Atomistry » Magnesium » PDB 3vdb-3vsq » 3vdb
Atomistry »
  Magnesium »
    PDB 3vdb-3vsq »
      3vdb »

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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Go back to Magnesium Binding Sites List in 3vdb
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy