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Magnesium in PDB 3vd7: E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole

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

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7 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) 44.78 / 2.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.460, 152.370, 135.110, 90.00, 104.25, 90.00
R / Rfree (%) 18.8 / 25

Other elements in 3vd7:

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

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole (pdb code 3vd7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3vd7

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Magnesium binding site 1 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:44.8
occ:1.00
 O A:HOH4060 2.0 41.6 1.0
OE1 A:GLU461 2.1 35.1 1.0
O A:HOH4059 2.1 31.4 1.0
OE2 A:GLU416 2.3 34.4 1.0
O A:HOH4058 2.3 36.5 1.0
ND1 A:HIS418 2.4 30.9 1.0
CE1 A:HIS418 3.2 27.7 1.0
CD A:GLU461 3.3 38.5 1.0
CD A:GLU416 3.4 34.5 1.0
CG A:HIS418 3.4 28.9 1.0
CB A:HIS418 3.8 25.7 1.0
OD1 A:ASN102 3.9 53.8 1.0
OE1 A:GLU416 3.9 37.6 1.0
OE2 A:GLU461 4.1 44.7 1.0
CG A:GLU461 4.1 33.9 1.0
O4 A:GTZ2001 4.2 81.0 1.0
CB A:ASP201 4.2 46.5 1.0
N A:ASP201 4.3 42.3 1.0
O3 A:GTZ2001 4.3 68.3 1.0
NE2 A:HIS418 4.4 25.6 1.0
C2 A:GTZ2001 4.4 76.6 1.0
CB A:GLU461 4.4 32.5 1.0
O A:ASP199 4.5 32.4 1.0
CD2 A:HIS418 4.5 26.0 1.0
O A:ASN102 4.6 47.9 1.0
CG A:GLU416 4.6 28.8 1.0
CA A:ASP201 4.8 44.3 1.0
C3 A:GTZ2001 4.8 75.8 1.0
C1 A:GTZ2001 4.8 79.6 1.0
C A:GLN200 4.9 39.6 1.0

Magnesium binding site 2 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 2 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:31.0
occ:1.00
 O B:HOH4092 1.9 56.1 1.0
OE1 B:GLU461 2.0 31.1 1.0
O B:HOH4077 2.2 27.0 1.0
OE2 B:GLU416 2.3 28.0 1.0
O B:HOH4002 2.5 23.1 1.0
ND1 B:HIS418 2.7 27.9 1.0
CD B:GLU461 3.3 30.6 1.0
CD B:GLU416 3.4 27.2 1.0
CE1 B:HIS418 3.5 30.0 1.0
CG B:HIS418 3.7 29.2 1.0
OD1 B:ASN102 3.8 48.0 1.0
CB B:ASP201 3.8 43.1 1.0
N B:ASP201 3.9 40.6 1.0
OE2 B:GLU461 4.0 34.1 1.0
CB B:HIS418 4.0 24.1 1.0
OE1 B:GLU416 4.0 27.2 1.0
O4 B:GTZ2001 4.1 67.3 1.0
O B:ASP199 4.1 37.6 1.0
O3 B:GTZ2001 4.2 60.2 1.0
CG B:GLU461 4.3 28.5 1.0
CA B:ASP201 4.4 42.0 1.0
C2 B:GTZ2001 4.5 74.7 1.0
CG B:GLU416 4.6 23.4 1.0
NE2 B:HIS418 4.7 30.5 1.0
O B:ASN102 4.7 38.8 1.0
C B:GLN200 4.7 38.0 1.0
C3 B:GTZ2001 4.8 71.5 1.0
CD2 B:HIS418 4.8 29.0 1.0
CA B:GLN200 4.8 39.1 1.0
CG B:ASN102 4.9 44.3 1.0
C1 B:GTZ2001 5.0 77.0 1.0
CG B:ASP201 5.0 45.7 1.0

Magnesium binding site 3 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 3 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:36.2
occ:1.00
 OD2 B:ASP193 2.1 28.1 1.0
OE1 B:GLN163 2.3 36.5 1.0
O B:ASP15 2.3 35.6 1.0
O B:VAL21 2.3 30.6 1.0
O B:ASN18 2.7 32.6 1.0
CG B:ASP193 2.9 26.8 1.0
OD1 B:ASP193 3.1 30.2 1.0
CD B:GLN163 3.2 39.2 1.0
C B:ASP15 3.4 35.6 1.0
NE2 B:GLN163 3.4 32.4 1.0
C B:VAL21 3.5 29.3 1.0
C B:ASN18 3.5 32.2 1.0
OH B:TYR161 3.7 28.9 1.0
N B:ASN18 3.8 31.5 1.0
CA B:TRP16 3.8 30.1 1.0
C B:TRP16 4.1 29.5 1.0
CA B:ASN18 4.1 31.9 1.0
N B:TRP16 4.1 32.5 1.0
CE2 B:TYR161 4.2 30.3 1.0
CA B:VAL21 4.3 29.9 1.0
CB B:ASP193 4.4 24.0 1.0
N B:PRO19 4.4 31.6 1.0
CZ B:TYR161 4.4 25.6 1.0
N B:GLU17 4.4 31.4 1.0
CB B:VAL21 4.4 29.5 1.0
N B:THR22 4.4 27.7 1.0
O B:TRP16 4.5 31.5 1.0
N B:VAL21 4.5 31.0 1.0
CA B:THR22 4.6 23.7 1.0
CG B:GLN163 4.6 35.9 1.0
CA B:ASP15 4.6 35.8 1.0
CA B:PRO19 4.6 31.5 1.0
CB B:ASN18 4.6 32.2 1.0
CG1 B:VAL21 4.7 25.0 1.0
C B:GLU17 4.9 31.4 1.0
CB B:ASP15 5.0 34.9 1.0

Magnesium binding site 4 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 4 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:35.7
occ:1.00
 O C:HOH4075 1.8 33.0 1.0
OE1 C:GLU461 2.1 25.9 1.0
O C:HOH4003 2.2 25.9 1.0
OE2 C:GLU416 2.2 36.1 1.0
O C:HOH4076 2.3 33.8 1.0
ND1 C:HIS418 2.4 31.0 1.0
CD C:GLU461 3.2 26.7 1.0
CE1 C:HIS418 3.3 33.9 1.0
CG C:HIS418 3.4 31.8 1.0
CD C:GLU416 3.5 38.6 1.0
CB C:HIS418 3.6 31.1 1.0
CG C:GLU461 4.0 23.1 1.0
OD1 C:ASN102 4.1 39.4 1.0
OE1 C:GLU416 4.2 39.7 1.0
OE2 C:GLU461 4.2 30.9 1.0
O C:ASP199 4.2 31.8 1.0
CB C:GLU461 4.2 19.4 1.0
O C:ASN102 4.2 41.0 1.0
CB C:ASP201 4.3 33.9 1.0
N C:ASP201 4.3 35.7 1.0
O4 C:GTZ2001 4.4 60.9 1.0
NE2 C:HIS418 4.4 33.7 1.0
CD2 C:HIS418 4.5 36.0 1.0
CG C:GLU416 4.5 32.9 1.0
O3 C:GTZ2001 4.6 64.3 1.0
C2 C:GTZ2001 4.7 62.7 1.0
CA C:ASP201 4.8 34.1 1.0
C C:GLN200 4.9 32.3 1.0
CA C:GLN200 5.0 31.5 1.0

Magnesium binding site 5 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 5 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:31.9
occ:1.00
 OD2 C:ASP193 2.1 32.9 1.0
OE1 C:GLN163 2.3 28.4 1.0
O C:VAL21 2.3 30.2 1.0
O C:ASP15 2.3 37.3 1.0
O C:ASN18 2.3 32.9 1.0
CG C:ASP193 3.1 28.4 1.0
C C:ASN18 3.2 30.8 1.0
CD C:GLN163 3.3 33.6 1.0
OD1 C:ASP193 3.4 37.4 1.0
C C:ASP15 3.4 37.9 1.0
C C:VAL21 3.5 29.3 1.0
N C:ASN18 3.7 30.2 1.0
NE2 C:GLN163 3.8 36.3 1.0
OH C:TYR161 3.8 40.3 1.0
CA C:ASN18 3.9 30.4 1.0
N C:PRO19 4.1 29.6 1.0
CA C:TRP16 4.1 34.0 1.0
CE2 C:TYR161 4.2 33.4 1.0
N C:TRP16 4.2 35.5 1.0
CA C:PRO19 4.2 31.0 1.0
C C:TRP16 4.3 32.4 1.0
CA C:VAL21 4.3 30.5 1.0
N C:THR22 4.4 28.1 1.0
CB C:ASP193 4.4 29.0 1.0
N C:VAL21 4.4 29.7 1.0
CB C:ASN18 4.4 29.6 1.0
CB C:VAL21 4.4 31.9 1.0
CA C:ASP15 4.5 39.6 1.0
CA C:THR22 4.5 29.9 1.0
CZ C:TYR161 4.5 33.0 1.0
N C:GLU17 4.5 30.5 1.0
CG C:GLN163 4.6 36.6 1.0
CG1 C:VAL21 4.7 32.2 1.0
O C:TRP16 4.8 31.9 1.0
CB C:ASP15 4.8 40.2 1.0
C C:PRO19 4.8 31.9 1.0
C C:GLU17 4.9 30.1 1.0

Magnesium binding site 6 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 6 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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

b:37.1
occ:1.00
 O D:HOH4122 1.8 29.5 1.0
OE1 D:GLU461 2.1 37.0 1.0
O D:HOH4121 2.1 43.6 1.0
O D:HOH4003 2.2 12.9 1.0
OE2 D:GLU416 2.3 21.6 1.0
ND1 D:HIS418 2.6 22.9 1.0
CD D:GLU461 3.3 32.7 1.0
CD D:GLU416 3.4 25.1 1.0
CE1 D:HIS418 3.4 19.3 1.0
CG D:HIS418 3.7 26.7 1.0
OE1 D:GLU416 3.8 25.7 1.0
CB D:ASP201 4.0 41.9 1.0
CB D:HIS418 4.0 26.4 1.0
OD1 D:ASN102 4.1 40.5 1.0
N D:ASP201 4.2 38.8 1.0
OE2 D:GLU461 4.2 36.2 1.0
C2 D:GTZ2001 4.2 82.4 1.0
CG D:GLU461 4.2 27.0 1.0
O D:ASN102 4.2 38.1 1.0
O3 D:GTZ2001 4.2 78.6 1.0
O D:ASP199 4.4 31.6 1.0
O4 D:GTZ2001 4.5 80.4 1.0
CB D:GLU461 4.5 24.9 1.0
NE2 D:HIS418 4.6 26.6 1.0
CA D:ASP201 4.6 39.4 1.0
CG D:GLU416 4.7 21.3 1.0
C1 D:GTZ2001 4.7 86.9 1.0
CD2 D:HIS418 4.8 27.3 1.0
C3 D:GTZ2001 4.8 80.6 1.0
C D:GLN200 4.9 37.7 1.0
N1 D:GTZ2001 5.0 90.9 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 12:55:31 2024

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