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Magnesium in PDB 3vdb: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone, PDB code: 3vdb was solved by R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 75.05 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.443, 161.643, 202.155, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 20.5

Other elements in 3vdb:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone 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 (N460T) in Complex with Galactonolactone (pdb code 3vdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone, PDB code: 3vdb:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3vdb

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Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:23.4
occ:1.00
 OE1 A:GLU461 2.0 22.3 1.0
OE2 A:GLU416 2.1 20.1 1.0
O A:HOH4691 2.1 15.3 1.0
O A:HOH4626 2.1 18.9 1.0
O A:HOH4736 2.1 17.0 1.0
ND1 A:HIS418 2.4 19.0 1.0
CD A:GLU416 3.2 18.6 1.0
CD A:GLU461 3.2 36.6 1.0
CE1 A:HIS418 3.3 22.5 1.0
CG A:HIS418 3.4 21.7 1.0
CB A:HIS418 3.7 11.8 1.0
OE1 A:GLU416 3.7 21.1 1.0
OD1 A:ASN102 4.0 21.9 1.0
CG A:GLU461 4.0 28.6 1.0
OE2 A:GLU461 4.1 45.2 1.0
CB A:ASP201 4.1 19.4 1.0
O4 A:1492001 4.1 20.7 1.0
O A:ASP199 4.1 20.8 1.0
N A:ASP201 4.2 19.6 1.0
C2 A:1492001 4.2 26.4 1.0
CB A:GLU461 4.2 20.6 1.0
O3 A:1492001 4.4 19.9 1.0
CG A:GLU416 4.4 17.5 1.0
NE2 A:HIS418 4.5 22.5 1.0
CD2 A:HIS418 4.5 17.4 1.0
CA A:ASP201 4.7 19.2 1.0
O2 A:1492001 4.7 28.4 1.0
O A:ASN102 4.7 22.7 1.0
C3 A:1492001 4.8 22.7 1.0
CG2 A:VAL103 4.9 23.8 1.0
C A:GLN200 4.9 23.1 1.0
CA A:GLN200 5.0 22.2 1.0

Magnesium binding site 2 out of 9 in 3vdb

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Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:25.0
occ:1.00
 OD2 A:ASP193 2.1 18.6 1.0
O A:ASN18 2.3 24.5 1.0
OE1 A:GLN163 2.3 29.1 1.0
O A:ASP15 2.3 27.8 1.0
O A:VAL21 2.3 28.5 1.0
CG A:ASP193 2.8 26.0 1.0
OD1 A:ASP193 2.9 27.4 1.0
CD A:GLN163 3.1 25.2 1.0
C A:ASN18 3.2 26.0 1.0
NE2 A:GLN163 3.4 20.2 1.0
C A:VAL21 3.4 26.7 1.0
C A:ASP15 3.5 26.7 1.0
N A:ASN18 3.7 28.0 1.0
CA A:ASN18 3.9 26.4 1.0
CA A:TRP16 4.0 25.4 1.0
OH A:TYR161 4.1 20.5 1.0
N A:PRO19 4.1 26.7 1.0
N A:TRP16 4.2 27.1 1.0
CA A:VAL21 4.2 28.0 1.0
CB A:ASN18 4.2 25.7 1.0
C A:TRP16 4.3 26.1 1.0
N A:VAL21 4.3 28.9 1.0
CB A:ASP193 4.3 23.3 1.0
CB A:VAL21 4.3 29.4 1.0
CA A:PRO19 4.4 28.2 1.0
N A:THR22 4.4 25.0 1.0
CE2 A:TYR161 4.5 22.3 1.0
N A:GLU17 4.5 27.1 1.0
CG A:GLN163 4.5 22.5 1.0
CA A:ASP15 4.6 29.4 1.0
CA A:THR22 4.7 26.6 1.0
CZ A:TYR161 4.7 18.9 1.0
O A:TRP16 4.8 26.8 1.0
C A:GLU17 4.9 28.4 1.0
CG1 A:VAL21 4.9 21.2 1.0
C A:PRO19 4.9 29.2 1.0

Magnesium binding site 3 out of 9 in 3vdb

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Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:21.1
occ:1.00
 OE2 B:GLU461 1.9 23.5 1.0
O B:HOH4163 2.0 15.0 1.0
OE2 B:GLU416 2.1 16.0 1.0
O B:HOH4744 2.1 12.7 1.0
O B:HOH4680 2.1 14.8 1.0
ND1 B:HIS418 2.4 15.2 1.0
CD B:GLU461 3.1 28.7 1.0
CD B:GLU416 3.2 14.1 1.0
CE1 B:HIS418 3.3 22.7 1.0
CG B:HIS418 3.4 16.5 1.0
OE1 B:GLU416 3.7 20.7 1.0
CB B:HIS418 3.7 13.8 1.0
CG B:GLU461 4.0 22.3 1.0
OE1 B:GLU461 4.0 44.2 1.0
OD1 B:ASN102 4.1 19.7 1.0
O4 B:1492001 4.2 21.6 1.0
C2 B:1492001 4.2 27.3 1.0
CB B:GLU461 4.2 15.4 1.0
O B:ASP199 4.2 18.0 1.0
N B:ASP201 4.2 17.2 1.0
CB B:ASP201 4.2 16.3 1.0
O3 B:1492001 4.4 19.2 1.0
CG B:GLU416 4.4 15.8 1.0
NE2 B:HIS418 4.4 20.4 1.0
CD2 B:HIS418 4.5 15.3 1.0
O B:ASN102 4.6 19.4 1.0
O2 B:1492001 4.7 24.1 1.0
C3 B:1492001 4.8 28.3 1.0
CA B:ASP201 4.8 18.9 1.0
C B:GLN200 4.9 20.5 1.0
CG2 B:VAL103 5.0 24.0 1.0
CA B:GLN200 5.0 16.7 1.0

Magnesium binding site 4 out of 9 in 3vdb

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Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:24.8
occ:1.00
 OD2 B:ASP193 2.1 26.3 1.0
O B:ASN18 2.3 23.3 1.0
O B:ASP15 2.3 19.9 1.0
O B:VAL21 2.3 24.0 1.0
OE1 B:GLN163 2.3 24.4 1.0
CG B:ASP193 2.9 23.8 1.0
OD1 B:ASP193 3.0 29.4 1.0
CD B:GLN163 3.1 23.9 1.0
C B:ASN18 3.2 21.9 1.0
NE2 B:GLN163 3.4 26.4 1.0
C B:VAL21 3.4 25.4 1.0
C B:ASP15 3.5 19.9 1.0
N B:ASN18 3.6 24.7 1.0
CA B:ASN18 3.9 22.8 1.0
OH B:TYR161 4.0 21.8 1.0
CA B:TRP16 4.1 23.7 1.0
N B:PRO19 4.1 24.0 1.0
N B:TRP16 4.2 18.6 1.0
CA B:VAL21 4.2 24.4 1.0
CB B:ASN18 4.2 20.7 1.0
C B:TRP16 4.3 25.8 1.0
CB B:ASP193 4.3 20.9 1.0
N B:VAL21 4.3 27.1 1.0
CE2 B:TYR161 4.3 26.6 1.0
CA B:PRO19 4.4 27.1 1.0
CB B:VAL21 4.4 25.7 1.0
N B:THR22 4.4 21.3 1.0
N B:GLU17 4.4 28.3 1.0
CG B:GLN163 4.5 24.0 1.0
CA B:THR22 4.6 23.5 1.0
CA B:ASP15 4.6 22.6 1.0
CZ B:TYR161 4.7 21.6 1.0
C B:PRO19 4.8 25.8 1.0
C B:GLU17 4.8 26.9 1.0
O B:TRP16 4.9 25.9 1.0
CG1 B:VAL21 5.0 26.8 1.0

Magnesium binding site 5 out of 9 in 3vdb

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Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:37.2
occ:1.00
 O B:HOH4894 1.9 29.9 1.0
O B:HOH4703 2.0 34.0 1.0
O B:HOH4528 2.1 24.3 1.0
O B:HOH4925 2.1 35.1 1.0
O B:HOH4924 2.1 19.8 1.0
O B:HOH4926 2.2 30.4 1.0
OE1 B:GLU369 3.9 27.7 1.0
O B:HOH4634 4.1 29.0 1.0
O B:HOH4584 4.1 29.3 1.0
O B:HOH4643 4.2 36.1 1.0
OE2 B:GLU369 4.3 29.7 1.0
O B:HOH4705 4.5 41.2 1.0
CD B:GLU369 4.5 27.4 1.0

Magnesium binding site 6 out of 9 in 3vdb

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Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:19.5
occ:1.00
 OE2 C:GLU461 2.0 20.4 1.0
O C:HOH4880 2.0 16.2 1.0
O C:HOH4786 2.0 14.4 1.0
OE2 C:GLU416 2.1 14.8 1.0
O C:HOH4672 2.1 15.6 1.0
ND1 C:HIS418 2.4 14.1 1.0
CD C:GLU416 3.2 19.3 1.0
CD C:GLU461 3.2 31.9 1.0
CE1 C:HIS418 3.3 18.2 1.0
CG C:HIS418 3.4 20.4 1.0
OE1 C:GLU416 3.6 18.0 1.0
CB C:HIS418 3.7 14.1 1.0
OD1 C:ASN102 3.9 13.8 1.0
O C:ASP199 4.0 16.0 1.0
N C:ASP201 4.0 17.6 1.0
CB C:ASP201 4.0 16.1 1.0
CG C:GLU461 4.0 25.8 1.0
OE1 C:GLU461 4.1 44.5 1.0
O4 C:1492001 4.3 18.9 1.0
CB C:GLU461 4.3 13.0 1.0
C2 C:1492001 4.3 22.9 1.0
O C:ASN102 4.4 18.2 1.0
CG C:GLU416 4.4 16.4 1.0
NE2 C:HIS418 4.5 19.1 1.0
O3 C:1492001 4.5 14.7 1.0
CD2 C:HIS418 4.5 14.8 1.0
CA C:ASP201 4.5 18.6 1.0
C C:GLN200 4.7 17.3 1.0
CA C:GLN200 4.8 18.6 1.0
O2 C:1492001 4.8 24.1 1.0
C3 C:1492001 4.9 21.6 1.0
CG2 C:VAL103 5.0 18.5 1.0

Magnesium binding site 7 out of 9 in 3vdb

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Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:18.2
occ:1.00
 OD2 C:ASP193 2.1 21.0 1.0
O C:ASN18 2.3 22.4 1.0
O C:ASP15 2.3 21.2 1.0
O C:VAL21 2.3 20.3 1.0
OE1 C:GLN163 2.3 19.9 1.0
CG C:ASP193 2.8 23.5 1.0
OD1 C:ASP193 2.9 22.2 1.0
CD C:GLN163 3.1 17.8 1.0
C C:ASN18 3.2 22.0 1.0
C C:VAL21 3.4 20.7 1.0
C C:ASP15 3.4 23.3 1.0
NE2 C:GLN163 3.5 23.9 1.0
N C:ASN18 3.7 25.0 1.0
CA C:ASN18 4.0 25.7 1.0
OH C:TYR161 4.0 24.7 1.0
CA C:TRP16 4.0 20.3 1.0
N C:TRP16 4.2 20.7 1.0
CA C:VAL21 4.2 24.6 1.0
N C:PRO19 4.2 25.1 1.0
C C:TRP16 4.2 22.8 1.0
CB C:ASP193 4.3 20.2 1.0
CB C:VAL21 4.3 23.0 1.0
N C:VAL21 4.3 25.8 1.0
CB C:ASN18 4.4 23.1 1.0
CA C:PRO19 4.4 25.7 1.0
N C:THR22 4.4 20.1 1.0
CG C:GLN163 4.4 21.5 1.0
CE2 C:TYR161 4.4 18.2 1.0
N C:GLU17 4.5 19.5 1.0
CA C:ASP15 4.6 23.9 1.0
CA C:THR22 4.6 20.8 1.0
CZ C:TYR161 4.7 19.3 1.0
O C:TRP16 4.8 20.4 1.0
CG1 C:VAL21 4.9 22.1 1.0
C C:PRO19 4.9 25.3 1.0
C C:GLU17 4.9 23.4 1.0
CB C:ASP15 5.0 19.0 1.0

