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Magnesium in PDB 4dux: E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose, PDB code: 4dux was solved by R.W.Wheatley, S.Lo, L.J.Janzcewicz, M.L.Dugdale, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 86.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 150.648, 168.103, 201.881, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22.1

Other elements in 4dux:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose also contains other interesting chemical elements:

Sodium (Na) 14 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose (pdb code 4dux). 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 (N460S) in Complex with L-Ribose, PDB code: 4dux:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 4dux

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:27.4
occ:1.00
 O A:HOH4634 2.0 21.4 1.0
OE2 A:GLU461 2.1 25.4 1.0
OE2 A:GLU416 2.1 25.7 1.0
O A:HOH4635 2.1 26.2 1.0
O A:HOH4143 2.2 27.3 1.0
ND1 A:HIS418 2.4 25.3 1.0
CD A:GLU416 3.1 19.9 1.0
CE1 A:HIS418 3.2 27.7 1.0
CD A:GLU461 3.2 28.1 1.0
CG A:HIS418 3.5 27.4 1.0
OE1 A:GLU416 3.6 24.2 1.0
CB A:HIS418 3.8 25.5 1.0
OE1 A:GLU461 4.0 31.0 1.0
N A:ASP201 4.0 27.1 1.0
O2 A:0MK2001 4.1 19.6 1.0
CB A:ASP201 4.1 27.3 1.0
OD1 A:ASN102 4.1 25.6 1.0
CB A:GLU461 4.2 18.4 1.0
CG A:GLU461 4.2 26.5 1.0
O A:ASP199 4.3 24.0 1.0
O3 A:0MK2001 4.3 22.2 1.0
NE2 A:HIS418 4.4 22.6 1.0
CG A:GLU416 4.4 20.4 1.0
C1 A:0MK2001 4.5 20.4 1.0
CD2 A:HIS418 4.5 30.8 1.0
CA A:ASP201 4.7 25.2 1.0
O1 A:0MK2001 4.7 28.4 1.0
O A:ASN102 4.8 26.3 1.0
CA A:GLN200 4.8 23.9 1.0
C2 A:0MK2001 4.8 24.9 1.0
C A:GLN200 4.8 26.2 1.0
OG A:SER460 4.9 23.6 1.0

Magnesium binding site 2 out of 8 in 4dux

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:29.5
occ:1.00
 OD2 A:ASP193 2.1 25.2 1.0
O A:ASN18 2.3 31.9 1.0
OE1 A:GLN163 2.3 30.6 1.0
O A:ASP15 2.3 31.7 1.0
O A:VAL21 2.3 29.9 1.0
CG A:ASP193 2.9 30.9 1.0
OD1 A:ASP193 3.0 31.9 1.0
CD A:GLN163 3.2 27.2 1.0
C A:ASN18 3.2 33.3 1.0
C A:VAL21 3.4 29.4 1.0
C A:ASP15 3.5 34.0 1.0
NE2 A:GLN163 3.5 31.4 1.0
N A:ASN18 3.6 34.5 1.0
CA A:ASN18 3.9 34.8 1.0
OH A:TYR161 4.1 25.3 1.0
CA A:TRP16 4.1 32.0 1.0
N A:PRO19 4.1 31.0 1.0
N A:TRP16 4.2 32.3 1.0
CA A:VAL21 4.3 28.5 1.0
CB A:ASN18 4.3 33.0 1.0
C A:TRP16 4.3 28.9 1.0
N A:GLU17 4.3 30.6 1.0
CA A:PRO19 4.3 31.7 1.0
N A:VAL21 4.3 30.9 1.0
CB A:ASP193 4.3 28.0 1.0
CB A:VAL21 4.4 32.0 1.0
N A:THR22 4.4 28.8 1.0
CE2 A:TYR161 4.4 21.9 1.0
CG A:GLN163 4.5 24.2 1.0
CA A:THR22 4.6 28.2 1.0
CA A:ASP15 4.6 34.3 1.0
CZ A:TYR161 4.7 26.2 1.0
C A:GLU17 4.8 32.9 1.0
CG1 A:VAL21 4.8 24.2 1.0
C A:PRO19 4.8 32.0 1.0
O A:TRP16 5.0 30.6 1.0

Magnesium binding site 3 out of 8 in 4dux

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:30.0
occ:1.00
 O B:HOH4568 1.9 28.3 1.0
OE2 B:GLU461 2.1 31.2 1.0
OE2 B:GLU416 2.1 27.6 1.0
O B:HOH4032 2.1 27.6 1.0
O B:HOH4159 2.3 24.2 1.0
ND1 B:HIS418 2.4 29.5 1.0
CD B:GLU461 3.2 32.1 1.0
CE1 B:HIS418 3.2 27.4 1.0
CD B:GLU416 3.2 30.1 1.0
CG B:HIS418 3.5 25.5 1.0
OE1 B:GLU416 3.7 32.7 1.0
OE1 B:GLU461 3.8 28.7 1.0
CB B:HIS418 3.9 25.1 1.0
CB B:ASP201 4.0 28.9 1.0
N B:ASP201 4.0 27.6 1.0
OD1 B:ASN102 4.0 22.9 1.0
O2 B:0MK2001 4.1 24.6 1.0
O3 B:0MK2001 4.2 25.9 1.0
CG B:GLU461 4.2 29.9 1.0
CB B:GLU461 4.2 28.1 1.0
O B:ASP199 4.3 23.7 1.0
NE2 B:HIS418 4.4 30.0 1.0
CG B:GLU416 4.4 27.4 1.0
C1 B:0MK2001 4.5 24.8 1.0
CD2 B:HIS418 4.5 20.6 1.0
CA B:ASP201 4.6 29.0 1.0
O1 B:0MK2001 4.7 29.0 1.0
O B:ASN102 4.7 25.2 1.0
C B:GLN200 4.8 28.2 1.0
C2 B:0MK2001 4.8 25.0 1.0
CA B:GLN200 4.9 25.5 1.0
C5 B:0MK2002 4.9 83.5 1.0

Magnesium binding site 4 out of 8 in 4dux

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:34.7
occ:1.00
 OD2 B:ASP193 2.1 33.3 1.0
O B:ASN18 2.3 34.5 1.0
OE1 B:GLN163 2.3 33.5 1.0
O B:ASP15 2.3 36.9 1.0
O B:VAL21 2.3 31.4 1.0
CG B:ASP193 2.9 33.2 1.0
OD1 B:ASP193 3.1 29.9 1.0
C B:ASN18 3.1 35.7 1.0
CD B:GLN163 3.2 36.0 1.0
C B:ASP15 3.5 38.5 1.0
C B:VAL21 3.5 33.9 1.0
NE2 B:GLN163 3.6 33.1 1.0
N B:ASN18 3.6 35.8 1.0
CA B:ASN18 3.8 36.0 1.0
OH B:TYR161 4.0 30.4 1.0
CA B:TRP16 4.1 37.5 1.0
N B:PRO19 4.1 35.8 1.0
N B:TRP16 4.2 36.8 1.0
C B:TRP16 4.2 36.8 1.0
CB B:ASN18 4.3 34.2 1.0
CA B:VAL21 4.3 32.2 1.0
CB B:ASP193 4.3 28.3 1.0
CA B:PRO19 4.4 37.8 1.0
N B:VAL21 4.4 36.2 1.0
CB B:VAL21 4.4 34.7 1.0
N B:GLU17 4.4 38.1 1.0
CE2 B:TYR161 4.5 24.9 1.0
N B:THR22 4.5 34.7 1.0
CG B:GLN163 4.6 33.9 1.0
CA B:ASP15 4.6 40.2 1.0
CA B:THR22 4.6 36.8 1.0
CZ B:TYR161 4.7 28.2 1.0
O B:TRP16 4.8 37.1 1.0
C B:GLU17 4.8 38.3 1.0
C B:PRO19 4.9 37.8 1.0
CB B:ASP15 5.0 40.0 1.0
CG1 B:VAL21 5.0 30.2 1.0

