Atomistry » Magnesium » PDB 3i5y-3ig8 » 3iaq
Atomistry »
  Magnesium »
    PDB 3i5y-3ig8 »
      3iaq »

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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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

Go back to Magnesium Binding Sites List in 3iaq
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: Wed Aug 14 16:01:35 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy