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Magnesium in PDB 3t08: E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex, PDB code: 3t08 was solved by L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.52 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.160, 161.590, 202.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.3

Other elements in 3t08:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex also contains other interesting chemical elements:

Sodium (Na) 13 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex (pdb code 3t08). 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 (S796A) Iptg Complex, PDB code: 3t08:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3t08

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:32.8
occ:1.00
 O A:HOH4699 2.0 26.1 1.0
ND1 A:HIS418 2.1 28.5 1.0
OE2 A:GLU416 2.1 28.6 1.0
OE1 A:GLU461 2.1 30.8 1.0
O A:HOH4643 2.1 27.5 1.0
O A:HOH4606 2.2 29.9 1.0
CE1 A:HIS418 3.0 31.3 1.0
CG A:HIS418 3.1 29.3 1.0
CD A:GLU461 3.2 35.6 1.0
CD A:GLU416 3.2 24.8 1.0
CB A:HIS418 3.5 26.1 1.0
OE1 A:GLU416 3.7 26.5 1.0
OE2 A:GLU461 3.9 38.2 1.0
CB A:GLU461 4.1 28.6 1.0
OD1 A:ASN102 4.1 30.7 1.0
NE2 A:HIS418 4.1 32.0 1.0
CG A:GLU461 4.2 32.4 1.0
CD2 A:HIS418 4.2 31.5 1.0
CB A:ASP201 4.2 32.4 1.0
O A:ASP199 4.3 28.2 1.0
N A:ASP201 4.3 29.9 1.0
O A:HOH4001 4.3 37.2 1.0
CG A:GLU416 4.4 25.4 1.0
ND2 A:ASN460 4.4 29.3 1.0
O A:HOH4231 4.4 43.9 1.0
O4 A:IPT2001 4.6 38.4 0.9
O A:ASN102 4.6 37.5 1.0
CA A:ASP201 4.8 32.4 1.0
C2 A:IPT2001 4.9 45.0 0.9
O3 A:IPT2001 4.9 44.6 0.9
CG2 A:VAL103 4.9 31.6 1.0
CA A:HIS418 5.0 28.2 1.0
C A:GLN200 5.0 32.1 1.0

Magnesium binding site 2 out of 9 in 3t08

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:36.6
occ:1.00
 OD2 A:ASP193 2.1 38.9 1.0
O A:ASP15 2.1 39.2 1.0
O A:ASN18 2.3 35.0 1.0
OE1 A:GLN163 2.3 40.5 1.0
O A:VAL21 2.3 35.8 1.0
CG A:ASP193 2.9 41.1 1.0
OD1 A:ASP193 3.1 39.3 1.0
C A:ASN18 3.2 38.7 1.0
CD A:GLN163 3.2 38.6 1.0
C A:ASP15 3.3 39.5 1.0
C A:VAL21 3.4 35.5 1.0
NE2 A:GLN163 3.6 36.0 1.0
N A:ASN18 3.6 41.9 1.0
CA A:ASN18 3.8 39.5 1.0
OH A:TYR161 3.9 34.6 1.0
CA A:TRP16 4.0 37.7 1.0
N A:TRP16 4.1 37.5 1.0
CB A:ASN18 4.2 38.8 1.0
N A:PRO19 4.2 40.4 1.0
CA A:VAL21 4.2 35.9 1.0
C A:TRP16 4.2 37.1 1.0
CB A:VAL21 4.3 36.7 1.0
N A:VAL21 4.3 38.7 1.0
CE2 A:TYR161 4.3 35.1 1.0
CB A:ASP193 4.4 35.4 1.0
N A:GLU17 4.4 36.8 1.0
CA A:ASP15 4.4 39.8 1.0
CA A:PRO19 4.5 41.3 1.0
N A:THR22 4.5 35.0 1.0
CG A:GLN163 4.5 39.4 1.0
CZ A:TYR161 4.6 35.4 1.0
CA A:THR22 4.7 37.4 1.0
O A:TRP16 4.7 38.2 1.0
C A:GLU17 4.8 38.7 1.0
CG1 A:VAL21 4.8 32.9 1.0
CB A:ASP15 4.9 38.4 1.0
C A:PRO19 4.9 40.0 1.0

Magnesium binding site 3 out of 9 in 3t08

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:31.8
occ:1.00
 ND1 B:HIS418 2.1 22.7 1.0
OE2 B:GLU416 2.1 29.9 1.0
OE1 B:GLU461 2.1 33.1 1.0
O B:HOH4572 2.1 29.5 1.0
O B:HOH4142 2.2 30.4 1.0
O B:HOH4725 2.2 30.9 1.0
CE1 B:HIS418 2.9 30.4 1.0
CG B:HIS418 3.1 24.1 1.0
CD B:GLU461 3.2 32.4 1.0
CD B:GLU416 3.2 26.6 1.0
CB B:HIS418 3.6 27.0 1.0
OE1 B:GLU416 3.7 29.4 1.0
OE2 B:GLU461 3.9 29.8 1.0
OD1 B:ASN102 4.0 36.0 1.0
NE2 B:HIS418 4.1 29.3 1.0
CB B:GLU461 4.1 29.6 1.0
O B:ASP199 4.2 29.0 1.0
CG B:GLU461 4.2 34.2 1.0
CD2 B:HIS418 4.2 25.5 1.0
N B:ASP201 4.3 30.4 1.0
CB B:ASP201 4.3 27.4 1.0
ND2 B:ASN460 4.4 25.2 1.0
CG B:GLU416 4.4 29.7 1.0
O B:HOH4010 4.4 28.6 1.0
O4 B:IPT2001 4.5 35.0 1.0
O B:ASN102 4.7 33.1 1.0
O B:HOH4247 4.8 43.8 1.0
CA B:ASP201 4.8 26.0 1.0
O3 B:IPT2001 4.9 42.6 1.0
C2 B:IPT2001 4.9 42.4 1.0
C B:GLN200 4.9 31.9 1.0
CA B:GLN200 5.0 31.5 1.0
CG2 B:VAL103 5.0 33.6 1.0

Magnesium binding site 4 out of 9 in 3t08

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:33.4
occ:1.00
 OD2 B:ASP193 2.1 41.3 1.0
O B:ASP15 2.1 33.4 1.0
O B:ASN18 2.3 32.0 1.0
OE1 B:GLN163 2.3 35.5 1.0
O B:VAL21 2.3 35.7 1.0
CG B:ASP193 2.9 35.6 1.0
OD1 B:ASP193 3.0 41.9 1.0
CD B:GLN163 3.1 41.7 1.0
C B:ASN18 3.2 35.3 1.0
C B:ASP15 3.3 35.0 1.0
NE2 B:GLN163 3.4 39.3 1.0
C B:VAL21 3.5 35.6 1.0
N B:ASN18 3.6 35.1 1.0
CA B:ASN18 3.8 34.4 1.0
OH B:TYR161 3.9 34.1 1.0
CA B:TRP16 4.0 35.4 1.0
N B:TRP16 4.1 33.9 1.0
N B:PRO19 4.1 36.1 1.0
C B:TRP16 4.2 33.8 1.0
CB B:ASN18 4.2 34.9 1.0
CA B:VAL21 4.3 36.2 1.0
CB B:ASP193 4.3 33.3 1.0
N B:GLU17 4.3 34.7 1.0
N B:VAL21 4.4 37.9 1.0
CE2 B:TYR161 4.4 28.9 1.0
CB B:VAL21 4.4 37.2 1.0
CA B:PRO19 4.4 38.4 1.0
CA B:ASP15 4.5 36.3 1.0
CG B:GLN163 4.5 35.8 1.0
N B:THR22 4.5 34.0 1.0
CZ B:TYR161 4.6 30.2 1.0
CA B:THR22 4.7 35.6 1.0
C B:GLU17 4.7 37.6 1.0
O B:TRP16 4.8 36.1 1.0
CB B:ASP15 4.9 34.8 1.0
C B:PRO19 4.9 38.5 1.0
CG1 B:VAL21 5.0 36.5 1.0

Magnesium binding site 5 out of 9 in 3t08

Go back to Magnesium Binding Sites List in 3t08
Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:56.6
occ:1.00
 O B:HOH4746 2.0 43.3 1.0
O B:HOH4470 2.2 50.2 1.0
O B:HOH4697 2.2 48.7 1.0
O B:HOH4466 2.3 44.9 1.0
O B:HOH4586 2.3 45.0 1.0
OE1 B:GLU369 3.7 46.6 1.0
OE2 B:GLU369 4.1 43.4 1.0
CD B:GLU369 4.3 44.1 1.0
O B:HOH4348 4.7 45.6 1.0
O B:HOH4636 4.9 52.0 1.0

Magnesium binding site 6 out of 9 in 3t08

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:33.2
occ:1.00
 O C:HOH4704 2.0 24.7 1.0
ND1 C:HIS418 2.1 30.1 1.0
OE2 C:GLU416 2.1 31.2 1.0
OE1 C:GLU461 2.1 34.7 1.0
O C:HOH4757 2.1 26.4 1.0
O C:HOH4731 2.2 28.7 1.0
CE1 C:HIS418 2.9 33.4 1.0
CG C:HIS418 3.2 29.0 1.0
CD C:GLU416 3.2 27.9 1.0
CD C:GLU461 3.2 32.6 1.0
CB C:HIS418 3.6 27.5 1.0
OE1 C:GLU416 3.7 29.6 1.0
OE2 C:GLU461 3.9 32.5 1.0
OD1 C:ASN102 4.0 31.1 1.0
NE2 C:HIS418 4.1 26.6 1.0
CB C:GLU461 4.1 26.2 1.0
CG C:GLU461 4.2 29.8 1.0
CD2 C:HIS418 4.2 29.8 1.0
O C:ASP199 4.2 29.1 1.0
N C:ASP201 4.2 27.0 1.0
CB C:ASP201 4.2 27.1 1.0
ND2 C:ASN460 4.3 27.2 1.0
O C:HOH4012 4.3 25.6 1.0
CG C:GLU416 4.4 28.1 1.0
O C:HOH4238 4.4 48.3 1.0
O4 C:IPT2001 4.5 36.9 1.0
O C:ASN102 4.7 33.5 1.0
CA C:ASP201 4.8 27.1 1.0
O3 C:IPT2001 4.8 43.4 1.0
C2 C:IPT2001 4.9 46.3 1.0
CA C:GLN200 4.9 28.2 1.0
C C:GLN200 4.9 30.1 1.0

Magnesium binding site 7 out of 9 in 3t08

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:29.4
occ:1.00
 OD2 C:ASP193 2.1 36.0 1.0
O C:ASP15 2.1 35.2 1.0
OE1 C:GLN163 2.3 31.7 1.0
O C:ASN18 2.3 35.7 1.0
O C:VAL21 2.3 32.0 1.0
CG C:ASP193 2.8 35.8 1.0
OD1 C:ASP193 2.9 35.9 1.0
CD C:GLN163 3.2 37.7 1.0
C C:ASN18 3.2 36.6 1.0
C C:ASP15 3.3 34.2 1.0
C C:VAL21 3.4 35.6 1.0
NE2 C:GLN163 3.5 34.0 1.0
N C:ASN18 3.7 37.8 1.0
CA C:ASN18 3.9 37.2 1.0
OH C:TYR161 3.9 29.8 1.0
CA C:TRP16 4.0 33.3 1.0
N C:TRP16 4.1 34.1 1.0
C C:TRP16 4.2 33.0 1.0
CA C:VAL21 4.2 36.6 1.0
N C:PRO19 4.2 36.6 1.0
CB C:ASP193 4.3 33.1 1.0
CB C:ASN18 4.3 34.8 1.0
N C:VAL21 4.3 39.1 1.0
CB C:VAL21 4.3 37.6 1.0
CE2 C:TYR161 4.4 24.5 1.0
N C:GLU17 4.4 31.8 1.0
CA C:PRO19 4.5 35.8 1.0
CA C:ASP15 4.5 35.7 1.0
N C:THR22 4.5 31.0 1.0
CG C:GLN163 4.5 34.6 1.0
CZ C:TYR161 4.7 28.6 1.0
O C:TRP16 4.7 31.8 1.0
CA C:THR22 4.7 33.0 1.0
CG1 C:VAL21 4.8 33.7 1.0
C C:GLU17 4.8 35.9 1.0
CB C:ASP15 4.9 32.7 1.0
C C:PRO19 4.9 36.1 1.0

Magnesium binding site 8 out of 9 in 3t08

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:35.4
occ:1.00
 ND1 D:HIS418 2.0 36.5 1.0
O D:HOH4651 2.1 34.1 1.0
OE1 D:GLU461 2.1 35.9 1.0
OE2 D:GLU416 2.1 30.4 1.0
O D:HOH4525 2.1 27.9 1.0
O D:HOH4022 2.4 30.5 1.0
CE1 D:HIS418 2.9 34.1 1.0
CD D:GLU461 3.1 35.2 1.0
CG D:HIS418 3.1 28.1 1.0
CD D:GLU416 3.2 29.8 1.0
CB D:HIS418 3.6 30.9 1.0
OE2 D:GLU461 3.8 37.2 1.0
OE1 D:GLU416 3.8 27.3 1.0
OD1 D:ASN102 4.0 35.2 1.0
NE2 D:HIS418 4.1 28.7 1.0
CB D:GLU461 4.1 31.4 1.0
CG D:GLU461 4.2 33.1 1.0
O D:HOH4014 4.2 30.0 1.0
CB D:ASP201 4.2 33.3 1.0
CD2 D:HIS418 4.2 32.8 1.0
O D:ASP199 4.2 36.7 1.0
N D:ASP201 4.4 34.6 1.0
CG D:GLU416 4.4 32.8 1.0
ND2 D:ASN460 4.4 39.3 1.0
O4 D:IPT2001 4.4 39.7 1.0
O D:HOH4221 4.4 48.9 1.0
O D:ASN102 4.6 39.6 1.0
O3 D:IPT2001 4.8 45.8 1.0
CA D:ASP201 4.8 34.0 1.0
C2 D:IPT2001 4.9 45.4 1.0
CG2 D:VAL103 5.0 40.8 1.0

Magnesium binding site 9 out of 9 in 3t08

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (S796A) Iptg Complex


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 (S796A) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:36.9
occ:1.00
 OD2 D:ASP193 2.1 47.0 1.0
O D:ASP15 2.1 36.7 1.0
O D:ASN18 2.3 37.0 1.0
OE1 D:GLN163 2.3 41.3 1.0
O D:VAL21 2.3 34.4 1.0
CG D:ASP193 2.9 44.8 1.0
OD1 D:ASP193 3.0 46.2 1.0
CD D:GLN163 3.2 42.1 1.0
C D:ASN18 3.3 38.5 1.0
C D:ASP15 3.3 38.7 1.0
C D:VAL21 3.5 35.4 1.0
NE2 D:GLN163 3.5 36.9 1.0
N D:ASN18 3.7 37.5 1.0
CA D:TRP16 3.9 39.6 1.0
OH D:TYR161 3.9 37.4 1.0
CA D:ASN18 3.9 38.5 1.0
N D:TRP16 4.0 38.9 1.0
C D:TRP16 4.2 38.3 1.0
CA D:VAL21 4.2 35.4 1.0
N D:PRO19 4.2 36.8 1.0
CB D:VAL21 4.3 37.0 1.0
CB D:ASN18 4.3 39.9 1.0
CB D:ASP193 4.3 38.3 1.0
CE2 D:TYR161 4.3 34.9 1.0
N D:VAL21 4.4 38.2 1.0
N D:GLU17 4.4 37.0 1.0
CA D:ASP15 4.4 39.7 1.0
N D:THR22 4.5 35.2 1.0
CA D:PRO19 4.5 39.1 1.0
CG D:GLN163 4.5 39.1 1.0
CZ D:TYR161 4.6 36.9 1.0
CA D:THR22 4.7 34.7 1.0
CG1 D:VAL21 4.8 33.8 1.0
O D:TRP16 4.8 37.4 1.0
CB D:ASP15 4.8 35.2 1.0
C D:GLU17 4.8 36.9 1.0
C D:PRO19 5.0 38.9 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Ser-796 of Beta-Galactosidase (E. Coli) Plays A Key Role in Maintaining An Optimum Balance Between the Opened and Closed Conformations of the Catalytically Important Active Site Loop Arch.Biochem.Biophys. V. 517 111 2012.
ISSN: ISSN 0003-9861
PubMed: 22155115
DOI: 10.1016/J.ABB.2011.11.017
Page generated: Thu Aug 15 11:12:41 2024

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