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Magnesium in PDB 3czj: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One, PDB code: 3czj was solved by R.E.Huber, M.L.Dugdale, M.E.Fraser, S.D.Tammam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.05 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.443, 161.643, 202.155, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.1

Other elements in 3czj:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One (pdb code 3czj). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One, PDB code: 3czj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3czj

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:19.7
occ:1.00
 OE1 A:GLU461 2.0 20.9 1.0
OE2 A:GLU416 2.1 10.6 1.0
O A:HOH8719 2.2 7.0 1.0
O A:HOH8770 2.2 11.5 1.0
O A:HOH9255 2.2 14.5 1.0
ND1 A:HIS418 2.4 11.1 1.0
CD A:GLU461 3.0 23.8 1.0
CD A:GLU416 3.3 12.7 1.0
CE1 A:HIS418 3.3 14.4 1.0
CG A:HIS418 3.4 12.3 1.0
CB A:HIS418 3.6 8.5 1.0
OE2 A:GLU461 3.6 28.5 1.0
OE1 A:GLU416 3.8 14.1 1.0
ND2 A:ASN102 4.0 11.9 1.0
CG A:GLU461 4.1 21.0 1.0
C2 A:1492001 4.1 18.6 1.0
CB A:GLU461 4.2 16.0 1.0
CB A:ASP201 4.2 13.2 1.0
O A:ASP199 4.2 14.7 1.0
O4 A:1492001 4.2 16.5 1.0
N A:ASP201 4.3 14.4 1.0
NE2 A:HIS418 4.5 14.5 1.0
CG A:GLU416 4.5 10.4 1.0
CD2 A:HIS418 4.5 11.0 1.0
O3 A:1492001 4.5 16.1 1.0
O2 A:1492001 4.6 22.0 1.0
O A:ASN102 4.8 13.8 1.0
CA A:ASP201 4.8 13.3 1.0
CG2 A:VAL103 4.9 14.3 1.0
C3 A:1492001 4.9 17.4 1.0
C A:GLN200 5.0 15.7 1.0

Magnesium binding site 2 out of 9 in 3czj

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:19.8
occ:1.00
 O A:ASN18 2.2 19.0 1.0
O A:VAL21 2.3 20.7 1.0
O A:ASP15 2.3 22.8 1.0
OE1 A:GLN163 2.3 19.7 1.0
OD2 A:ASP193 2.3 10.8 1.0
OD1 A:ASP193 2.9 15.6 1.0
CG A:ASP193 3.0 15.4 1.0
C A:ASN18 3.2 20.0 1.0
CD A:GLN163 3.2 17.6 1.0
C A:VAL21 3.4 20.8 1.0
C A:ASP15 3.5 22.2 1.0
NE2 A:GLN163 3.5 15.2 1.0
N A:ASN18 3.6 21.1 1.0
CA A:ASN18 3.9 20.6 1.0
OH A:TYR161 4.0 13.9 1.0
CA A:TRP16 4.1 20.6 1.0
N A:PRO19 4.1 20.7 1.0
CA A:VAL21 4.1 21.3 1.0
CB A:VAL21 4.1 21.8 1.0
N A:VAL21 4.2 21.6 1.0
CB A:ASN18 4.2 19.4 1.0
C A:TRP16 4.3 20.6 1.0
N A:TRP16 4.3 21.6 1.0
CE2 A:TYR161 4.4 14.6 1.0
CA A:PRO19 4.4 21.4 1.0
N A:THR22 4.4 19.4 1.0
N A:GLU17 4.4 20.4 1.0
CB A:ASP193 4.4 14.7 1.0
CG A:GLN163 4.5 15.8 1.0
CA A:ASP15 4.6 23.2 1.0
CA A:THR22 4.6 19.4 1.0
CZ A:TYR161 4.7 14.4 1.0
CG1 A:VAL21 4.7 18.7 1.0
O A:TRP16 4.8 20.3 1.0
C A:PRO19 4.8 22.1 1.0
C A:GLU17 4.8 21.2 1.0