Magnesium binding site 5 out of 8 in 4dux

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:29.8
occ:1.00
 O C:HOH4633 2.0 29.6 1.0
OE2 C:GLU416 2.1 25.8 1.0
OE2 C:GLU461 2.1 28.6 1.0
O C:HOH4632 2.2 22.0 1.0
O C:HOH4631 2.2 25.4 1.0
ND1 C:HIS418 2.4 30.1 1.0
CD C:GLU416 3.2 30.8 1.0
CD C:GLU461 3.2 26.0 1.0
CE1 C:HIS418 3.2 27.1 1.0
CG C:HIS418 3.5 27.6 1.0
OE1 C:GLU416 3.6 29.8 1.0
CB C:HIS418 3.8 26.6 1.0
OE1 C:GLU461 3.9 27.2 1.0
OD1 C:ASN102 4.0 30.3 1.0
CB C:ASP201 4.1 30.0 1.0
N C:ASP201 4.1 29.0 1.0
O2 C:0MK2001 4.1 25.5 1.0
CG C:GLU461 4.2 25.0 1.0
CB C:GLU461 4.2 25.4 1.0
O C:ASP199 4.3 25.6 1.0
O3 C:0MK2001 4.3 25.0 1.0
NE2 C:HIS418 4.4 31.1 1.0
CG C:GLU416 4.4 23.9 1.0
CD2 C:HIS418 4.5 28.6 1.0
C1 C:0MK2001 4.5 24.7 1.0
CA C:ASP201 4.7 29.0 1.0
O C:ASN102 4.7 33.5 1.0
O1 C:0MK2001 4.8 25.1 1.0
C2 C:0MK2001 4.8 28.4 1.0
C C:GLN200 4.8 28.0 1.0
CA C:GLN200 4.9 25.5 1.0

Magnesium binding site 6 out of 8 in 4dux

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:39.7
occ:1.00
 OD2 C:ASP193 2.1 39.3 1.0
O C:ASN18 2.3 40.9 1.0
O C:VAL21 2.3 35.5 1.0
O C:ASP15 2.3 44.7 1.0
OE1 C:GLN163 2.3 36.2 1.0
CG C:ASP193 2.9 36.8 1.0
OD1 C:ASP193 2.9 40.7 1.0
CD C:GLN163 3.2 32.7 1.0
C C:ASN18 3.2 40.4 1.0
C C:ASP15 3.5 43.9 1.0
C C:VAL21 3.5 36.8 1.0
NE2 C:GLN163 3.5 33.6 1.0
N C:ASN18 3.6 39.4 1.0
CA C:ASN18 3.9 40.1 1.0
OH C:TYR161 4.0 32.9 1.0
CA C:TRP16 4.0 39.0 1.0
N C:PRO19 4.1 39.0 1.0
N C:TRP16 4.2 41.2 1.0
C C:TRP16 4.2 40.2 1.0
CB C:ASP193 4.3 34.0 1.0
CB C:ASN18 4.3 39.4 1.0
CE2 C:TYR161 4.3 20.4 1.0
CA C:VAL21 4.3 36.1 1.0
N C:VAL21 4.4 35.4 1.0
N C:GLU17 4.5 39.4 1.0
N C:THR22 4.5 35.5 1.0
CA C:PRO19 4.5 40.1 1.0
CG C:GLN163 4.5 31.5 1.0
CA C:THR22 4.6 34.7 1.0
CB C:VAL21 4.6 40.1 1.0
CA C:ASP15 4.6 45.5 1.0
CZ C:TYR161 4.7 31.5 1.0
O C:TRP16 4.8 39.7 1.0
C C:GLU17 4.8 41.6 1.0
C C:PRO19 5.0 40.6 1.0

