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Magnesium in PDB 3iaq: E. Coli (Lacz) Beta-Galactosidase (E416V)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E416V)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E416V):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E416V), PDB code: 3iaq was solved by S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 83.33 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.380, 168.300, 200.730, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 25.3

Other elements in 3iaq:

The structure of E. Coli (Lacz) Beta-Galactosidase (E416V) also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (E416V) (pdb code 3iaq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (E416V), PDB code: 3iaq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 3iaq

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Magnesium binding site 1 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:28.1
occ:1.00
 O A:ASP15 2.1 26.6 1.0
O A:ASN18 2.2 23.6 1.0
OE1 A:GLN163 2.3 19.2 1.0
O A:VAL21 2.3 19.2 1.0
OD2 A:ASP193 2.4 22.5 1.0
CG A:ASP193 3.1 20.3 1.0
OD1 A:ASP193 3.2 24.4 1.0
C A:ASN18 3.2 23.4 1.0
C A:ASP15 3.3 25.7 1.0
CD A:GLN163 3.3 17.9 1.0
C A:VAL21 3.5 18.9 1.0
N A:ASN18 3.7 22.9 1.0
NE2 A:GLN163 3.8 16.7 1.0
CA A:ASN18 3.9 23.2 1.0
OH A:TYR161 4.0 15.6 1.0
CA A:TRP16 4.0 21.3 1.0
N A:TRP16 4.1 23.6 1.0
CB A:ASN18 4.2 23.3 1.0
CA A:VAL21 4.2 19.3 1.0
CB A:VAL21 4.2 19.0 1.0
CE1 A:TYR161 4.2 15.7 1.0
C A:TRP16 4.3 21.7 1.0
N A:PRO19 4.3 23.2 1.0
N A:VAL21 4.3 20.8 1.0
CA A:ASP15 4.4 26.5 1.0
N A:GLU17 4.4 22.0 1.0
N A:THR22 4.5 18.1 1.0
CA A:PRO19 4.5 23.9 1.0
CZ A:TYR161 4.6 16.7 1.0
CB A:ASP193 4.6 18.8 1.0
CG A:GLN163 4.6 14.5 1.0
CG1 A:VAL21 4.7 17.2 1.0
CA A:THR22 4.8 17.5 1.0
CB A:ASP15 4.8 26.6 1.0
O A:TRP16 4.8 23.1 1.0
C A:GLU17 4.9 22.7 1.0

Magnesium binding site 2 out of 13 in 3iaq

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Magnesium binding site 2 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:48.8
occ:1.00
 O A:ASN597 2.5 35.1 1.0
N A:ASN597 3.1 36.9 1.0
O A:HOH4283 3.3 27.6 1.0
C A:ASN597 3.4 35.0 1.0
CB A:PRO596 3.6 39.1 1.0
C A:PRO596 3.8 37.3 1.0
CA A:ASN597 3.8 36.1 1.0
CA A:PRO596 3.8 38.5 1.0
O A:HOH4348 4.2 23.6 1.0
N A:ASP598 4.5 34.7 1.0
O A:HOH4265 4.7 16.1 1.0
OD1 A:ASP598 4.8 36.4 1.0
CG A:ASN597 4.9 36.1 1.0
O A:PRO596 4.9 36.8 1.0
CA A:ASP598 4.9 34.2 1.0
CG A:PRO596 5.0 38.7 1.0
CB A:ASN597 5.0 35.8 1.0

Magnesium binding site 3 out of 13 in 3iaq

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Magnesium binding site 3 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:45.5
occ:1.00
 OE1 A:GLN718 2.8 16.3 1.0
CD A:GLN718 3.5 18.3 1.0
O A:HOH4188 3.6 16.5 1.0
NE2 A:GLN718 3.9 20.6 1.0
O A:GLN719 4.1 20.5 1.0
CG A:GLN718 4.5 16.3 1.0
O A:HOH4233 4.5 14.6 1.0
O A:HOH4059 4.8 11.9 1.0

Magnesium binding site 4 out of 13 in 3iaq

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Magnesium binding site 4 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3004

b:36.7
occ:1.00
 O A:HOH4333 3.9 11.5 1.0
OE1 A:GLU314 4.0 25.2 1.0
OE2 A:GLU314 4.6 26.4 1.0
O A:HOH4312 4.7 29.9 1.0
CD A:GLU314 4.8 23.0 1.0
OE1 A:GLN266 4.9 16.0 1.0

Magnesium binding site 5 out of 13 in 3iaq

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Magnesium binding site 5 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:23.1
occ:1.00
 O B:ASP15 2.0 21.6 1.0
OD2 B:ASP193 2.0 22.8 1.0
OE1 B:GLN163 2.2 22.7 1.0
O B:ASN18 2.6 15.1 1.0
O B:VAL21 2.6 24.8 1.0
CG B:ASP193 3.1 18.8 1.0
C B:ASP15 3.2 21.6 1.0
CD B:GLN163 3.3 24.8 1.0
C B:ASN18 3.5 16.6 1.0
N B:ASN18 3.6 16.7 1.0
OH B:TYR161 3.6 17.4 1.0
NE2 B:GLN163 3.6 26.2 1.0
OD1 B:ASP193 3.7 22.9 1.0
CA B:TRP16 3.7 18.8 1.0
C B:VAL21 3.7 23.6 1.0
N B:TRP16 3.9 20.1 1.0
C B:TRP16 3.9 18.6 1.0
CA B:ASN18 3.9 16.5 1.0
N B:GLU17 4.2 18.4 1.0
CE1 B:TYR161 4.2 14.9 1.0
CB B:ASN18 4.2 17.2 1.0
CA B:ASP15 4.3 23.0 1.0
O B:TRP16 4.4 19.1 1.0
CZ B:TYR161 4.4 16.4 1.0
CB B:ASP193 4.4 15.5 1.0
N B:PRO19 4.5 17.3 1.0
CG B:GLN163 4.6 20.6 1.0
CA B:VAL21 4.6 23.8 1.0
N B:THR22 4.6 23.4 1.0
CA B:THR22 4.7 22.1 1.0
C B:GLU17 4.7 17.8 1.0
CB B:VAL21 4.7 23.8 1.0
CB B:ASP15 4.8 23.3 1.0
N B:VAL21 4.8 23.2 1.0
CA B:GLU17 4.9 18.1 1.0
CA B:PRO19 4.9 18.4 1.0

Magnesium binding site 6 out of 13 in 3iaq

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Magnesium binding site 6 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:91.6
occ:1.00
 O B:HOH4495 2.0 29.3 1.0
O B:HOH4468 2.6 16.7 1.0
OE1 B:GLU369 3.2 35.9 1.0
O B:HOH4330 3.7 2.0 1.0
CD B:GLU369 4.1 30.7 1.0
OE2 B:GLU369 4.4 29.3 1.0

Magnesium binding site 7 out of 13 in 3iaq

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Magnesium binding site 7 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3003

b:42.5
occ:1.00
 O B:HOH4281 2.8 26.7 1.0
O B:HOH4222 2.9 28.0 1.0
O B:ASN597 2.9 27.9 1.0
N B:ASN597 3.2 29.4 1.0
CB B:PRO596 3.6 31.3 1.0
CA B:PRO596 3.7 31.4 1.0
C B:ASN597 3.9 28.4 1.0
C B:PRO596 3.9 31.1 1.0
O B:HOH4628 4.0 24.3 1.0
CA B:ASN597 4.1 28.4 1.0
ND2 B:ASN597 4.6 24.6 1.0
CG B:ASN597 4.6 26.5 1.0
O B:HOH4283 4.8 28.6 1.0
OD1 B:ASN597 4.9 24.4 1.0
CG B:PRO596 4.9 30.4 1.0
CB B:ASN597 5.0 27.3 1.0

Magnesium binding site 8 out of 13 in 3iaq

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Magnesium binding site 8 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3004

b:57.0
occ:1.00
 OE1 B:GLN718 2.7 25.8 1.0
O B:THR911 3.1 18.7 1.0
O B:HOH4186 3.1 15.1 1.0
NE2 B:HIS622 3.2 7.7 1.0
CD B:GLN718 3.6 23.3 1.0
NE2 B:GLN718 3.8 22.5 1.0
C B:THR911 4.0 16.8 1.0
CE1 B:HIS622 4.0 10.9 1.0
CA B:THR911 4.1 16.3 1.0
CB B:THR911 4.2 15.7 1.0
CD2 B:HIS622 4.3 7.7 1.0
O B:DMS7017 4.3 45.3 1.0
O B:HOH4055 4.5 8.7 1.0
CG2 B:THR911 5.0 8.8 1.0

Magnesium binding site 9 out of 13 in 3iaq

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Magnesium binding site 9 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:16.9
occ:1.00
 O C:VAL21 2.2 19.0 1.0
O C:ASP15 2.2 22.1 1.0
O C:ASN18 2.2 19.8 1.0
OE1 C:GLN163 2.3 17.8 1.0
OD2 C:ASP193 2.5 20.2 1.0
OD1 C:ASP193 3.1 19.1 1.0
CG C:ASP193 3.2 19.0 1.0
C C:ASN18 3.2 19.1 1.0
C C:VAL21 3.3 18.3 1.0
CD C:GLN163 3.3 16.4 1.0
C C:ASP15 3.3 22.5 1.0
N C:ASN18 3.7 17.1 1.0
NE2 C:GLN163 3.7 14.0 1.0
CA C:ASN18 3.9 18.5 1.0
CA C:VAL21 4.0 18.8 1.0
OH C:TYR161 4.0 18.3 1.0
CB C:VAL21 4.1 20.1 1.0
CA C:TRP16 4.1 18.9 1.0
N C:TRP16 4.1 21.4 1.0
N C:VAL21 4.1 20.3 1.0
N C:PRO19 4.2 18.6 1.0
CB C:ASN18 4.3 18.6 1.0
N C:THR22 4.3 17.8 1.0
C C:TRP16 4.3 17.7 1.0
CE1 C:TYR161 4.4 20.2 1.0
CA C:PRO19 4.4 18.2 1.0
N C:GLU17 4.4 16.8 1.0
CA C:ASP15 4.4 23.9 1.0
CG1 C:VAL21 4.5 19.4 1.0
CA C:THR22 4.6 16.4 1.0
CG C:GLN163 4.6 14.4 1.0
CB C:ASP193 4.6 17.1 1.0
CZ C:TYR161 4.7 18.2 1.0
CB C:ASP15 4.8 24.4 1.0
C C:GLU17 4.9 17.9 1.0
C C:PRO19 4.9 18.5 1.0
O C:TRP16 5.0 18.0 1.0

Magnesium binding site 10 out of 13 in 3iaq

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Magnesium binding site 10 out of 13 in the E. Coli (Lacz) Beta-Galactosidase (E416V)


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 (E416V) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:45.9
occ:1.00
 O C:HOH4295 2.7 44.0 1.0
O C:ASN597 2.7 20.9 1.0
N C:ASN597 3.5 23.5 1.0
CB C:PRO596 3.6 25.4 1.0
C C:ASN597 3.7 21.5 1.0
CA C:PRO596 4.1 25.1 1.0
C C:PRO596 4.2 24.3 1.0
CA C:ASN597 4.2 22.2 1.0
N C:ASP598 4.9 22.3 1.0
CG C:ASN597 5.0 20.5 1.0

Reference:

S.Lo, M.L.Dugdale, N.Jeerh, T.Ku, N.J.Roth, R.E.Huber. Studies of Glu-416 Variants of Beta-Galactosidase (E. Coli) Show That the Active Site Mg(2+) Is Not Important For Structure and Indicate That the Main Role of Mg (2+) Is to Mediate Optimization of Active Site Chemistry Protein J. V. 29 26 2010.
ISSN: ISSN 1572-3887
PubMed: 19936901
DOI: 10.1007/S10930-009-9216-X
Page generated: Mon Dec 14 08:16:34 2020

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