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Magnesium in PDB 3t2o: E. Coli (Lacz) Beta-Galactosidase (S796D)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (S796D)

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (S796D), PDB code: 3t2o 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) 61.03 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.260, 168.360, 200.640, 90.00, 90.00, 90.00
R / Rfree (%) 15.2 / 18.2

Other elements in 3t2o:

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

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (S796D) (pdb code 3t2o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (S796D), PDB code: 3t2o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in 3t2o

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Magnesium binding site 1 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:13.8
occ:1.00
 ND1 A:HIS418 2.1 13.2 1.0
OE2 A:GLU416 2.1 15.0 1.0
OE1 A:GLU461 2.1 14.4 1.0
O A:HOH4991 2.1 10.3 1.0
O A:HOH4896 2.1 11.2 1.0
O A:HOH4012 2.3 13.3 1.0
CE1 A:HIS418 2.9 18.4 1.0
CG A:HIS418 3.1 15.2 1.0
CD A:GLU461 3.2 18.3 1.0
CD A:GLU416 3.2 13.5 1.0
CB A:HIS418 3.6 12.8 1.0
OE1 A:GLU416 3.7 12.8 1.0
OE2 A:GLU461 3.9 15.1 1.0
CB A:GLU461 4.1 12.8 1.0
NE2 A:HIS418 4.1 15.2 1.0
OD1 A:ASN102 4.1 17.0 1.0
CG A:GLU461 4.2 12.2 1.0
O A:HOH4812 4.2 34.5 1.0
CD2 A:HIS418 4.2 15.6 1.0
O A:ASP199 4.2 16.2 1.0
N A:ASP201 4.3 13.8 1.0
CB A:ASP201 4.3 14.2 1.0
O A:HOH4001 4.4 19.1 1.0
CG A:GLU416 4.4 11.5 1.0
ND2 A:ASN460 4.4 12.8 1.0
O A:HOH4283 4.6 23.0 1.0
O A:ASN102 4.6 15.5 1.0
CA A:ASP201 4.9 13.5 1.0
CG2 A:VAL103 4.9 16.1 1.0
CA A:GLN200 5.0 8.9 1.0
C A:GLN200 5.0 11.1 1.0

Magnesium binding site 2 out of 16 in 3t2o

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Magnesium binding site 2 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:14.8
occ:1.00
 O A:ASP15 2.1 16.1 1.0
OD2 A:ASP193 2.1 19.0 1.0
O A:ASN18 2.3 17.7 1.0
OE1 A:GLN163 2.3 16.5 1.0
O A:VAL21 2.3 15.3 1.0
CG A:ASP193 2.9 17.2 1.0
OD1 A:ASP193 3.1 19.0 1.0
C A:ASN18 3.2 17.3 1.0
CD A:GLN163 3.2 16.1 1.0
C A:ASP15 3.3 15.8 1.0
C A:VAL21 3.5 15.7 1.0
NE2 A:GLN163 3.5 16.3 1.0
N A:ASN18 3.7 18.2 1.0
CA A:ASN18 3.9 19.1 1.0
OH A:TYR161 3.9 12.6 1.0
CA A:TRP16 3.9 14.5 1.0
N A:TRP16 4.0 14.4 1.0
N A:PRO19 4.2 17.8 1.0
C A:TRP16 4.2 16.3 1.0
CA A:VAL21 4.2 16.1 1.0
CB A:ASN18 4.3 18.8 1.0
CE2 A:TYR161 4.3 15.6 1.0
N A:VAL21 4.4 17.1 1.0
CB A:ASP193 4.4 15.2 1.0
N A:GLU17 4.4 15.7 1.0
CB A:VAL21 4.4 18.1 1.0
CA A:ASP15 4.4 17.1 1.0
CA A:PRO19 4.4 16.9 1.0
N A:THR22 4.5 15.0 1.0
CG A:GLN163 4.6 15.9 1.0
CZ A:TYR161 4.6 12.7 1.0
CA A:THR22 4.7 17.4 1.0
O A:TRP16 4.8 17.4 1.0
C A:GLU17 4.8 19.6 1.0
CB A:ASP15 4.9 16.9 1.0
CG1 A:VAL21 4.9 19.4 1.0
C A:PRO19 5.0 17.2 1.0

Magnesium binding site 3 out of 16 in 3t2o

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Magnesium binding site 3 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:39.0
occ:1.00
 O A:HOH5075 2.1 29.8 1.0
O A:HOH4992 2.2 27.9 1.0
O A:HOH4897 2.2 20.7 1.0
O A:HOH4591 2.2 37.7 1.0
OE1 A:GLN718 2.3 23.4 1.0
O A:HOH4414 2.4 31.8 1.0
CD A:GLN718 3.2 20.1 1.0
NE2 A:GLN718 3.5 15.8 1.0
O A:HOH4401 4.1 31.9 1.0
C2 A:DMS8020 4.1 78.3 1.0
O A:THR911 4.1 13.7 1.0
O A:HOH4271 4.2 35.5 1.0
NE2 A:HIS622 4.2 12.7 1.0
O A:GLN719 4.4 14.7 1.0
O A:HOH5141 4.5 31.0 1.0
O A:HOH4077 4.5 14.8 1.0
CG A:GLN718 4.6 14.2 1.0
N A:GLN719 4.6 10.4 1.0
O A:DMS8020 4.8 78.9 1.0
O A:HOH4247 4.8 22.1 1.0
CE1 A:HIS622 4.8 16.1 1.0

Magnesium binding site 4 out of 16 in 3t2o

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Magnesium binding site 4 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:43.3
occ:1.00
 O A:HOH5144 2.0 41.3 1.0
O A:HOH5179 2.0 31.2 1.0
O A:HOH5175 2.1 46.1 1.0
O A:HOH4844 2.1 34.5 1.0
O A:HOH4562 2.2 29.7 1.0
O A:DMS8006 3.4 64.0 1.0
O A:HOH5108 4.1 52.7 1.0
O A:HOH4729 4.2 39.0 1.0
O A:HOH4599 4.3 25.9 1.0
C1 A:DMS8006 4.3 62.7 1.0
OE1 A:GLU314 4.3 22.3 1.0
OE2 A:GLU314 4.4 24.7 1.0
S A:DMS8006 4.6 66.4 1.0
O A:HOH5186 4.7 40.8 1.0
CD A:GLU314 4.8 25.4 1.0
O A:HOH4593 4.8 30.0 1.0

Magnesium binding site 5 out of 16 in 3t2o

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Magnesium binding site 5 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3006

b:27.0
occ:1.00
 O A:HOH5136 1.9 24.7 1.0
O A:HOH5199 2.0 27.5 1.0
O A:HOH5171 2.0 37.0 1.0
O A:HOH4741 2.1 36.8 1.0
O A:HOH4782 2.1 30.9 1.0
O A:HOH4804 2.2 32.3 1.0
O A:HOH5030 4.2 36.8 1.0
OE1 A:GLU136 4.4 28.3 1.0
O A:HOH4785 4.4 44.6 1.0
O A:HOH4663 4.4 35.6 1.0
NE2 A:GLN135 4.5 43.2 1.0
CB A:GLN135 4.6 24.3 1.0

Magnesium binding site 6 out of 16 in 3t2o

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Magnesium binding site 6 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:12.5
occ:1.00
 O B:HOH5172 2.0 10.5 1.0
ND1 B:HIS418 2.1 11.2 1.0
OE2 B:GLU416 2.1 11.6 1.0
OE1 B:GLU461 2.1 12.3 1.0
O B:HOH5206 2.1 13.0 1.0
O B:HOH4023 2.3 13.2 1.0
CE1 B:HIS418 2.9 13.9 1.0
CD B:GLU461 3.1 14.2 1.0
CG B:HIS418 3.2 12.6 1.0
CD B:GLU416 3.2 10.6 1.0
CB B:HIS418 3.6 13.6 1.0
OE1 B:GLU416 3.6 11.6 1.0
OE2 B:GLU461 3.8 15.2 1.0
CB B:GLU461 4.1 11.0 1.0
NE2 B:HIS418 4.1 14.2 1.0
OD1 B:ASN102 4.1 15.7 1.0
CG B:GLU461 4.1 10.8 1.0
CD2 B:HIS418 4.2 13.2 1.0
O B:ASP199 4.3 12.2 1.0
O B:HOH4011 4.3 18.9 1.0
CB B:ASP201 4.3 11.9 1.0
N B:ASP201 4.3 11.4 1.0
O B:HOH4523 4.3 29.4 1.0
ND2 B:ASN460 4.4 11.8 1.0
CG B:GLU416 4.4 10.9 1.0
O B:HOH4294 4.6 21.7 1.0
O B:ASN102 4.7 15.7 1.0
CA B:ASP201 4.9 12.6 1.0
CG2 B:VAL103 4.9 16.1 1.0
CA B:GLN200 5.0 10.5 1.0

Magnesium binding site 7 out of 16 in 3t2o

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Magnesium binding site 7 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:14.8
occ:1.00
 O B:ASP15 2.1 14.7 1.0
OD2 B:ASP193 2.1 17.9 1.0
O B:ASN18 2.3 16.6 1.0
OE1 B:GLN163 2.3 17.7 1.0
O B:VAL21 2.3 16.6 1.0
CG B:ASP193 2.9 14.3 1.0
OD1 B:ASP193 3.1 17.7 1.0
CD B:GLN163 3.2 19.1 1.0
C B:ASN18 3.2 18.2 1.0
C B:ASP15 3.3 13.0 1.0
C B:VAL21 3.5 17.2 1.0
NE2 B:GLN163 3.6 17.5 1.0
N B:ASN18 3.7 17.6 1.0
CA B:ASN18 3.9 17.6 1.0
OH B:TYR161 3.9 15.0 1.0
CA B:TRP16 3.9 14.4 1.0
N B:TRP16 4.1 13.9 1.0
N B:PRO19 4.2 19.0 1.0
C B:TRP16 4.2 15.4 1.0
CB B:ASN18 4.2 16.6 1.0
CA B:VAL21 4.3 17.6 1.0
CE2 B:TYR161 4.4 13.7 1.0
CB B:VAL21 4.4 16.1 1.0
CB B:ASP193 4.4 12.0 1.0
N B:GLU17 4.4 16.3 1.0
N B:VAL21 4.4 19.1 1.0
CA B:PRO19 4.4 18.9 1.0
N B:THR22 4.5 15.5 1.0
CA B:ASP15 4.5 16.7 1.0
CG B:GLN163 4.5 17.8 1.0
CZ B:TYR161 4.6 16.4 1.0
CA B:THR22 4.6 16.7 1.0
O B:TRP16 4.8 14.8 1.0
C B:GLU17 4.8 18.2 1.0
CG1 B:VAL21 4.8 18.4 1.0
CB B:ASP15 4.9 14.2 1.0
C B:PRO19 4.9 20.1 1.0

Magnesium binding site 8 out of 16 in 3t2o

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Magnesium binding site 8 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:33.1
occ:1.00
 O B:HOH4924 2.2 18.4 1.0
O B:HOH4368 2.2 27.1 1.0
O B:HOH4579 2.2 27.6 1.0
O B:HOH4428 2.2 24.0 1.0
OE1 B:GLN718 2.3 22.0 1.0
O B:HOH4631 2.4 29.2 1.0
CD B:GLN718 3.2 19.1 1.0
NE2 B:GLN718 3.5 18.2 1.0
O B:THR911 4.1 14.2 1.0
O B:HOH4281 4.1 37.4 1.0
O B:HOH4413 4.1 29.0 1.0
NE2 B:HIS622 4.2 13.6 1.0
O B:DMS8020 4.3 48.0 1.0
C1 B:DMS8020 4.4 45.0 1.0
O B:GLN719 4.4 13.8 1.0
N B:GLN719 4.6 13.5 1.0
CG B:GLN718 4.6 12.3 1.0
O B:HOH4088 4.6 12.7 1.0
O B:HOH4257 4.6 19.3 1.0
CE1 B:HIS622 4.8 15.3 1.0
O B:HOH4244 4.8 40.4 1.0
S B:DMS8020 5.0 46.7 1.0

Magnesium binding site 9 out of 16 in 3t2o

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Magnesium binding site 9 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:13.4
occ:1.00
 ND1 C:HIS418 2.1 11.8 1.0
OE2 C:GLU416 2.1 13.8 1.0
OE1 C:GLU461 2.1 11.6 1.0
O C:HOH5123 2.1 11.3 1.0
O C:HOH4957 2.1 11.2 1.0
O C:HOH4032 2.3 12.1 1.0
CE1 C:HIS418 2.9 16.2 1.0
CG C:HIS418 3.1 11.5 1.0
CD C:GLU461 3.2 19.5 1.0
CD C:GLU416 3.2 14.7 1.0
CB C:HIS418 3.5 12.0 1.0
OE1 C:GLU416 3.7 11.8 1.0
OE2 C:GLU461 3.9 16.3 1.0
CB C:GLU461 4.0 11.1 1.0
NE2 C:HIS418 4.1 13.2 1.0
CG C:GLU461 4.1 9.8 1.0
OD1 C:ASN102 4.2 18.2 1.0
CD2 C:HIS418 4.2 13.8 1.0
O C:ASP199 4.3 11.6 1.0
O C:HOH4523 4.3 29.0 1.0
O C:HOH4020 4.3 17.1 1.0
CB C:ASP201 4.3 11.2 1.0
N C:ASP201 4.3 12.9 1.0
ND2 C:ASN460 4.4 11.9 1.0
CG C:GLU416 4.4 9.7 1.0
O C:HOH4309 4.6 23.7 1.0
O C:ASN102 4.7 15.8 1.0
CA C:ASP201 4.9 12.8 1.0
CG2 C:VAL103 4.9 17.2 1.0
CA C:HIS418 5.0 12.5 1.0
CA C:GLN200 5.0 13.8 1.0

Magnesium binding site 10 out of 16 in 3t2o

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Magnesium binding site 10 out of 16 in the E. Coli (Lacz) Beta-Galactosidase (S796D)


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

b:14.6
occ:1.00
 OD2 C:ASP193 2.1 20.9 1.0
O C:ASP15 2.1 14.8 1.0
O C:ASN18 2.3 16.1 1.0
OE1 C:GLN163 2.3 15.1 1.0
O C:VAL21 2.3 15.2 1.0
CG C:ASP193 2.9 15.2 1.0
OD1 C:ASP193 3.1 18.3 1.0
CD C:GLN163 3.2 16.7 1.0
C C:ASN18 3.2 16.1 1.0
C C:ASP15 3.3 14.8 1.0
C C:VAL21 3.4 13.8 1.0
NE2 C:GLN163 3.6 14.3 1.0
N C:ASN18 3.7 18.3 1.0
OH C:TYR161 3.9 15.5 1.0
CA C:ASN18 3.9 16.6 1.0
CA C:TRP16 4.0 14.4 1.0
N C:TRP16 4.1 14.3 1.0
N C:PRO19 4.2 17.1 1.0
C C:TRP16 4.2 15.6 1.0
CA C:VAL21 4.3 15.0 1.0
CE2 C:TYR161 4.3 10.1 1.0
CB C:ASN18 4.3 16.3 1.0
N C:VAL21 4.4 16.3 1.0
CB C:VAL21 4.4 15.7 1.0
CB C:ASP193 4.4 13.2 1.0
N C:GLU17 4.4 16.4 1.0
N C:THR22 4.4 12.8 1.0
CA C:PRO19 4.4 18.2 1.0
CA C:ASP15 4.5 16.4 1.0
CG C:GLN163 4.5 15.4 1.0
CZ C:TYR161 4.6 14.2 1.0
CA C:THR22 4.6 15.5 1.0
O C:TRP16 4.7 15.6 1.0
C C:GLU17 4.9 19.7 1.0
CB C:ASP15 4.9 14.2 1.0
CG1 C:VAL21 4.9 17.4 1.0
C C:PRO19 5.0 18.5 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 11:49:40 2024

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