Magnesium binding site 3 out of 9 in 3czj

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:13.2
occ:1.00
 OE2 B:GLU461 2.0 16.0 1.0
OE2 B:GLU416 2.0 7.8 1.0
O B:HOH9284 2.2 12.6 1.0
O B:HOH9224 2.2 6.6 1.0
O B:HOH9356 2.3 7.0 1.0
ND1 B:HIS418 2.3 7.6 1.0
CD B:GLU461 2.9 17.3 1.0
CD B:GLU416 3.1 8.8 1.0
CE1 B:HIS418 3.2 11.9 1.0
CG B:HIS418 3.3 8.0 1.0
OE1 B:GLU461 3.5 21.4 1.0
OE1 B:GLU416 3.6 11.7 1.0
CB B:HIS418 3.7 8.1 1.0
CG B:GLU461 4.0 13.0 1.0
CB B:GLU461 4.0 8.4 1.0
C2 B:1492001 4.1 17.9 1.0
ND2 B:ASN102 4.3 10.1 1.0
O4 B:1492001 4.3 15.9 1.0
O B:ASP199 4.3 10.2 1.0
NE2 B:HIS418 4.3 10.4 1.0
CB B:ASP201 4.3 9.6 1.0
CG B:GLU416 4.3 9.9 1.0
N B:ASP201 4.3 10.1 1.0
CD2 B:HIS418 4.4 8.0 1.0
O3 B:1492001 4.5 15.3 1.0
O2 B:1492001 4.6 17.4 1.0
C3 B:1492001 4.8 17.7 1.0
O B:ASN102 4.8 10.8 1.0
CA B:ASP201 4.9 10.7 1.0

Magnesium binding site 4 out of 9 in 3czj

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:22.2
occ:1.00
 O B:ASP15 2.2 14.3 1.0
O B:VAL21 2.3 16.6 1.0
O B:ASN18 2.3 17.0 1.0
OD2 B:ASP193 2.4 16.9 1.0
OE1 B:GLN163 2.5 16.5 1.0
OD1 B:ASP193 3.1 17.3 1.0
CG B:ASP193 3.1 16.1 1.0
C B:ASN18 3.2 17.6 1.0
CD B:GLN163 3.3 16.5 1.0
C B:VAL21 3.4 17.7 1.0
C B:ASP15 3.4 15.4 1.0
NE2 B:GLN163 3.6 16.8 1.0
N B:ASN18 3.6 18.1 1.0
CA B:ASN18 3.9 17.6 1.0
CA B:TRP16 4.0 16.1 1.0
OH B:TYR161 4.0 15.1 1.0
N B:PRO19 4.1 18.0 1.0
CA B:VAL21 4.1 17.5 1.0
N B:TRP16 4.2 14.6 1.0
CB B:VAL21 4.2 19.0 1.0
N B:VAL21 4.2 19.3 1.0
C B:TRP16 4.2 17.9 1.0
CB B:ASN18 4.2 18.1 1.0
N B:GLU17 4.3 18.7 1.0
CE2 B:TYR161 4.3 14.9 1.0
CA B:PRO19 4.4 19.2 1.0
N B:THR22 4.4 15.5 1.0
CB B:ASP193 4.5 15.0 1.0
CA B:ASP15 4.6 16.7 1.0
CG B:GLN163 4.6 17.0 1.0
CA B:THR22 4.6 16.1 1.0
CZ B:TYR161 4.6 14.0 1.0
C B:PRO19 4.8 19.5 1.0
C B:GLU17 4.8 19.2 1.0
CG1 B:VAL21 4.8 17.7 1.0
O B:TRP16 4.9 18.0 1.0
CB B:ASP15 5.0 16.9 1.0

Magnesium binding site 5 out of 9 in 3czj

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:36.3
occ:1.00
 O B:HOH9806 2.2 26.9 1.0
O B:HOH9735 2.2 15.7 1.0
O B:HOH9825 2.3 38.6 1.0
O B:HOH9851 2.3 15.8 1.0
O B:HOH9826 2.3 19.7 1.0
O B:HOH9827 2.4 35.5 1.0
OE1 B:GLU369 3.8 17.9 1.0
O B:HOH9824 4.0 60.5 1.0
OE2 B:GLU369 4.2 18.9 1.0
O B:HOH9805 4.3 32.1 1.0
O B:HOH9849 4.3 23.0 1.0
O B:HOH9832 4.3 44.7 1.0
O B:HOH9828 4.4 25.2 1.0
CD B:GLU369 4.4 17.8 1.0
O B:HOH9831 4.9 50.7 1.0
O B:HOH9633 5.0 26.4 1.0

