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Magnesium in PDB 3t2p: E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg, PDB code: 3t2p 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) 74.67 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.869, 166.171, 200.786, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 24.2

Other elements in 3t2p:

The structure of E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg also contains other interesting chemical elements:

Sodium (Na) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg (pdb code 3t2p). 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 (S796D) in Complex with Iptg, PDB code: 3t2p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3t2p

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:51.9
occ:1.00
 O A:HOH4280 2.0 61.0 1.0
ND1 A:HIS418 2.0 52.6 1.0
OE2 A:GLU416 2.1 47.4 1.0
OE1 A:GLU461 2.1 46.3 1.0
O A:HOH4041 2.1 39.9 1.0
O A:HOH4339 2.2 28.2 1.0
CD A:GLU461 2.9 45.2 1.0
CE1 A:HIS418 2.9 45.0 1.0
CG A:HIS418 3.1 47.0 1.0
CD A:GLU416 3.3 44.7 1.0
OE2 A:GLU461 3.4 46.4 1.0
CB A:HIS418 3.6 42.7 1.0
OE1 A:GLU416 3.8 40.5 1.0
CG A:GLU461 4.0 43.6 1.0
CB A:GLU461 4.0 36.4 1.0
NE2 A:HIS418 4.1 47.0 1.0
OD1 A:ASN102 4.1 54.2 1.0
O A:HOH4001 4.1 48.9 1.0
CD2 A:HIS418 4.2 47.1 1.0
CB A:ASP201 4.3 51.6 1.0
O A:ASP199 4.3 41.0 1.0
N A:ASP201 4.4 48.8 1.0
ND2 A:ASN460 4.4 34.4 1.0
CG A:GLU416 4.4 38.2 1.0
O A:ASN102 4.5 56.4 1.0
O4 A:IPT2001 4.6 55.7 0.9
O3 A:IPT2001 4.9 74.3 0.9
C2 A:IPT2001 4.9 62.9 0.9
CA A:ASP201 4.9 48.7 1.0
CG2 A:VAL103 4.9 47.8 1.0
CA A:HIS418 5.0 41.5 1.0

Magnesium binding site 2 out of 8 in 3t2p

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:48.7
occ:1.00
 OD2 A:ASP193 2.1 54.5 1.0
O A:ASP15 2.1 57.9 1.0
OE1 A:GLN163 2.3 48.7 1.0
O A:ASN18 2.3 47.6 1.0
O A:VAL21 2.3 45.4 1.0
CG A:ASP193 2.9 46.2 1.0
OD1 A:ASP193 3.0 57.5 1.0
C A:ASN18 3.2 49.4 1.0
CD A:GLN163 3.2 44.4 1.0
C A:ASP15 3.3 58.1 1.0
C A:VAL21 3.4 43.1 1.0
N A:ASN18 3.6 52.7 1.0
NE2 A:GLN163 3.7 46.8 1.0
OH A:TYR161 3.8 42.2 1.0
CA A:ASN18 3.9 52.2 1.0
CA A:TRP16 4.0 55.4 1.0
N A:TRP16 4.1 57.4 1.0
N A:PRO19 4.2 48.9 1.0
C A:TRP16 4.2 52.9 1.0
CA A:VAL21 4.2 44.1 1.0
CB A:ASN18 4.3 51.7 1.0
CE2 A:TYR161 4.3 45.9 1.0
N A:GLU17 4.3 52.1 1.0
CB A:VAL21 4.3 42.0 1.0
CB A:ASP193 4.3 40.1 1.0
N A:VAL21 4.4 48.0 1.0
CA A:ASP15 4.4 58.4 1.0
CA A:PRO19 4.4 48.8 1.0
N A:THR22 4.5 42.3 1.0
CG A:GLN163 4.5 36.3 1.0
CZ A:TYR161 4.5 47.4 1.0
CA A:THR22 4.6 44.3 1.0
CB A:ASP15 4.7 58.7 1.0
C A:GLU17 4.8 51.6 1.0
O A:TRP16 4.9 52.4 1.0
CG1 A:VAL21 4.9 39.1 1.0
C A:PRO19 5.0 47.9 1.0

Magnesium binding site 3 out of 8 in 3t2p

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:57.2
occ:1.00
 ND1 B:HIS418 2.0 47.6 1.0
O B:HOH4262 2.0 40.5 1.0
OE2 B:GLU416 2.1 45.8 1.0
OE1 B:GLU461 2.1 57.8 1.0
O B:HOH4225 2.3 46.9 1.0
O B:HOH4228 2.3 40.5 1.0
CE1 B:HIS418 2.9 41.3 1.0
CD B:GLU461 3.0 51.8 1.0
CG B:HIS418 3.1 46.7 1.0
CD B:GLU416 3.3 44.6 1.0
CB B:HIS418 3.5 44.0 1.0
OE2 B:GLU461 3.7 53.0 1.0
CB B:GLU461 3.9 38.0 1.0
CG B:GLU461 3.9 45.5 1.0
OE1 B:GLU416 3.9 44.9 1.0
NE2 B:HIS418 4.1 47.8 1.0
CD2 B:HIS418 4.2 45.3 1.0
OD1 B:ASN102 4.2 55.0 1.0
ND2 B:ASN460 4.3 46.8 1.0
CG B:GLU416 4.4 42.7 1.0
O B:ASP199 4.4 41.6 1.0
CB B:ASP201 4.4 45.1 1.0
N B:ASP201 4.4 43.8 1.0
O4 B:IPT2001 4.7 71.3 1.0
C2 B:IPT2001 4.8 70.3 1.0
O B:ASN102 4.9 49.6 1.0
O3 B:IPT2001 4.9 72.8 1.0
CA B:HIS418 4.9 42.2 1.0
CA B:ASP201 5.0 43.6 1.0

Magnesium binding site 4 out of 8 in 3t2p

Go back to Magnesium Binding Sites List in 3t2p
Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:57.3
occ:1.00
 OD2 B:ASP193 2.1 54.9 1.0
O B:ASP15 2.1 59.5 1.0
O B:ASN18 2.3 53.7 1.0
O B:VAL21 2.3 49.9 1.0
OE1 B:GLN163 2.3 45.4 1.0
CG B:ASP193 3.0 49.2 1.0
C B:ASN18 3.2 54.9 1.0
OD1 B:ASP193 3.2 56.6 1.0
C B:ASP15 3.3 61.4 1.0
CD B:GLN163 3.4 52.1 1.0
C B:VAL21 3.5 50.7 1.0
N B:ASN18 3.6 56.9 1.0
OH B:TYR161 3.7 49.6 1.0
CA B:ASN18 3.8 55.9 1.0
CA B:TRP16 3.9 56.9 1.0
NE2 B:GLN163 3.9 59.5 1.0
N B:TRP16 4.0 58.1 1.0
C B:TRP16 4.1 57.5 1.0
N B:PRO19 4.1 55.1 1.0
CB B:ASN18 4.2 54.0 1.0
CA B:VAL21 4.2 51.5 1.0
N B:GLU17 4.3 57.9 1.0
CB B:VAL21 4.3 50.4 1.0
N B:VAL21 4.4 53.7 1.0
CB B:ASP193 4.4 43.0 1.0
CA B:ASP15 4.4 64.1 1.0
CA B:PRO19 4.4 55.6 1.0
CE2 B:TYR161 4.5 47.2 1.0
N B:THR22 4.5 49.8 1.0
CZ B:TYR161 4.5 52.1 1.0
O B:TRP16 4.6 56.2 1.0
CG B:GLN163 4.6 50.6 1.0
CA B:THR22 4.7 50.2 1.0
C B:GLU17 4.7 57.1 1.0
CB B:ASP15 4.9 64.3 1.0
CG1 B:VAL21 4.9 47.5 1.0
C B:PRO19 5.0 56.4 1.0
N B:ASP193 5.0 42.5 1.0

Magnesium binding site 5 out of 8 in 3t2p

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:52.6
occ:1.00
 O C:HOH4309 1.9 46.0 1.0
ND1 C:HIS418 2.0 51.8 1.0
OE2 C:GLU416 2.1 45.6 1.0
OE1 C:GLU461 2.1 49.6 1.0
O C:HOH4269 2.1 43.9 1.0
O C:HOH4308 2.3 42.2 1.0
CE1 C:HIS418 2.9 43.7 1.0
CD C:GLU461 3.1 48.2 1.0
CG C:HIS418 3.1 48.4 1.0
CD C:GLU416 3.3 46.9 1.0
CB C:HIS418 3.6 45.1 1.0
OE2 C:GLU461 3.7 48.2 1.0
OE1 C:GLU416 3.9 44.5 1.0
OD1 C:ASN102 4.0 57.0 1.0
NE2 C:HIS418 4.1 44.3 1.0
CG C:GLU461 4.1 45.8 1.0
CB C:GLU461 4.1 40.2 1.0
CB C:ASP201 4.2 49.2 1.0
CD2 C:HIS418 4.2 47.5 1.0
N C:ASP201 4.3 48.7 1.0
O C:ASP199 4.3 41.8 1.0
O C:HOH4282 4.3 56.4 1.0
CG C:GLU416 4.4 44.2 1.0
ND2 C:ASN460 4.4 38.9 1.0
O C:ASN102 4.7 59.6 1.0
O4 C:IPT2001 4.7 61.0 1.0
CA C:ASP201 4.8 48.5 1.0
C2 C:IPT2001 4.8 68.7 1.0
O3 C:IPT2001 4.9 75.9 1.0

Magnesium binding site 6 out of 8 in 3t2p

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:58.8
occ:1.00
 OD2 C:ASP193 2.1 58.7 1.0
O C:ASP15 2.1 64.1 1.0
O C:ASN18 2.3 54.6 1.0
OE1 C:GLN163 2.3 52.6 1.0
O C:VAL21 2.3 48.4 1.0
CG C:ASP193 2.9 56.0 1.0
OD1 C:ASP193 3.1 64.0 1.0
C C:ASN18 3.2 55.0 1.0
C C:ASP15 3.3 65.1 1.0
CD C:GLN163 3.3 47.4 1.0
C C:VAL21 3.5 48.6 1.0
N C:ASN18 3.6 56.5 1.0
NE2 C:GLN163 3.8 55.3 1.0
CA C:ASN18 3.9 56.6 1.0
OH C:TYR161 3.9 51.7 1.0
CA C:TRP16 4.0 59.0 1.0
N C:TRP16 4.1 61.8 1.0
N C:PRO19 4.1 53.6 1.0
C C:TRP16 4.2 58.5 1.0
CB C:ASP193 4.3 49.6 1.0
CA C:VAL21 4.3 50.4 1.0
N C:GLU17 4.3 58.1 1.0
CB C:ASN18 4.4 57.9 1.0
CE2 C:TYR161 4.4 52.5 1.0
CA C:ASP15 4.4 65.7 1.0
CA C:PRO19 4.4 53.8 1.0
N C:VAL21 4.4 51.5 1.0
N C:THR22 4.5 48.1 1.0
CB C:VAL21 4.5 53.4 1.0
CG C:GLN163 4.6 43.5 1.0
CA C:THR22 4.6 48.8 1.0
CZ C:TYR161 4.6 50.1 1.0
O C:TRP16 4.7 59.9 1.0
C C:GLU17 4.8 57.7 1.0
CB C:ASP15 4.8 65.6 1.0
C C:PRO19 4.9 54.0 1.0

Magnesium binding site 7 out of 8 in 3t2p

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:45.6
occ:1.00
 O D:HOH4321 1.9 46.6 1.0
ND1 D:HIS418 2.0 39.9 1.0
OE1 D:GLU461 2.1 44.0 1.0
OE2 D:GLU416 2.1 51.8 1.0
O D:HOH4106 2.2 37.9 1.0
O D:HOH4030 2.5 24.4 1.0
CD D:GLU461 2.9 40.2 1.0
CE1 D:HIS418 2.9 29.6 1.0
CG D:HIS418 3.1 39.8 1.0
CD D:GLU416 3.3 46.5 1.0
OE2 D:GLU461 3.5 40.7 1.0
CB D:HIS418 3.5 36.3 1.0
CB D:GLU461 3.9 38.3 1.0
OE1 D:GLU416 3.9 44.6 1.0
CG D:GLU461 3.9 41.2 1.0
NE2 D:HIS418 4.1 32.2 1.0
OD1 D:ASN102 4.1 59.3 1.0
CD2 D:HIS418 4.2 32.0 1.0
O D:HOH4324 4.3 56.7 1.0
ND2 D:ASN460 4.3 37.5 1.0
CB D:ASP201 4.3 45.7 1.0
CG D:GLU416 4.4 40.2 1.0
O D:ASP199 4.5 41.1 1.0
N D:ASP201 4.5 43.1 1.0
O D:ASN102 4.6 57.8 1.0
O4 D:IPT2001 4.6 53.9 1.0
O3 D:IPT2001 4.7 60.1 1.0
C2 D:IPT2001 4.9 61.8 1.0
CA D:HIS418 4.9 37.1 1.0

Magnesium binding site 8 out of 8 in 3t2p

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (S796D) in Complex with Iptg


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 (S796D) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:53.6
occ:1.00
 O D:ASP15 2.1 53.3 1.0
OD2 D:ASP193 2.1 47.6 1.0
O D:ASN18 2.2 52.4 1.0
OE1 D:GLN163 2.3 51.9 1.0
O D:VAL21 2.3 48.7 1.0
CG D:ASP193 2.9 41.3 1.0
OD1 D:ASP193 2.9 53.0 1.0
C D:ASN18 3.2 53.5 1.0
CD D:GLN163 3.3 48.6 1.0
C D:ASP15 3.3 50.5 1.0
C D:VAL21 3.5 43.7 1.0
NE2 D:GLN163 3.7 48.3 1.0
N D:ASN18 3.7 54.2 1.0
OH D:TYR161 3.9 48.0 1.0
CA D:TRP16 3.9 49.7 1.0
CA D:ASN18 3.9 53.9 1.0
N D:TRP16 4.0 51.1 1.0
N D:PRO19 4.1 53.5 1.0
C D:TRP16 4.2 49.2 1.0
CB D:ASP193 4.3 40.4 1.0
CE2 D:TYR161 4.3 47.3 1.0
CA D:PRO19 4.3 53.2 1.0
CA D:VAL21 4.3 44.0 1.0
CB D:ASN18 4.4 53.6 1.0
CA D:ASP15 4.4 51.5 1.0
N D:THR22 4.4 41.5 1.0
N D:VAL21 4.4 48.6 1.0
N D:GLU17 4.5 48.9 1.0
CB D:VAL21 4.5 44.6 1.0
CG D:GLN163 4.5 42.9 1.0
CA D:THR22 4.6 42.5 1.0
CZ D:TYR161 4.6 46.5 1.0
O D:TRP16 4.8 50.0 1.0
CB D:ASP15 4.9 51.1 1.0
C D:PRO19 4.9 53.2 1.0
C D:GLU17 4.9 53.5 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 11:50:10 2024

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