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Magnesium in PDB 3t0b: E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex, PDB code: 3t0b 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) 67.79 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.970, 163.140, 204.020, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 23.3

Other elements in 3t0b:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex (pdb code 3t0b). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (S796T) Iptg Complex, PDB code: 3t0b:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:21.0
occ:1.00
 O A:HOH4811 2.0 13.1 1.0
ND1 A:HIS418 2.0 13.2 1.0
OE1 A:GLU461 2.1 17.9 1.0
OE2 A:GLU416 2.1 14.2 1.0
O A:HOH4072 2.2 13.0 1.0
O A:HOH4013 2.3 22.5 1.0
CE1 A:HIS418 2.9 6.8 1.0
CD A:GLU461 3.1 19.8 1.0
CG A:HIS418 3.1 8.9 1.0
CD A:GLU416 3.2 12.2 1.0
CB A:HIS418 3.5 12.0 1.0
OE2 A:GLU461 3.8 17.3 1.0
OE1 A:GLU416 3.8 17.4 1.0
OD1 A:ASN102 4.0 14.8 1.0
NE2 A:HIS418 4.1 12.6 1.0
CB A:GLU461 4.1 15.0 1.0
CG A:GLU461 4.2 16.9 1.0
CD2 A:HIS418 4.2 3.2 1.0
O A:ASP199 4.3 11.2 1.0
CB A:ASP201 4.3 15.5 1.0
N A:ASP201 4.3 18.5 1.0
O A:HOH4001 4.4 13.3 1.0
ND2 A:ASN460 4.4 9.4 1.0
CG A:GLU416 4.4 15.1 1.0
O A:ASN102 4.5 20.6 1.0
O4 A:IPT2001 4.5 14.4 0.9
CG2 A:VAL103 4.8 13.3 1.0
CA A:ASP201 4.9 17.4 1.0
C2 A:IPT2001 4.9 18.8 0.9
O3 A:IPT2001 4.9 32.3 0.9
CA A:HIS418 5.0 13.0 1.0

Magnesium binding site 2 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:22.9
occ:1.00
 O A:ASP15 2.1 27.1 1.0
OD2 A:ASP193 2.1 30.0 1.0
O A:ASN18 2.3 23.4 1.0
OE1 A:GLN163 2.3 28.8 1.0
O A:VAL21 2.3 23.0 1.0
CG A:ASP193 3.0 27.1 1.0
C A:ASN18 3.1 26.4 1.0
OD1 A:ASP193 3.1 27.4 1.0
CD A:GLN163 3.2 26.0 1.0
C A:ASP15 3.3 27.8 1.0
C A:VAL21 3.4 24.4 1.0
N A:ASN18 3.5 27.8 1.0
NE2 A:GLN163 3.5 20.1 1.0
CA A:ASN18 3.7 28.2 1.0
OH A:TYR161 3.9 32.4 1.0
CA A:TRP16 4.0 24.4 1.0
N A:PRO19 4.0 28.4 1.0
N A:TRP16 4.1 27.2 1.0
CB A:ASN18 4.2 27.9 1.0
CA A:VAL21 4.2 24.2 1.0
C A:TRP16 4.2 25.9 1.0
N A:VAL21 4.3 26.1 1.0
CB A:VAL21 4.3 27.8 1.0
N A:GLU17 4.4 24.0 1.0
CB A:ASP193 4.4 22.6 1.0
CA A:PRO19 4.4 27.6 1.0
CA A:ASP15 4.4 27.5 1.0
CE2 A:TYR161 4.4 24.5 1.0
N A:THR22 4.5 23.1 1.0
CG A:GLN163 4.6 22.4 1.0
CZ A:TYR161 4.6 25.5 1.0
CA A:THR22 4.7 24.2 1.0
C A:GLU17 4.7 26.9 1.0
CG1 A:VAL21 4.8 22.2 1.0
O A:TRP16 4.8 28.5 1.0
CB A:ASP15 4.9 26.9 1.0
C A:PRO19 4.9 29.4 1.0

Magnesium binding site 3 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:14.0
occ:1.00
 ND1 B:HIS418 2.1 11.1 1.0
OE1 B:GLU461 2.1 13.7 1.0
O B:HOH4908 2.1 13.0 1.0
OE2 B:GLU416 2.1 10.9 1.0
O B:HOH4160 2.2 6.3 1.0
O B:HOH4020 2.5 7.1 1.0
CE1 B:HIS418 2.9 11.0 1.0
CD B:GLU461 3.0 15.7 1.0
CG B:HIS418 3.2 9.6 1.0
CD B:GLU416 3.2 11.6 1.0
CB B:HIS418 3.7 5.7 1.0
OE2 B:GLU461 3.7 17.0 1.0
OE1 B:GLU416 3.8 10.8 1.0
CB B:GLU461 4.0 10.4 1.0
NE2 B:HIS418 4.1 16.8 1.0
OD1 B:ASN102 4.1 12.8 1.0
CG B:GLU461 4.1 12.7 1.0
O B:HOH4008 4.2 15.5 1.0
CD2 B:HIS418 4.2 8.4 1.0
ND2 B:ASN460 4.2 9.9 1.0
CB B:ASP201 4.3 12.5 1.0
N B:ASP201 4.4 13.0 1.0
O B:HOH4290 4.4 22.1 1.0
O B:ASP199 4.4 11.6 1.0
CG B:GLU416 4.4 8.0 1.0
O4 B:IPT2001 4.5 15.3 1.0
O B:ASN102 4.7 12.4 1.0
O3 B:IPT2001 4.7 11.8 1.0
C2 B:IPT2001 4.8 12.3 1.0
CA B:ASP201 4.9 13.4 1.0

Magnesium binding site 4 out of 8 in 3t0b

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:16.8
occ:1.00
 OD2 B:ASP193 2.1 14.8 1.0
O B:ASP15 2.1 18.6 1.0
O B:ASN18 2.3 17.1 1.0
O B:VAL21 2.3 16.4 1.0
OE1 B:GLN163 2.3 16.9 1.0
CG B:ASP193 2.8 15.9 1.0
OD1 B:ASP193 2.9 15.0 1.0
C B:ASN18 3.1 17.7 1.0
CD B:GLN163 3.2 17.4 1.0
C B:ASP15 3.3 17.3 1.0
C B:VAL21 3.4 17.7 1.0
NE2 B:GLN163 3.5 18.1 1.0
N B:ASN18 3.6 18.8 1.0
CA B:ASN18 3.8 17.4 1.0
OH B:TYR161 3.9 14.5 1.0
CA B:TRP16 4.0 17.3 1.0
N B:TRP16 4.1 15.2 1.0
N B:PRO19 4.1 18.7 1.0
CA B:VAL21 4.2 18.2 1.0
C B:TRP16 4.2 18.0 1.0
CB B:ASN18 4.2 17.5 1.0
N B:VAL21 4.2 20.0 1.0
CB B:VAL21 4.3 20.9 1.0
CB B:ASP193 4.3 13.7 1.0
CA B:PRO19 4.4 18.0 1.0
CA B:ASP15 4.4 17.5 1.0
CE2 B:TYR161 4.4 18.3 1.0
N B:GLU17 4.4 18.5 1.0
N B:THR22 4.5 13.8 1.0
CG B:GLN163 4.5 16.2 1.0
CZ B:TYR161 4.6 17.4 1.0
CA B:THR22 4.7 15.3 1.0
O B:TRP16 4.7 16.9 1.0
C B:GLU17 4.8 17.5 1.0
CB B:ASP15 4.9 18.1 1.0
C B:PRO19 4.9 19.8 1.0
CG1 B:VAL21 4.9 17.1 1.0