Magnesium binding site 6 out of 9 in 3czj

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:14.5
occ:1.00
 OE2 C:GLU461 1.9 15.4 1.0
OE2 C:GLU416 2.1 8.7 1.0
O C:HOH8666 2.2 7.6 1.0
O C:HOH8592 2.2 9.3 1.0
O C:HOH8532 2.2 4.5 1.0
ND1 C:HIS418 2.3 5.6 1.0
CD C:GLU461 3.0 19.3 1.0
CD C:GLU416 3.1 10.2 1.0
CE1 C:HIS418 3.2 10.4 1.0
CG C:HIS418 3.3 9.8 1.0
CB C:HIS418 3.6 6.8 1.0
OE1 C:GLU416 3.6 10.1 1.0
OE1 C:GLU461 3.7 25.1 1.0
CG C:GLU461 4.0 15.6 1.0
ND2 C:ASN102 4.1 6.5 1.0
CB C:GLU461 4.2 9.3 1.0
O C:ASP199 4.2 9.3 1.0
N C:ASP201 4.2 11.2 1.0
CB C:ASP201 4.2 10.3 1.0
C2 C:1492001 4.3 14.9 1.0
NE2 C:HIS418 4.3 9.4 1.0
CG C:GLU416 4.4 8.6 1.0
CD2 C:HIS418 4.4 7.7 1.0
O4 C:1492001 4.4 11.4 1.0
O3 C:1492001 4.6 11.0 1.0
O C:ASN102 4.6 10.0 1.0
O2 C:1492001 4.7 16.1 1.0
CA C:ASP201 4.8 10.8 1.0
CA C:GLN200 4.9 11.1 1.0
C C:GLN200 4.9 10.1 1.0
C3 C:1492001 5.0 14.6 1.0

Magnesium binding site 7 out of 9 in 3czj

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:10.9
occ:1.00
 O C:VAL21 2.2 11.6 1.0
O C:ASP15 2.3 13.8 1.0
O C:ASN18 2.3 17.4 1.0
OD2 C:ASP193 2.3 13.3 1.0
OE1 C:GLN163 2.4 11.7 1.0
OD1 C:ASP193 3.0 13.2 1.0
CG C:ASP193 3.0 14.7 1.0
CD C:GLN163 3.2 12.3 1.0
C C:ASN18 3.3 16.3 1.0
C C:VAL21 3.4 13.8 1.0
C C:ASP15 3.5 15.2 1.0
NE2 C:GLN163 3.5 12.9 1.0
N C:ASN18 3.7 17.6 1.0
CA C:ASN18 4.0 18.0 1.0
OH C:TYR161 4.0 13.1 1.0
CA C:TRP16 4.0 14.0 1.0
CA C:VAL21 4.1 13.5 1.0
CB C:VAL21 4.1 14.5 1.0
N C:PRO19 4.2 17.2 1.0
N C:TRP16 4.2 14.3 1.0
N C:VAL21 4.2 16.2 1.0
C C:TRP16 4.3 14.7 1.0
CB C:ASN18 4.3 17.2 1.0
CE2 C:TYR161 4.3 10.8 1.0
N C:THR22 4.4 13.6 1.0
CA C:PRO19 4.4 18.0 1.0
N C:GLU17 4.4 14.0 1.0
CB C:ASP193 4.5 13.0 1.0
CG C:GLN163 4.5 13.3 1.0
CA C:THR22 4.5 13.9 1.0
CA C:ASP15 4.6 15.9 1.0
CG1 C:VAL21 4.6 13.3 1.0
CZ C:TYR161 4.6 10.5 1.0
C C:PRO19 4.8 18.4 1.0
O C:TRP16 4.8 13.0 1.0
C C:GLU17 4.9 16.6 1.0
CB C:ASP15 4.9 13.5 1.0

