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Magnesium in PDB 3i3e: E. Coli (Lacz) Beta-Galactosidase (M542A)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (M542A):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A), PDB code: 3i3e was solved by M.L.Dugdale, D.Dymianiw, B.Minhas, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.70 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.701, 168.417, 200.709, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.1

Other elements in 3i3e:

The structure of E. Coli (Lacz) Beta-Galactosidase (M542A) also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (M542A) (pdb code 3i3e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (M542A), PDB code: 3i3e:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 3i3e

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Magnesium binding site 1 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:17.3
occ:1.00
 O A:HOH4078 2.1 9.5 1.0
OE2 A:GLU416 2.1 11.0 1.0
O A:HOH4156 2.2 12.4 1.0
OE1 A:GLU461 2.2 12.0 1.0
ND1 A:HIS418 2.3 12.1 1.0
O A:HOH4014 2.3 13.4 1.0
CE1 A:HIS418 3.1 14.1 1.0
CD A:GLU416 3.3 11.4 1.0
CD A:GLU461 3.3 13.3 1.0
CG A:HIS418 3.3 11.8 1.0
CB A:HIS418 3.7 10.2 1.0
OE1 A:GLU416 3.8 9.7 1.0
OE2 A:GLU461 3.9 12.8 1.0
OD1 A:ASN102 3.9 20.7 1.0
CB A:ASP201 4.1 17.3 1.0
N A:ASP201 4.2 14.0 1.0
O A:ASP199 4.3 17.2 1.0
CB A:GLU461 4.3 9.5 1.0
NE2 A:HIS418 4.3 12.8 1.0
CG A:GLU461 4.3 11.5 1.0
ND2 A:ASN460 4.4 8.3 1.0
CD2 A:HIS418 4.4 13.1 1.0
CG A:GLU416 4.5 10.7 1.0
O A:HOH7308 4.5 23.1 1.0
O A:ASN102 4.6 17.2 1.0
O A:HOH7309 4.7 40.7 1.0
O A:HOH4298 4.7 44.6 1.0
CA A:ASP201 4.7 15.1 1.0
CG2 A:VAL103 4.9 13.7 1.0
C A:GLN200 4.9 13.1 1.0
CA A:GLN200 5.0 11.7 1.0

Magnesium binding site 2 out of 15 in 3i3e

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Magnesium binding site 2 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:15.4
occ:1.00
 O A:ASP15 2.2 15.8 1.0
OE1 A:GLN163 2.2 14.4 1.0
O A:VAL21 2.3 15.2 1.0
O A:ASN18 2.3 16.1 1.0
OD2 A:ASP193 2.3 15.6 1.0
OD1 A:ASP193 3.0 13.2 1.0
CG A:ASP193 3.0 15.5 1.0
CD A:GLN163 3.2 14.4 1.0
C A:ASN18 3.2 16.4 1.0
C A:ASP15 3.4 15.9 1.0
C A:VAL21 3.4 14.7 1.0
NE2 A:GLN163 3.6 14.2 1.0
N A:ASN18 3.6 18.9 1.0
CA A:ASN18 3.9 17.6 1.0
OH A:TYR161 3.9 9.0 1.0
CA A:TRP16 4.0 16.7 1.0
N A:TRP16 4.2 16.1 1.0
C A:TRP16 4.2 16.6 1.0
N A:PRO19 4.2 16.0 1.0
CA A:VAL21 4.2 15.4 1.0
CB A:ASN18 4.2 17.3 1.0
CB A:VAL21 4.2 16.1 1.0
CE2 A:TYR161 4.3 12.3 1.0
N A:VAL21 4.3 15.8 1.0
N A:GLU17 4.4 16.9 1.0
N A:THR22 4.4 15.3 1.0
CB A:ASP193 4.5 12.6 1.0
CA A:ASP15 4.5 17.4 1.0
CG A:GLN163 4.5 12.4 1.0
CA A:PRO19 4.5 14.0 1.0
CZ A:TYR161 4.6 10.0 1.0
CA A:THR22 4.6 15.4 1.0
O A:TRP16 4.7 15.7 1.0
CG1 A:VAL21 4.8 14.6 1.0
C A:GLU17 4.8 19.0 1.0
CB A:ASP15 4.8 16.3 1.0
C A:PRO19 4.9 14.9 1.0

Magnesium binding site 3 out of 15 in 3i3e

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Magnesium binding site 3 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:56.9
occ:1.00
 O A:HOH4649 2.2 35.5 1.0
OE1 A:GLN718 2.3 21.1 1.0
O A:HOH4268 2.3 29.2 1.0
O A:HOH4384 2.3 38.5 1.0
O A:HOH4450 2.4 44.9 1.0
O A:HOH4721 2.7 50.1 1.0
CD A:GLN718 3.3 19.3 1.0
NE2 A:GLN718 3.7 17.6 1.0
O A:THR911 4.1 12.7 1.0
NE2 A:HIS622 4.2 15.3 1.0
C2 A:DMS8427 4.3 84.4 1.0
O A:HOH4433 4.3 45.6 1.0
O A:GLN719 4.5 11.7 1.0
O A:HOH4284 4.5 39.1 1.0
N A:GLN719 4.7 11.8 1.0
O A:HOH4258 4.7 21.7 1.0
CG A:GLN718 4.7 15.4 1.0
O A:HOH4080 4.7 13.4 1.0
O A:HOH7352 4.7 46.9 1.0
O A:DMS8427 4.8 84.2 1.0
CE1 A:HIS622 4.9 13.8 1.0

Magnesium binding site 4 out of 15 in 3i3e

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Magnesium binding site 4 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3009

b:43.9
occ:1.00
 O A:HOH5173 2.4 25.2 1.0
O A:HOH4674 2.5 25.3 1.0
O A:HOH5175 2.7 45.0 1.0
O A:HOH7017 2.8 38.1 1.0
O A:HOH4706 4.1 39.5 1.0
O A:HOH7401 4.1 69.3 1.0
O A:HOH4736 4.2 32.5 1.0
OE2 A:GLU314 4.5 14.7 1.0
OE1 A:GLU314 4.5 13.5 1.0
CD A:GLU314 5.0 14.1 1.0

Magnesium binding site 5 out of 15 in 3i3e

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Magnesium binding site 5 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:40.7
occ:1.00
 O A:HOH7323 2.2 73.2 1.0
O A:HOH7322 2.8 60.5 1.0
O A:HOH7321 3.5 33.2 1.0
OE1 A:GLU136 4.3 33.5 1.0
O A:HOH5134 4.5 33.2 1.0
CB A:GLN135 4.5 28.7 1.0
OE1 A:GLN135 4.8 41.1 1.0

Magnesium binding site 6 out of 15 in 3i3e

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Magnesium binding site 6 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:14.4
occ:1.00
 OE1 B:GLU461 2.0 13.2 1.0
OE2 B:GLU416 2.1 8.6 1.0
O B:HOH4156 2.2 9.8 1.0
O B:HOH4078 2.2 11.9 1.0
ND1 B:HIS418 2.3 10.9 1.0
O B:HOH4014 2.4 11.5 1.0
CD B:GLU461 3.1 11.1 1.0
CE1 B:HIS418 3.2 11.5 1.0
CD B:GLU416 3.2 8.3 1.0
CG B:HIS418 3.3 8.9 1.0
CB B:HIS418 3.6 10.2 1.0
OE2 B:GLU461 3.7 11.8 1.0
OE1 B:GLU416 3.8 8.0 1.0
OD1 B:ASN102 4.1 18.3 1.0
CG B:GLU461 4.1 9.2 1.0
CB B:GLU461 4.1 7.1 1.0
O B:ASP199 4.3 11.5 1.0
CB B:ASP201 4.3 15.7 1.0
N B:ASP201 4.3 13.2 1.0
ND2 B:ASN460 4.3 4.0 1.0
NE2 B:HIS418 4.3 10.8 1.0
CD2 B:HIS418 4.4 10.8 1.0
CG B:GLU416 4.4 9.9 1.0
O B:HOH7190 4.5 25.0 1.0
O B:HOH7189 4.7 35.1 1.0
O B:ASN102 4.7 15.0 1.0
O B:HOH7191 4.8 25.9 1.0
O B:HOH7193 4.8 47.9 1.0
CA B:ASP201 4.9 14.6 1.0

Magnesium binding site 7 out of 15 in 3i3e

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Magnesium binding site 7 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:11.5
occ:1.00
 OE1 B:GLN163 2.2 13.5 1.0
OD2 B:ASP193 2.2 13.0 1.0
O B:ASP15 2.3 10.2 1.0
O B:ASN18 2.4 13.6 1.0
O B:VAL21 2.4 13.8 1.0
OD1 B:ASP193 2.9 13.7 1.0
CG B:ASP193 2.9 13.7 1.0
CD B:GLN163 3.2 11.2 1.0
C B:ASN18 3.2 14.9 1.0
C B:ASP15 3.5 13.0 1.0
NE2 B:GLN163 3.5 7.5 1.0
C B:VAL21 3.5 14.0 1.0
N B:ASN18 3.6 15.0 1.0
CA B:ASN18 3.9 15.2 1.0
OH B:TYR161 3.9 11.7 1.0
CA B:TRP16 4.0 11.8 1.0
N B:PRO19 4.2 15.9 1.0
N B:TRP16 4.2 11.9 1.0
C B:TRP16 4.2 12.8 1.0
CE2 B:TYR161 4.3 10.6 1.0
CB B:ASN18 4.3 14.4 1.0
N B:GLU17 4.3 12.5 1.0
CA B:VAL21 4.3 16.0 1.0
CB B:VAL21 4.4 16.1 1.0
CB B:ASP193 4.4 10.5 1.0
N B:VAL21 4.4 16.0 1.0
CA B:PRO19 4.5 16.6 1.0
N B:THR22 4.5 13.7 1.0
CG B:GLN163 4.5 10.6 1.0
CZ B:TYR161 4.6 12.4 1.0
CA B:ASP15 4.6 14.8 1.0
CA B:THR22 4.6 14.0 1.0
O B:TRP16 4.8 11.5 1.0
C B:GLU17 4.8 15.1 1.0
CG1 B:VAL21 4.9 16.3 1.0
C B:PRO19 4.9 16.5 1.0
CB B:ASP15 5.0 13.8 1.0

Magnesium binding site 8 out of 15 in 3i3e

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Magnesium binding site 8 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:38.0
occ:1.00
 O B:HOH4649 2.1 27.7 1.0
O B:HOH4268 2.3 17.1 1.0
O B:HOH4450 2.3 34.5 1.0
O B:HOH4384 2.3 20.4 1.0
OE1 B:GLN718 2.5 18.9 1.0
O B:HOH4721 2.6 23.8 1.0
CD B:GLN718 3.4 17.4 1.0
NE2 B:GLN718 3.6 16.5 1.0
O B:THR911 4.0 10.8 1.0
NE2 B:HIS622 4.3 9.0 1.0
O B:HOH4284 4.3 28.9 1.0
C1 B:DMS8427 4.3 53.0 1.0
O B:HOH4433 4.4 24.8 1.0
O B:DMS8427 4.5 53.1 1.0
O B:HOH4080 4.5 7.9 1.0
O B:HOH4258 4.6 19.6 1.0
O B:GLN719 4.7 13.1 1.0
O B:HOH4244 4.7 31.3 1.0
N B:GLN719 4.8 10.8 1.0
CG B:GLN718 4.8 12.3 1.0
C B:THR911 4.9 11.3 1.0
CA B:THR911 4.9 10.1 1.0
CB B:THR911 4.9 9.8 1.0
CE1 B:HIS622 4.9 8.8 1.0
S B:DMS8427 5.0 54.4 1.0