Magnesium binding site 8 out of 9 in 3vdb

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Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:22.9
occ:1.00
 O D:HOH4797 2.0 18.4 1.0
OE2 D:GLU461 2.0 28.5 1.0
OE2 D:GLU416 2.1 19.4 1.0
O D:HOH4670 2.1 18.1 1.0
O D:HOH4044 2.2 21.1 1.0
ND1 D:HIS418 2.4 19.7 1.0
CD D:GLU461 3.2 34.6 1.0
CD D:GLU416 3.2 19.2 1.0
CE1 D:HIS418 3.3 22.2 1.0
CG D:HIS418 3.4 19.7 1.0
CB D:HIS418 3.6 16.8 1.0
OE1 D:GLU416 3.7 21.6 1.0
OE1 D:GLU461 4.0 49.3 1.0
OD1 D:ASN102 4.1 23.2 1.0
CG D:GLU461 4.1 25.7 1.0
O D:ASP199 4.1 23.4 1.0
C2 D:1492001 4.2 24.5 1.0
O4 D:1492001 4.2 25.0 1.0
CB D:ASP201 4.2 21.1 1.0
N D:ASP201 4.2 17.6 1.0
CB D:GLU461 4.3 16.6 1.0
O3 D:1492001 4.4 17.6 1.0
CG D:GLU416 4.4 20.5 1.0
NE2 D:HIS418 4.4 25.3 1.0
CD2 D:HIS418 4.5 17.5 1.0
O D:ASN102 4.6 22.8 1.0
O2 D:1492001 4.7 31.9 1.0
CA D:ASP201 4.8 17.3 1.0
C3 D:1492001 4.8 25.5 1.0
C D:GLN200 4.9 20.5 1.0
CA D:GLN200 5.0 20.0 1.0

Magnesium binding site 9 out of 9 in 3vdb

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Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Galactonolactone


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 (N460T) in Complex with Galactonolactone within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:28.6
occ:1.00
 OD2 D:ASP193 2.1 30.1 1.0
O D:ASN18 2.3 28.1 1.0
OE1 D:GLN163 2.3 35.1 1.0
O D:ASP15 2.3 28.9 1.0
O D:VAL21 2.3 26.8 1.0
CG D:ASP193 2.8 27.4 1.0
OD1 D:ASP193 2.9 32.5 1.0
CD D:GLN163 3.2 30.6 1.0
C D:ASN18 3.2 27.1 1.0
C D:VAL21 3.5 28.4 1.0
C D:ASP15 3.5 28.6 1.0
NE2 D:GLN163 3.5 30.2 1.0
N D:ASN18 3.7 26.5 1.0
CA D:ASN18 3.9 28.3 1.0
OH D:TYR161 3.9 23.9 1.0
CA D:TRP16 4.0 29.9 1.0
N D:PRO19 4.2 26.4 1.0
N D:TRP16 4.2 29.0 1.0
CA D:VAL21 4.3 28.1 1.0
CB D:ASP193 4.3 26.9 1.0
C D:TRP16 4.3 28.9 1.0
CB D:ASN18 4.3 28.2 1.0
CB D:VAL21 4.4 33.3 1.0
CE2 D:TYR161 4.4 24.1 1.0
N D:VAL21 4.4 29.2 1.0
CA D:PRO19 4.4 26.5 1.0
N D:THR22 4.5 25.2 1.0
N D:GLU17 4.5 28.2 1.0
CG D:GLN163 4.6 26.1 1.0
CA D:ASP15 4.6 30.5 1.0
CZ D:TYR161 4.6 24.5 1.0
CA D:THR22 4.6 23.5 1.0
CG1 D:VAL21 4.8 30.0 1.0
O D:TRP16 4.9 26.5 1.0
C D:GLU17 4.9 27.6 1.0
C D:PRO19 4.9 30.0 1.0

Reference:

R.W.Wheatley, J.C.Kappelhoff, J.N.Hahn, M.L.Dugdale, M.J.Dutkoski, S.D.Tamman, M.E.Fraser, R.E.Huber. Substitution For ASN460 Cripples {Beta}-Galactosidase (Escherichia Coli) By Increasing Substrate Affinity and Decreasing Transition State Stability. Arch.Biochem.Biophys. V. 521 51 2012.
ISSN: ISSN 0003-9861
PubMed: 22446164
DOI: 10.1016/J.ABB.2012.03.014
Page generated: Thu Aug 15 13:01:00 2024

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