Magnesium binding site 8 out of 9 in 3czj

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:15.6
occ:1.00
 OE2 D:GLU461 1.9 22.3 1.0
OE2 D:GLU416 2.0 10.5 1.0
O D:HOH8876 2.1 9.8 1.0
O D:HOH8806 2.2 11.9 1.0
ND1 D:HIS418 2.3 10.6 1.0
O D:HOH8748 2.4 15.1 1.0
CD D:GLU461 2.9 22.6 1.0
CD D:GLU416 3.2 11.3 1.0
CE1 D:HIS418 3.2 12.7 1.0
CG D:HIS418 3.2 12.0 1.0
OE1 D:GLU461 3.5 29.2 1.0
CB D:HIS418 3.5 10.6 1.0
OE1 D:GLU416 3.7 10.3 1.0
CG D:GLU461 4.0 19.6 1.0
CB D:GLU461 4.2 13.5 1.0
C2 D:1492001 4.2 19.7 1.0
ND2 D:ASN102 4.2 15.8 1.0
O D:ASP199 4.2 15.1 1.0
NE2 D:HIS418 4.3 13.7 1.0
CB D:ASP201 4.4 12.0 1.0
CD2 D:HIS418 4.4 11.6 1.0
O4 D:1492001 4.4 18.0 1.0
CG D:GLU416 4.4 11.2 1.0
N D:ASP201 4.4 11.9 1.0
O2 D:1492001 4.6 23.0 1.0
O3 D:1492001 4.6 14.7 1.0
O D:ASN102 4.7 16.9 1.0
CA D:ASP201 5.0 11.2 1.0
C3 D:1492001 5.0 18.2 1.0
CA D:HIS418 5.0 11.6 1.0

Magnesium binding site 9 out of 9 in 3czj

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 (N460T) in Complex with D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:22.4
occ:1.00
 O D:ASN18 2.2 19.6 1.0
O D:VAL21 2.3 20.3 1.0
O D:ASP15 2.3 21.3 1.0
OD2 D:ASP193 2.3 19.0 1.0
OE1 D:GLN163 2.4 26.1 1.0
OD1 D:ASP193 2.9 19.6 1.0
CG D:ASP193 3.0 18.0 1.0
C D:ASN18 3.2 20.2 1.0
CD D:GLN163 3.3 23.7 1.0
C D:VAL21 3.4 21.1 1.0
C D:ASP15 3.5 22.4 1.0
NE2 D:GLN163 3.6 23.5 1.0
N D:ASN18 3.7 21.3 1.0
CA D:ASN18 3.9 21.2 1.0
OH D:TYR161 4.0 16.3 1.0
CA D:TRP16 4.1 22.3 1.0
N D:PRO19 4.1 19.3 1.0
CA D:VAL21 4.2 21.7 1.0
CB D:VAL21 4.2 24.2 1.0
N D:VAL21 4.2 22.5 1.0
N D:TRP16 4.2 22.4 1.0
CB D:ASN18 4.3 22.5 1.0
C D:TRP16 4.3 22.2 1.0
N D:GLU17 4.4 21.7 1.0
CE2 D:TYR161 4.4 15.7 1.0
CA D:PRO19 4.4 19.9 1.0
CB D:ASP193 4.4 18.2 1.0
N D:THR22 4.4 18.9 1.0
CA D:ASP15 4.6 23.2 1.0
CA D:THR22 4.6 17.6 1.0
CG D:GLN163 4.6 22.0 1.0
CZ D:TYR161 4.7 15.4 1.0
CG1 D:VAL21 4.7 23.0 1.0
C D:PRO19 4.8 20.8 1.0
C D:GLU17 4.8 21.6 1.0
O D:TRP16 4.9 21.0 1.0
CB D:ASP15 5.0 21.0 1.0

Reference:

J.C.Kappelhoff, S.Y.Liu, M.L.Dugdale, D.L.Dymianiw, L.R.Linton, R.E.Huber. Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-Beta-Galactosidase (E. Coli) As Examples. Protein J. V. 28 96 2009.
ISSN: ISSN 1572-3887
PubMed: 19229596
DOI: 10.1007/S10930-009-9168-1
Page generated: Wed Aug 14 11:59:11 2024

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