Magnesium binding site 5 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:17.0
occ:1.00
 O C:HOH4984 2.0 4.7 1.0
ND1 C:HIS418 2.1 17.7 1.0
OE1 C:GLU461 2.1 11.6 1.0
OE2 C:GLU416 2.1 11.5 1.0
O C:HOH4895 2.1 15.5 1.0
O C:HOH4038 2.2 7.3 1.0
CE1 C:HIS418 2.9 8.8 1.0
CD C:GLU461 3.2 20.0 1.0
CG C:HIS418 3.2 10.4 1.0
CD C:GLU416 3.2 13.4 1.0
CB C:HIS418 3.7 8.5 1.0
OE1 C:GLU416 3.8 11.5 1.0
OE2 C:GLU461 3.9 19.5 1.0
NE2 C:HIS418 4.1 12.1 1.0
OD1 C:ASN102 4.1 12.0 1.0
CB C:ASP201 4.1 12.7 1.0
CB C:GLU461 4.1 9.8 1.0
N C:ASP201 4.2 10.8 1.0
CG C:GLU461 4.2 10.6 1.0
CD2 C:HIS418 4.2 10.1 1.0
O C:HOH4026 4.3 18.2 1.0
O C:ASP199 4.3 7.3 1.0
CG C:GLU416 4.4 7.4 1.0
O C:HOH4311 4.4 19.8 1.0
ND2 C:ASN460 4.4 10.9 1.0
O C:ASN102 4.5 11.2 1.0
O4 C:IPT2001 4.5 9.4 1.0
CA C:ASP201 4.7 13.2 1.0
O3 C:IPT2001 4.8 8.0 1.0
C C:GLN200 4.9 10.8 1.0
C2 C:IPT2001 4.9 14.3 1.0

Magnesium binding site 6 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:13.9
occ:1.00
 OD2 C:ASP193 2.1 16.2 1.0
O C:ASP15 2.1 16.7 1.0
OE1 C:GLN163 2.3 12.2 1.0
O C:ASN18 2.3 18.7 1.0
O C:VAL21 2.3 14.7 1.0
CG C:ASP193 2.9 17.6 1.0
OD1 C:ASP193 3.0 15.2 1.0
CD C:GLN163 3.2 15.8 1.0
C C:ASN18 3.2 19.0 1.0
C C:ASP15 3.3 19.9 1.0
C C:VAL21 3.4 17.0 1.0
NE2 C:GLN163 3.5 14.5 1.0
N C:ASN18 3.6 22.0 1.0
CA C:ASN18 3.8 19.3 1.0
OH C:TYR161 4.0 12.1 1.0
CA C:TRP16 4.0 18.5 1.0
N C:TRP16 4.1 17.6 1.0
N C:PRO19 4.2 16.8 1.0
C C:TRP16 4.2 18.7 1.0
CA C:VAL21 4.2 18.7 1.0
CB C:ASN18 4.2 18.4 1.0
CB C:ASP193 4.3 12.4 1.0
CB C:VAL21 4.3 16.9 1.0
N C:VAL21 4.3 20.7 1.0
N C:GLU17 4.4 17.7 1.0
CA C:PRO19 4.4 17.0 1.0
CA C:ASP15 4.4 21.0 1.0
N C:THR22 4.5 16.6 1.0
CG C:GLN163 4.5 13.8 1.0
CE2 C:TYR161 4.5 12.6 1.0
O C:TRP16 4.7 18.1 1.0
CZ C:TYR161 4.7 11.4 1.0
CG1 C:VAL21 4.7 10.5 1.0
CA C:THR22 4.7 17.8 1.0
C C:GLU17 4.8 22.0 1.0
CB C:ASP15 4.9 20.0 1.0

Magnesium binding site 7 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:22.3
occ:1.00
 ND1 D:HIS418 2.0 17.4 1.0
OE1 D:GLU461 2.1 18.0 1.0
OE2 D:GLU416 2.1 19.2 1.0
O D:HOH4848 2.1 14.1 1.0
O D:HOH4105 2.2 22.7 1.0
O D:HOH4042 2.5 14.1 1.0
CE1 D:HIS418 3.0 16.5 1.0
CD D:GLU461 3.1 20.5 1.0
CG D:HIS418 3.1 17.1 1.0
CD D:GLU416 3.2 21.4 1.0
CB D:HIS418 3.5 16.4 1.0
OE2 D:GLU461 3.7 17.6 1.0
OE1 D:GLU416 3.8 22.1 1.0
OD1 D:ASN102 4.0 21.1 1.0
NE2 D:HIS418 4.1 17.3 1.0
CB D:GLU461 4.1 12.7 1.0
CG D:GLU461 4.1 16.8 1.0
CD2 D:HIS418 4.2 11.7 1.0
O D:ASP199 4.3 14.8 1.0
O D:HOH4030 4.3 19.1 1.0
CB D:ASP201 4.3 23.3 1.0
N D:ASP201 4.3 22.4 1.0
CG D:GLU416 4.4 16.9 1.0
O D:ASN102 4.5 20.7 1.0
O D:HOH4297 4.5 34.0 1.0
ND2 D:ASN460 4.6 14.3 1.0
O4 D:IPT2001 4.6 18.0 1.0
CG2 D:VAL103 4.8 20.6 1.0
CA D:ASP201 4.9 20.1 1.0
C2 D:IPT2001 4.9 19.4 1.0
CA D:HIS418 4.9 16.0 1.0

Magnesium binding site 8 out of 8 in 3t0b

Go back to Magnesium Binding Sites List in 3t0b
Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796T) 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 (S796T) Iptg Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:24.0
occ:1.00
 OD2 D:ASP193 2.1 23.6 1.0
O D:ASP15 2.1 26.4 1.0
O D:ASN18 2.3 22.9 1.0
O D:VAL21 2.3 24.9 1.0
OE1 D:GLN163 2.3 28.9 1.0
CG D:ASP193 2.9 29.0 1.0
OD1 D:ASP193 3.1 29.0 1.0
CD D:GLN163 3.2 22.3 1.0
C D:ASN18 3.2 25.2 1.0
C D:ASP15 3.3 26.8 1.0
C D:VAL21 3.5 23.0 1.0
NE2 D:GLN163 3.5 21.3 1.0
N D:ASN18 3.6 26.6 1.0
CA D:ASN18 3.9 26.9 1.0
CA D:TRP16 4.0 24.4 1.0
OH D:TYR161 4.0 27.7 1.0
N D:TRP16 4.1 25.4 1.0
N D:PRO19 4.1 25.0 1.0
C D:TRP16 4.2 23.8 1.0
CA D:VAL21 4.3 22.5 1.0
CB D:ASN18 4.3 28.0 1.0
N D:GLU17 4.3 24.4 1.0
CB D:ASP193 4.3 24.7 1.0
CB D:VAL21 4.4 24.2 1.0
N D:VAL21 4.4 24.1 1.0
CA D:ASP15 4.4 28.2 1.0
CE2 D:TYR161 4.4 22.1 1.0
N D:THR22 4.4 20.8 1.0
CA D:PRO19 4.5 25.7 1.0
CG D:GLN163 4.5 20.0 1.0
CA D:THR22 4.6 22.3 1.0
CZ D:TYR161 4.7 19.4 1.0
O D:TRP16 4.7 25.3 1.0
C D:GLU17 4.8 25.5 1.0
CG1 D:VAL21 4.9 20.9 1.0
CB D:ASP15 4.9 25.5 1.0
C D:PRO19 5.0 24.5 1.0

Reference:

L.J.Jancewicz, R.W.Wheatley, G.Sutendra, M.Lee, M.E.Fraser, R.E.Huber. Er-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 11:12:48 2024

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