Magnesium binding site 9 out of 15 in 3i3e

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Magnesium binding site 9 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:14.6
occ:1.00
 OE1 C:GLU461 2.0 7.8 1.0
OE2 C:GLU416 2.0 13.2 1.0
O C:HOH4156 2.2 6.2 1.0
O C:HOH4014 2.3 14.7 1.0
ND1 C:HIS418 2.3 11.5 1.0
O C:HOH4078 2.4 13.3 1.0
CD C:GLU461 3.1 11.6 1.0
CD C:GLU416 3.1 7.9 1.0
CE1 C:HIS418 3.3 11.6 1.0
CG C:HIS418 3.3 8.4 1.0
CB C:HIS418 3.6 9.8 1.0
OE1 C:GLU416 3.6 7.8 1.0
OE2 C:GLU461 3.9 10.1 1.0
CB C:GLU461 4.1 7.0 1.0
CG C:GLU461 4.1 7.6 1.0
OD1 C:ASN102 4.2 20.2 1.0
ND2 C:ASN460 4.2 5.6 1.0
O C:ASP199 4.3 8.7 1.0
N C:ASP201 4.3 11.8 1.0
CG C:GLU416 4.3 8.7 1.0
CB C:ASP201 4.3 12.7 1.0
O C:HOH7251 4.4 16.7 1.0
NE2 C:HIS418 4.4 7.5 1.0
CD2 C:HIS418 4.5 9.9 1.0
O C:HOH7250 4.6 48.1 1.0
O C:ASN102 4.8 16.3 1.0
CA C:ASP201 4.9 12.2 1.0
CA C:GLN200 5.0 11.0 1.0
O C:HOH7252 5.0 32.4 1.0
C C:GLN200 5.0 11.4 1.0

Magnesium binding site 10 out of 15 in 3i3e

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Magnesium binding site 10 out of 15 in the E. Coli (Lacz) Beta-Galactosidase (M542A)


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 (M542A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:13.6
occ:1.00
 O C:VAL21 2.2 11.0 1.0
O C:ASP15 2.3 11.9 1.0
O C:ASN18 2.3 13.4 1.0
OE1 C:GLN163 2.4 15.7 1.0
OD2 C:ASP193 2.4 13.0 1.0
OD1 C:ASP193 3.1 16.4 1.0
CG C:ASP193 3.1 13.5 1.0
C C:ASN18 3.2 15.0 1.0
CD C:GLN163 3.3 15.3 1.0
C C:VAL21 3.3 12.1 1.0
C C:ASP15 3.5 13.4 1.0
NE2 C:GLN163 3.6 11.8 1.0
N C:ASN18 3.7 14.5 1.0
CA C:ASN18 3.9 13.4 1.0
OH C:TYR161 4.0 14.6 1.0
CA C:TRP16 4.1 11.9 1.0
CA C:VAL21 4.1 12.6 1.0
CB C:VAL21 4.1 13.0 1.0
N C:PRO19 4.2 14.5 1.0
N C:VAL21 4.2 12.7 1.0
N C:TRP16 4.2 11.7 1.0
CB C:ASN18 4.3 14.2 1.0
CE2 C:TYR161 4.3 11.1 1.0
C C:TRP16 4.3 13.1 1.0
N C:THR22 4.3 12.3 1.0
CA C:PRO19 4.4 14.9 1.0
N C:GLU17 4.4 14.7 1.0
CA C:THR22 4.5 13.8 1.0
CG C:GLN163 4.5 13.6 1.0
CA C:ASP15 4.6 14.4 1.0
CB C:ASP193 4.6 12.7 1.0
CZ C:TYR161 4.6 11.1 1.0
CG1 C:VAL21 4.7 12.1 1.0
C C:PRO19 4.9 14.2 1.0
O C:TRP16 4.9 12.5 1.0
C C:GLU17 4.9 15.3 1.0
CB C:ASP15 5.0 13.7 1.0

Reference:

M.L.Dugdale, D.L.Dymianiw, B.K.Minhas, I.D'angelo, R.E.Huber. Role of Met-542 As A Guide For the Conformational Changes of Phe-601 That Occur During the Reaction of β-Galactosidase (Escherichia Coli). Biochem.Cell Biol. V. 88 861 2010.
ISSN: ISSN 0829-8211
PubMed: 20921997
DOI: 10.1139/O10-009
Page generated: Mon Dec 14 08:15:26 2020

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