Magnesium binding site 7 out of 8 in 4dux

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:29.1
occ:1.00
 OE2 D:GLU461 2.1 23.3 1.0
OE2 D:GLU416 2.1 26.5 1.0
O D:HOH4185 2.1 20.1 1.0
O D:HOH4658 2.1 20.3 1.0
O D:HOH4659 2.2 18.4 1.0
ND1 D:HIS418 2.4 25.9 1.0
CD D:GLU416 3.2 21.3 1.0
CD D:GLU461 3.2 24.5 1.0
CE1 D:HIS418 3.3 25.5 1.0
CG D:HIS418 3.4 22.7 1.0
OE1 D:GLU416 3.7 23.6 1.0
CB D:HIS418 3.7 20.1 1.0
OD1 D:ASN102 4.0 31.8 1.0
OE1 D:GLU461 4.0 24.6 1.0
N D:ASP201 4.1 25.2 1.0
CB D:ASP201 4.1 25.0 1.0
O2 D:0MK2001 4.2 29.1 1.0
CB D:GLU461 4.2 21.3 1.0
CG D:GLU461 4.2 22.9 1.0
O D:ASP199 4.3 25.0 1.0
O3 D:0MK2001 4.3 24.3 1.0
CG D:GLU416 4.4 22.4 1.0
NE2 D:HIS418 4.4 20.6 1.0
CD2 D:HIS418 4.5 22.2 1.0
C1 D:0MK2001 4.7 27.7 1.0
CA D:ASP201 4.7 22.5 1.0
O D:ASN102 4.7 25.9 1.0
C D:GLN200 4.8 23.7 1.0
CA D:GLN200 4.8 23.2 1.0
O1 D:0MK2001 4.9 26.1 1.0
C2 D:0MK2001 4.9 28.0 1.0

Magnesium binding site 8 out of 8 in 4dux

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with L-Ribose


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 (N460S) in Complex with L-Ribose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:34.4
occ:1.00
 OD2 D:ASP193 2.1 27.5 1.0
O D:ASN18 2.3 30.3 1.0
OE1 D:GLN163 2.3 28.5 1.0
O D:ASP15 2.3 34.5 1.0
O D:VAL21 2.3 30.8 1.0
CG D:ASP193 2.8 28.3 1.0
OD1 D:ASP193 2.9 27.4 1.0
CD D:GLN163 3.2 28.0 1.0
C D:ASN18 3.2 34.7 1.0
C D:VAL21 3.4 29.5 1.0
C D:ASP15 3.5 32.4 1.0
NE2 D:GLN163 3.6 29.8 1.0
N D:ASN18 3.7 35.9 1.0
CA D:ASN18 3.9 33.8 1.0
CA D:TRP16 4.0 31.4 1.0
OH D:TYR161 4.0 31.6 1.0
N D:PRO19 4.2 35.3 1.0
N D:TRP16 4.2 32.2 1.0
C D:TRP16 4.2 32.0 1.0
CA D:VAL21 4.3 29.8 1.0
CB D:ASP193 4.3 28.8 1.0
CA D:PRO19 4.3 35.3 1.0
CB D:ASN18 4.4 34.1 1.0
N D:VAL21 4.4 31.4 1.0
N D:GLU17 4.4 31.8 1.0
CE2 D:TYR161 4.4 32.1 1.0
N D:THR22 4.4 30.0 1.0
CB D:VAL21 4.4 30.4 1.0
CG D:GLN163 4.5 27.7 1.0
CA D:THR22 4.6 30.2 1.0
CA D:ASP15 4.6 33.9 1.0
CZ D:TYR161 4.7 32.0 1.0
O D:TRP16 4.8 32.2 1.0
C D:PRO19 4.8 34.8 1.0
C D:GLU17 4.9 33.3 1.0
CG1 D:VAL21 5.0 27.2 1.0

Reference:

R.W.Wheatley, S.Lo, L.J.Jancewicz, M.L.Dugdale, R.E.Huber. Structural Explanation For Allolactose (Lac Operon Inducer) Synthesis By Lacz Beta-Galactosidase and the Evolutionary Relationship Between Allolactose Synthesis and the Lac Repressor. J.Biol.Chem. V. 288 12993 2013.
ISSN: ISSN 0021-9258
PubMed: 23486479
DOI: 10.1074/JBC.M113.455436
Page generated: Thu Aug 15 19:35:12 2024

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