:VAL103 4.8 22.9 1.0
C C:GLN200 4.9 20.9 1.0
CA C:GLN200 5.0 14.4 1.0
C3 C:1492001 5.0 26.4 1.0

Magnesium binding site 8 out of 11 in 1jz5

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Magnesium binding site 8 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:18.8
occ:1.00
 O C:VAL21 2.2 16.2 1.0
O C:ASN18 2.3 24.5 1.0
O C:ASP15 2.3 16.7 1.0
OD2 C:ASP193 2.4 19.8 1.0
OE1 C:GLN163 2.5 18.5 1.0
OD1 C:ASP193 3.1 20.7 1.0
CG C:ASP193 3.1 21.2 1.0
C C:ASN18 3.2 29.4 1.0
CD C:GLN163 3.4 29.0 1.0
C C:VAL21 3.4 21.9 1.0
C C:ASP15 3.5 22.6 1.0
N C:ASN18 3.6 24.2 1.0
NE2 C:GLN163 3.7 17.2 1.0
CA C:ASN18 3.9 18.3 1.0
OH C:TYR161 4.0 22.0 1.0
CA C:TRP16 4.1 23.6 1.0
N C:PRO19 4.1 26.0 1.0
CA C:VAL21 4.1 24.0 1.0
N C:TRP16 4.2 19.5 1.0
CB C:VAL21 4.3 23.9 1.0
CB C:ASN18 4.3 16.2 1.0
C C:TRP16 4.3 24.1 1.0
N C:VAL21 4.3 25.1 1.0
N C:THR22 4.4 13.0 1.0
CA C:PRO19 4.4 26.4 1.0
CE2 C:TYR161 4.4 15.3 1.0
N C:GLU17 4.4 22.7 1.0
CA C:THR22 4.5 19.1 1.0
CB C:ASP193 4.5 15.4 1.0
CA C:ASP15 4.6 17.1 1.0
CG C:GLN163 4.6 20.1 1.0
CZ C:TYR161 4.7 22.0 1.0
CG1 C:VAL21 4.8 23.6 1.0
O C:TRP16 4.8 20.0 1.0
C C:GLU17 4.9 31.5 1.0
C C:PRO19 4.9 24.5 1.0

Magnesium binding site 9 out of 11 in 1jz5

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Magnesium binding site 9 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:23.1
occ:1.00
 O D:HOH8824 2.0 16.9 1.0
OE1 D:GLU461 2.1 18.0 1.0
ND1 D:HIS418 2.2 16.5 1.0
O D:HOH8760 2.2 14.1 1.0
OE2 D:GLU416 2.3 23.3 1.0
O D:HOH8900 2.3 21.7 1.0
CE1 D:HIS418 3.0 21.3 1.0
CD D:GLU461 3.2 21.6 1.0
CG D:HIS418 3.3 16.3 1.0
CD D:GLU416 3.4 22.1 1.0
OE1 D:GLU416 3.7 18.3 1.0
CB D:HIS418 3.8 14.8 1.0
O4 D:1492001 4.0 19.3 1.0
OE2 D:GLU461 4.1 20.5 1.0
CB D:ASP201 4.1 18.9 1.0
C2 D:1492001 4.1 12.6 1.0
CG D:GLU461 4.1 16.3 1.0
CB D:GLU461 4.1 14.9 1.0
OD1 D:ASN102 4.2 25.8 1.0
NE2 D:HIS418 4.2 18.8 1.0
N D:ASP201 4.3 20.4 1.0
ND2 D:ASN460 4.3 17.2 1.0
O3 D:1492001 4.4 21.0 1.0
CD2 D:HIS418 4.4 19.0 1.0
O D:ASP199 4.4 18.6 1.0
O2 D:1492001 4.6 15.8 1.0
CG D:GLU416 4.6 12.1 1.0
CA D:ASP201 4.8 17.5 1.0
O D:ASN102 4.8 22.7 1.0
CG2 D:VAL103 4.8 18.6 1.0
C3 D:1492001 4.8 14.2 1.0
C1 D:1492001 4.9 25.1 1.0

Magnesium binding site 10 out of 11 in 1jz5

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Magnesium binding site 10 out of 11 in the E. Coli (Lacz) Beta-Galactosidase in Complex with D-Galctopyranosyl-1- on


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 D-Galctopyranosyl-1- on within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:20.7
occ:1.00
 O D:VAL21 2.2 23.5 1.0
OE1 D:GLN163 2.2 21.5 1.0
O D:ASN18 2.3 22.7 1.0
O D:ASP15 2.3 25.9 1.0
OD2 D:ASP193 2.5 26.4 1.0
OD1 D:ASP193 3.0 21.7 1.0
CG D:ASP193 3.1 25.8 1.0
CD D:GLN163 3.2 17.6 1.0
C D:ASN18 3.3 25.2 1.0
C D:VAL21 3.4 24.3 1.0
C D:ASP15 3.5 22.6 1.0
NE2 D:GLN163 3.5 20.2 1.0
N D:ASN18 3.7 20.4 1.0
CA D:ASN18 4.0 21.4 1.0
OH D:TYR161 4.0 23.8 1.0
CA D:TRP16 4.1 22.2 1.0
CB D:ASN18 4.2 25.6 1.0
CA D:VAL21 4.2 20.1 1.0
N D:PRO19 4.2 20.2 1.0
N D:VAL21 4.2 24.9 1.0
N D:TRP16 4.2 18.6 1.0
CB D:VAL21 4.3 26.2 1.0
C D:TRP16 4.3 26.5 1.0
N D:THR22 4.4 20.3 1.0
CE2 D:TYR161 4.4 20.1 1.0
CA D:PRO19 4.4 21.8 1.0
CG D:GLN163 4.4 17.1 1.0
CA D:THR22 4.5 17.3 1.0
N D:GLU17 4.5 19.7 1.0
CB D:ASP193 4.6 25.5 1.0
CA D:ASP15 4.6 19.8 1.0
CZ D:TYR161 4.7 15.9 1.0
CG1 D:VAL21 4.7 21.6 1.0
C D:PRO19 4.8 28.8 1.0
O D:TRP16 4.9 23.0 1.0
C D:GLU17 4.9 31.1 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 06:59:26 2024

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