Atomistry » Magnesium » PDB 3cpw-3d19 » 3czj
Atomistry »
  Magnesium »
    PDB 3cpw-3d19 »
      3czj »

Magnesium in PDB 3czj: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One, PDB code: 3czj was solved by R.E.Huber, M.L.Dugdale, M.E.Fraser, S.D.Tammam, 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 (%) 19.3 / 23.1

Other elements in 3czj:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One also contains other interesting chemical elements:

Sodium (Na) 16 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One (pdb code 3czj). 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 D- Galctopyranosyl-1-One, PDB code: 3czj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 1 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:19.7
occ:1.00
 OE1 A:GLU461 2.0 20.9 1.0
OE2 A:GLU416 2.1 10.6 1.0
O A:HOH8719 2.2 7.0 1.0
O A:HOH8770 2.2 11.5 1.0
O A:HOH9255 2.2 14.5 1.0
ND1 A:HIS418 2.4 11.1 1.0
CD A:GLU461 3.0 23.8 1.0
CD A:GLU416 3.3 12.7 1.0
CE1 A:HIS418 3.3 14.4 1.0
CG A:HIS418 3.4 12.3 1.0
CB A:HIS418 3.6 8.5 1.0
OE2 A:GLU461 3.6 28.5 1.0
OE1 A:GLU416 3.8 14.1 1.0
ND2 A:ASN102 4.0 11.9 1.0
CG A:GLU461 4.1 21.0 1.0
C2 A:1492001 4.1 18.6 1.0
CB A:GLU461 4.2 16.0 1.0
CB A:ASP201 4.2 13.2 1.0
O A:ASP199 4.2 14.7 1.0
O4 A:1492001 4.2 16.5 1.0
N A:ASP201 4.3 14.4 1.0
NE2 A:HIS418 4.5 14.5 1.0
CG A:GLU416 4.5 10.4 1.0
CD2 A:HIS418 4.5 11.0 1.0
O3 A:1492001 4.5 16.1 1.0
O2 A:1492001 4.6 22.0 1.0
O A:ASN102 4.8 13.8 1.0
CA A:ASP201 4.8 13.3 1.0
CG2 A:VAL103 4.9 14.3 1.0
C3 A:1492001 4.9 17.4 1.0
C A:GLN200 5.0 15.7 1.0

Magnesium binding site 2 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 2 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:19.8
occ:1.00
 O A:ASN18 2.2 19.0 1.0
O A:VAL21 2.3 20.7 1.0
O A:ASP15 2.3 22.8 1.0
OE1 A:GLN163 2.3 19.7 1.0
OD2 A:ASP193 2.3 10.8 1.0
OD1 A:ASP193 2.9 15.6 1.0
CG A:ASP193 3.0 15.4 1.0
C A:ASN18 3.2 20.0 1.0
CD A:GLN163 3.2 17.6 1.0
C A:VAL21 3.4 20.8 1.0
C A:ASP15 3.5 22.2 1.0
NE2 A:GLN163 3.5 15.2 1.0
N A:ASN18 3.6 21.1 1.0
CA A:ASN18 3.9 20.6 1.0
OH A:TYR161 4.0 13.9 1.0
CA A:TRP16 4.1 20.6 1.0
N A:PRO19 4.1 20.7 1.0
CA A:VAL21 4.1 21.3 1.0
CB A:VAL21 4.1 21.8 1.0
N A:VAL21 4.2 21.6 1.0
CB A:ASN18 4.2 19.4 1.0
C A:TRP16 4.3 20.6 1.0
N A:TRP16 4.3 21.6 1.0
CE2 A:TYR161 4.4 14.6 1.0
CA A:PRO19 4.4 21.4 1.0
N A:THR22 4.4 19.4 1.0
N A:GLU17 4.4 20.4 1.0
CB A:ASP193 4.4 14.7 1.0
CG A:GLN163 4.5 15.8 1.0
CA A:ASP15 4.6 23.2 1.0
CA A:THR22 4.6 19.4 1.0
CZ A:TYR161 4.7 14.4 1.0
CG1 A:VAL21 4.7 18.7 1.0
O A:TRP16 4.8 20.3 1.0
C A:PRO19 4.8 22.1 1.0
C A:GLU17 4.8 21.2 1.0

Magnesium binding site 3 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 3 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:13.2
occ:1.00
 OE2 B:GLU461 2.0 16.0 1.0
OE2 B:GLU416 2.0 7.8 1.0
O B:HOH9284 2.2 12.6 1.0
O B:HOH9224 2.2 6.6 1.0
O B:HOH9356 2.3 7.0 1.0
ND1 B:HIS418 2.3 7.6 1.0
CD B:GLU461 2.9 17.3 1.0
CD B:GLU416 3.1 8.8 1.0
CE1 B:HIS418 3.2 11.9 1.0
CG B:HIS418 3.3 8.0 1.0
OE1 B:GLU461 3.5 21.4 1.0
OE1 B:GLU416 3.6 11.7 1.0
CB B:HIS418 3.7 8.1 1.0
CG B:GLU461 4.0 13.0 1.0
CB B:GLU461 4.0 8.4 1.0
C2 B:1492001 4.1 17.9 1.0
ND2 B:ASN102 4.3 10.1 1.0
O4 B:1492001 4.3 15.9 1.0
O B:ASP199 4.3 10.2 1.0
NE2 B:HIS418 4.3 10.4 1.0
CB B:ASP201 4.3 9.6 1.0
CG B:GLU416 4.3 9.9 1.0
N B:ASP201 4.3 10.1 1.0
CD2 B:HIS418 4.4 8.0 1.0
O3 B:1492001 4.5 15.3 1.0
O2 B:1492001 4.6 17.4 1.0
C3 B:1492001 4.8 17.7 1.0
O B:ASN102 4.8 10.8 1.0
CA B:ASP201 4.9 10.7 1.0

Magnesium binding site 4 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 4 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:22.2
occ:1.00
 O B:ASP15 2.2 14.3 1.0
O B:VAL21 2.3 16.6 1.0
O B:ASN18 2.3 17.0 1.0
OD2 B:ASP193 2.4 16.9 1.0
OE1 B:GLN163 2.5 16.5 1.0
OD1 B:ASP193 3.1 17.3 1.0
CG B:ASP193 3.1 16.1 1.0
C B:ASN18 3.2 17.6 1.0
CD B:GLN163 3.3 16.5 1.0
C B:VAL21 3.4 17.7 1.0
C B:ASP15 3.4 15.4 1.0
NE2 B:GLN163 3.6 16.8 1.0
N B:ASN18 3.6 18.1 1.0
CA B:ASN18 3.9 17.6 1.0
CA B:TRP16 4.0 16.1 1.0
OH B:TYR161 4.0 15.1 1.0
N B:PRO19 4.1 18.0 1.0
CA B:VAL21 4.1 17.5 1.0
N B:TRP16 4.2 14.6 1.0
CB B:VAL21 4.2 19.0 1.0
N B:VAL21 4.2 19.3 1.0
C B:TRP16 4.2 17.9 1.0
CB B:ASN18 4.2 18.1 1.0
N B:GLU17 4.3 18.7 1.0
CE2 B:TYR161 4.3 14.9 1.0
CA B:PRO19 4.4 19.2 1.0
N B:THR22 4.4 15.5 1.0
CB B:ASP193 4.5 15.0 1.0
CA B:ASP15 4.6 16.7 1.0
CG B:GLN163 4.6 17.0 1.0
CA B:THR22 4.6 16.1 1.0
CZ B:TYR161 4.6 14.0 1.0
C B:PRO19 4.8 19.5 1.0
C B:GLU17 4.8 19.2 1.0
CG1 B:VAL21 4.8 17.7 1.0
O B:TRP16 4.9 18.0 1.0
CB B:ASP15 5.0 16.9 1.0

Magnesium binding site 5 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 5 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:36.3
occ:1.00
 O B:HOH9806 2.2 26.9 1.0
O B:HOH9735 2.2 15.7 1.0
O B:HOH9825 2.3 38.6 1.0
O B:HOH9851 2.3 15.8 1.0
O B:HOH9826 2.3 19.7 1.0
O B:HOH9827 2.4 35.5 1.0
OE1 B:GLU369 3.8 17.9 1.0
O B:HOH9824 4.0 60.5 1.0
OE2 B:GLU369 4.2 18.9 1.0
O B:HOH9805 4.3 32.1 1.0
O B:HOH9849 4.3 23.0 1.0
O B:HOH9832 4.3 44.7 1.0
O B:HOH9828 4.4 25.2 1.0
CD B:GLU369 4.4 17.8 1.0
O B:HOH9831 4.9 50.7 1.0
O B:HOH9633 5.0 26.4 1.0

Magnesium binding site 6 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 6 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:14.5
occ:1.00
 OE2 C:GLU461 1.9 15.4 1.0
OE2 C:GLU416 2.1 8.7 1.0
O C:HOH8666 2.2 7.6 1.0
O C:HOH8592 2.2 9.3 1.0
O C:HOH8532 2.2 4.5 1.0
ND1 C:HIS418 2.3 5.6 1.0
CD C:GLU461 3.0 19.3 1.0
CD C:GLU416 3.1 10.2 1.0
CE1 C:HIS418 3.2 10.4 1.0
CG C:HIS418 3.3 9.8 1.0
CB C:HIS418 3.6 6.8 1.0
OE1 C:GLU416 3.6 10.1 1.0
OE1 C:GLU461 3.7 25.1 1.0
CG C:GLU461 4.0 15.6 1.0
ND2 C:ASN102 4.1 6.5 1.0
CB C:GLU461 4.2 9.3 1.0
O C:ASP199 4.2 9.3 1.0
N C:ASP201 4.2 11.2 1.0
CB C:ASP201 4.2 10.3 1.0
C2 C:1492001 4.3 14.9 1.0
NE2 C:HIS418 4.3 9.4 1.0
CG C:GLU416 4.4 8.6 1.0
CD2 C:HIS418 4.4 7.7 1.0
O4 C:1492001 4.4 11.4 1.0
O3 C:1492001 4.6 11.0 1.0
O C:ASN102 4.6 10.0 1.0
O2 C:1492001 4.7 16.1 1.0
CA C:ASP201 4.8 10.8 1.0
CA C:GLN200 4.9 11.1 1.0
C C:GLN200 4.9 10.1 1.0
C3 C:1492001 5.0 14.6 1.0

Magnesium binding site 7 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 7 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:10.9
occ:1.00
 O C:VAL21 2.2 11.6 1.0
O C:ASP15 2.3 13.8 1.0
O C:ASN18 2.3 17.4 1.0
OD2 C:ASP193 2.3 13.3 1.0
OE1 C:GLN163 2.4 11.7 1.0
OD1 C:ASP193 3.0 13.2 1.0
CG C:ASP193 3.0 14.7 1.0
CD C:GLN163 3.2 12.3 1.0
C C:ASN18 3.3 16.3 1.0
C C:VAL21 3.4 13.8 1.0
C C:ASP15 3.5 15.2 1.0
NE2 C:GLN163 3.5 12.9 1.0
N C:ASN18 3.7 17.6 1.0
CA C:ASN18 4.0 18.0 1.0
OH C:TYR161 4.0 13.1 1.0
CA C:TRP16 4.0 14.0 1.0
CA C:VAL21 4.1 13.5 1.0
CB C:VAL21 4.1 14.5 1.0
N C:PRO19 4.2 17.2 1.0
N C:TRP16 4.2 14.3 1.0
N C:VAL21 4.2 16.2 1.0
C C:TRP16 4.3 14.7 1.0
CB C:ASN18 4.3 17.2 1.0
CE2 C:TYR161 4.3 10.8 1.0
N C:THR22 4.4 13.6 1.0
CA C:PRO19 4.4 18.0 1.0
N C:GLU17 4.4 14.0 1.0
CB C:ASP193 4.5 13.0 1.0
CG C:GLN163 4.5 13.3 1.0
CA C:THR22 4.5 13.9 1.0
CA C:ASP15 4.6 15.9 1.0
CG1 C:VAL21 4.6 13.3 1.0
CZ C:TYR161 4.6 10.5 1.0
C C:PRO19 4.8 18.4 1.0
O C:TRP16 4.8 13.0 1.0
C C:GLU17 4.9 16.6 1.0
CB C:ASP15 4.9 13.5 1.0

Magnesium binding site 8 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 8 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:15.6
occ:1.00
 OE2 D:GLU461 1.9 22.3 1.0
OE2 D:GLU416 2.0 10.5 1.0
O D:HOH8876 2.1 9.8 1.0
O D:HOH8806 2.2 11.9 1.0
ND1 D:HIS418 2.3 10.6 1.0
O D:HOH8748 2.4 15.1 1.0
CD D:GLU461 2.9 22.6 1.0
CD D:GLU416 3.2 11.3 1.0
CE1 D:HIS418 3.2 12.7 1.0
CG D:HIS418 3.2 12.0 1.0
OE1 D:GLU461 3.5 29.2 1.0
CB D:HIS418 3.5 10.6 1.0
OE1 D:GLU416 3.7 10.3 1.0
CG D:GLU461 4.0 19.6 1.0
CB D:GLU461 4.2 13.5 1.0
C2 D:1492001 4.2 19.7 1.0
ND2 D:ASN102 4.2 15.8 1.0
O D:ASP199 4.2 15.1 1.0
NE2 D:HIS418 4.3 13.7 1.0
CB D:ASP201 4.4 12.0 1.0
CD2 D:HIS418 4.4 11.6 1.0
O4 D:1492001 4.4 18.0 1.0
CG D:GLU416 4.4 11.2 1.0
N D:ASP201 4.4 11.9 1.0
O2 D:1492001 4.6 23.0 1.0
O3 D:1492001 4.6 14.7 1.0
O D:ASN102 4.7 16.9 1.0
CA D:ASP201 5.0 11.2 1.0
C3 D:1492001 5.0 18.2 1.0
CA D:HIS418 5.0 11.6 1.0

Magnesium binding site 9 out of 9 in 3czj

Go back to Magnesium Binding Sites List in 3czj
Magnesium binding site 9 out of 9 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with D- Galctopyranosyl-1-One


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 D- Galctopyranosyl-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:22.4
occ:1.00
 O D:ASN18 2.2 19.6 1.0
O D:VAL21 2.3 20.3 1.0
O D:ASP15 2.3 21.3 1.0
OD2 D:ASP193 2.3 19.0 1.0
OE1 D:GLN163 2.4 26.1 1.0
OD1 D:ASP193 2.9 19.6 1.0
CG D:ASP193 3.0 18.0 1.0
C D:ASN18 3.2 20.2 1.0
CD D:GLN163 3.3 23.7 1.0
C D:VAL21 3.4 21.1 1.0
C D:ASP15 3.5 22.4 1.0
NE2 D:GLN163 3.6 23.5 1.0
N D:ASN18 3.7 21.3 1.0
CA D:ASN18 3.9 21.2 1.0
OH D:TYR161 4.0 16.3 1.0
CA D:TRP16 4.1 22.3 1.0
N D:PRO19 4.1 19.3 1.0
CA D:VAL21 4.2 21.7 1.0
CB D:VAL21 4.2 24.2 1.0
N D:VAL21 4.2 22.5 1.0
N D:TRP16 4.2 22.4 1.0
CB D:ASN18 4.3 22.5 1.0
C D:TRP16 4.3 22.2 1.0
N D:GLU17 4.4 21.7 1.0
CE2 D:TYR161 4.4 15.7 1.0
CA D:PRO19 4.4 19.9 1.0
CB D:ASP193 4.4 18.2 1.0
N D:THR22 4.4 18.9 1.0
CA D:ASP15 4.6 23.2 1.0
CA D:THR22 4.6 17.6 1.0
CG D:GLN163 4.6 22.0 1.0
CZ D:TYR161 4.7 15.4 1.0
CG1 D:VAL21 4.7 23.0 1.0
C D:PRO19 4.8 20.8 1.0
C D:GLU17 4.8 21.6 1.0
O D:TRP16 4.9 21.0 1.0
CB D:ASP15 5.0 21.0 1.0

Reference:

J.C.Kappelhoff, S.Y.Liu, M.L.Dugdale, D.L.Dymianiw, L.R.Linton, R.E.Huber. Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-Beta-Galactosidase (E. Coli) As Examples. Protein J. V. 28 96 2009.
ISSN: ISSN 1572-3887
PubMed: 19229596
DOI: 10.1007/S10930-009-9168-1
Page generated: Mon Dec 14 08:02:53 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy