Atomistry » Magnesium » PDB 1jx2-1k9m » 1jz2
Atomistry »
  Magnesium »
    PDB 1jx2-1k9m »
      1jz2 »

Magnesium in PDB 1jz2: E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2 was solved by D.H.Juers, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.60 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.500, 167.700, 201.600, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 27

Other elements in 1jz2:

The structure of E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) also contains other interesting chemical elements:

Fluorine (F) 4 atoms
Sodium (Na) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) (pdb code 1jz2). 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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic), PDB code: 1jz2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:26.8
occ:1.00
 OE2 A:GLU416 2.0 18.5 1.0
OE1 A:GLU461 2.1 22.0 1.0
ND1 A:HIS418 2.2 25.3 1.0
O A:HOH8517 2.2 14.0 1.0
O A:HOH8656 2.2 23.0 1.0
O A:HOH8580 2.3 15.9 1.0
CE1 A:HIS418 3.0 21.2 1.0
CD A:GLU416 3.1 19.8 1.0
CD A:GLU461 3.2 33.0 1.0
CG A:HIS418 3.3 25.3 1.0
OE1 A:GLU416 3.4 13.2 1.0
CB A:HIS418 3.8 19.5 1.0
ND2 A:ASN460 4.0 21.2 1.0
N A:ASP201 4.0 23.7 1.0
OE2 A:GLU461 4.0 15.7 1.0
CB A:GLU461 4.0 17.3 1.0
OD1 A:ASN102 4.1 19.1 1.0
CB A:ASP201 4.1 18.4 1.0
O A:ASP199 4.1 19.6 1.0
CG A:GLU461 4.1 17.9 1.0
NE2 A:HIS418 4.2 21.6 1.0
O4 A:2FG2001 4.2 14.7 1.0
O3 A:2FG2001 4.2 29.4 1.0
CG A:GLU416 4.3 14.2 1.0
CD2 A:HIS418 4.4 23.8 1.0
C2 A:2FG2001 4.6 26.8 1.0
CA A:ASP201 4.6 22.8 1.0
O A:ASN102 4.7 18.6 1.0
C A:GLN200 4.7 22.1 1.0
O A:HOH8975 4.7 23.0 1.0
CA A:GLN200 4.8 15.1 1.0
F2 A:2FG2001 4.9 28.6 1.0
C3 A:2FG2001 4.9 23.0 1.0

Magnesium binding site 2 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:27.5
occ:1.00
 OE1 A:GLN163 2.1 24.6 1.0
O A:ASN18 2.2 29.8 1.0
O A:VAL21 2.2 18.1 1.0
OD2 A:ASP193 2.3 22.7 1.0
O A:ASP15 2.3 26.8 1.0
OD1 A:ASP193 2.9 25.1 1.0
CG A:ASP193 2.9 28.7 1.0
CD A:GLN163 3.0 34.9 1.0
C A:ASN18 3.0 22.4 1.0
NE2 A:GLN163 3.3 26.3 1.0
C A:VAL21 3.4 20.4 1.0
C A:ASP15 3.5 26.4 1.0
N A:ASN18 3.6 30.4 1.0
CA A:ASN18 3.8 27.3 1.0
OH A:TYR161 3.8 24.9 1.0
N A:PRO19 3.9 22.4 1.0
CA A:TRP16 4.1 27.2 1.0
N A:TRP16 4.2 25.4 1.0
CA A:VAL21 4.2 18.2 1.0
N A:VAL21 4.2 27.0 1.0
CA A:PRO19 4.2 23.0 1.0
CE2 A:TYR161 4.3 26.4 1.0
CB A:VAL21 4.3 27.5 1.0
CB A:ASN18 4.3 20.3 1.0
CG A:GLN163 4.3 15.6 1.0
C A:TRP16 4.3 27.9 1.0
N A:GLU17 4.4 28.9 1.0
N A:THR22 4.4 20.6 1.0
CB A:ASP193 4.4 15.1 1.0
CA A:THR22 4.4 14.3 1.0
CZ A:TYR161 4.5 37.6 1.0
CA A:ASP15 4.6 25.7 1.0
C A:GLU17 4.8 36.7 1.0
CG1 A:VAL21 4.8 26.8 1.0
C A:PRO19 4.8 28.5 1.0
CG2 A:THR22 4.8 19.1 1.0
O A:TRP16 5.0 24.5 1.0

Magnesium binding site 3 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:21.4
occ:1.00
 O B:HOH8599 1.8 13.8 1.0
OE1 B:GLU461 1.9 31.0 1.0
OE2 B:GLU416 2.0 22.6 1.0
O B:HOH8674 2.1 20.8 1.0
ND1 B:HIS418 2.2 19.0 1.0
O B:HOH8535 2.4 16.0 1.0
CD B:GLU461 2.9 14.7 1.0
CE1 B:HIS418 3.1 18.7 1.0
CD B:GLU416 3.2 30.6 1.0
CG B:HIS418 3.3 18.3 1.0
CB B:HIS418 3.7 19.3 1.0
OE1 B:GLU416 3.7 14.9 1.0
OE2 B:GLU461 3.7 16.4 1.0
O4 B:2FG2001 3.9 28.0 1.0
CG B:GLU461 4.0 17.4 1.0
OD1 B:ASN102 4.0 18.9 1.0
CB B:GLU461 4.1 11.2 1.0
CB B:ASP201 4.1 13.9 1.0
ND2 B:ASN460 4.2 17.8 1.0
NE2 B:HIS418 4.2 18.0 1.0
CD2 B:HIS418 4.4 16.8 1.0
N B:ASP201 4.4 23.2 1.0
O B:ASP199 4.4 13.5 1.0
CG B:GLU416 4.4 26.2 1.0
O3 B:2FG2001 4.4 17.6 1.0
O6 B:BTB2002 4.5 21.5 1.0
C2 B:2FG2001 4.5 21.2 1.0
F2 B:2FG2001 4.7 29.8 1.0
O B:ASN102 4.8 19.8 1.0
CA B:ASP201 4.8 20.3 1.0
C3 B:2FG2001 4.9 24.6 1.0
CG2 B:VAL103 5.0 17.1 1.0

Magnesium binding site 4 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:27.6
occ:1.00
 O B:VAL21 2.1 25.1 1.0
O B:ASP15 2.2 24.4 1.0
OE1 B:GLN163 2.3 17.6 1.0
O B:ASN18 2.3 23.5 1.0
OD2 B:ASP193 2.4 22.6 1.0
C B:ASN18 3.1 23.0 1.0
CG B:ASP193 3.2 33.3 1.0
OD1 B:ASP193 3.2 27.6 1.0
C B:VAL21 3.2 24.8 1.0
CD B:GLN163 3.3 39.6 1.0
C B:ASP15 3.4 28.2 1.0
N B:ASN18 3.6 32.7 1.0
NE2 B:GLN163 3.7 21.1 1.0
CA B:ASN18 3.8 19.7 1.0
CA B:TRP16 4.0 23.0 1.0
OH B:TYR161 4.0 32.2 1.0
CA B:VAL21 4.0 32.5 1.0
N B:PRO19 4.0 26.7 1.0
N B:TRP16 4.1 23.6 1.0
C B:TRP16 4.1 31.4 1.0
CB B:VAL21 4.2 39.7 1.0
CB B:ASN18 4.2 22.2 1.0
N B:VAL21 4.2 22.9 1.0
N B:THR22 4.3 29.6 1.0
N B:GLU17 4.3 30.0 1.0
CE2 B:TYR161 4.4 15.3 1.0
CA B:PRO19 4.5 26.0 1.0
CA B:ASP15 4.5 25.9 1.0
CG B:GLN163 4.5 20.2 1.0
CG1 B:VAL21 4.6 38.5 1.0
CA B:THR22 4.6 28.4 1.0
CB B:ASP193 4.6 25.9 1.0
CZ B:TYR161 4.7 47.8 1.0
O B:TRP16 4.7 22.9 1.0
C B:GLU17 4.8 34.0 1.0
C B:PRO19 4.9 37.9 1.0
CB B:ASP15 5.0 18.0 1.0

Magnesium binding site 5 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:23.0
occ:1.00
 O C:HOH8592 2.0 19.2 1.0
O C:HOH8670 2.0 18.2 1.0
OE2 C:GLU416 2.1 25.2 1.0
O C:HOH8528 2.1 14.3 1.0
OE1 C:GLU461 2.1 15.9 1.0
ND1 C:HIS418 2.3 23.3 1.0
CD C:GLU416 3.1 50.1 1.0
CD C:GLU461 3.2 26.1 1.0
CE1 C:HIS418 3.3 17.6 1.0
CG C:HIS418 3.4 20.0 1.0
OE1 C:GLU416 3.5 22.8 1.0
CB C:HIS418 3.7 15.4 1.0
OD1 C:ASN102 4.0 23.1 1.0
OE2 C:GLU461 4.0 20.2 1.0
CB C:ASP201 4.0 32.3 1.0
N C:ASP201 4.1 32.8 1.0
O C:ASP199 4.1 22.8 1.0
CG C:GLU461 4.2 18.7 1.0
CB C:GLU461 4.2 17.1 1.0
O4 C:2FG2001 4.2 19.7 1.0
ND2 C:ASN460 4.2 16.3 1.0
O3 C:2FG2001 4.3 20.9 1.0
CG C:GLU416 4.4 11.0 1.0
NE2 C:HIS418 4.5 19.1 1.0
CD2 C:HIS418 4.5 21.4 1.0
O C:ASN102 4.5 25.5 1.0
C2 C:2FG2001 4.6 24.1 1.0
CA C:ASP201 4.7 29.0 1.0
F2 C:2FG2001 4.8 24.7 1.0
CA C:GLN200 4.8 20.0 1.0
C C:GLN200 4.9 31.7 1.0
CG2 C:VAL103 4.9 23.8 1.0
C3 C:2FG2001 5.0 22.2 1.0
O C:HOH8983 5.0 19.6 1.0

Magnesium binding site 6 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:26.3
occ:1.00
 O C:ASN18 2.2 23.9 1.0
O C:VAL21 2.2 15.8 1.0
OE1 C:GLN163 2.2 23.0 1.0
OD2 C:ASP193 2.4 25.4 1.0
O C:ASP15 2.5 39.0 1.0
C C:ASN18 3.1 32.1 1.0
OD1 C:ASP193 3.1 28.2 1.0
CG C:ASP193 3.1 26.0 1.0
CD C:GLN163 3.2 33.6 1.0
C C:VAL21 3.4 29.6 1.0
NE2 C:GLN163 3.5 15.6 1.0
C C:ASP15 3.6 40.8 1.0
N C:ASN18 3.7 24.4 1.0
CA C:ASN18 3.9 26.8 1.0
N C:PRO19 4.0 34.0 1.0
OH C:TYR161 4.1 24.8 1.0
CA C:VAL21 4.2 30.1 1.0
N C:VAL21 4.2 28.2 1.0
CA C:TRP16 4.2 27.5 1.0
CB C:VAL21 4.2 37.8 1.0
C C:TRP16 4.3 30.2 1.0
CB C:ASN18 4.3 15.7 1.0
CA C:PRO19 4.3 32.1 1.0
CE2 C:TYR161 4.3 14.4 1.0
N C:TRP16 4.4 26.7 1.0
N C:THR22 4.4 24.2 1.0
CG C:GLN163 4.4 23.5 1.0
CA C:THR22 4.5 24.6 1.0
N C:GLU17 4.5 20.1 1.0
CB C:ASP193 4.6 19.5 1.0
CA C:ASP15 4.7 29.8 1.0
O C:TRP16 4.7 28.2 1.0
CZ C:TYR161 4.7 28.2 1.0
C C:PRO19 4.8 42.2 1.0
CG1 C:VAL21 4.8 33.1 1.0
C C:GLU17 4.8 35.9 1.0
CB C:ASP15 4.9 37.4 1.0

Magnesium binding site 7 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:19.9
occ:1.00
 O D:HOH8546 2.0 15.9 1.0
O D:HOH8685 2.0 19.6 1.0
OE1 D:GLU461 2.1 17.7 1.0
OE2 D:GLU416 2.1 19.0 1.0
O D:HOH8610 2.2 16.7 1.0
ND1 D:HIS418 2.2 18.6 1.0
CE1 D:HIS418 3.0 18.0 1.0
CD D:GLU461 3.2 22.8 1.0
CD D:GLU416 3.2 37.2 1.0
CG D:HIS418 3.3 21.8 1.0
OE1 D:GLU416 3.5 21.7 1.0
CB D:HIS418 3.7 16.9 1.0
CB D:GLU461 4.0 12.2 1.0
OE2 D:GLU461 4.0 15.5 1.0
OD1 D:ASN102 4.1 25.8 1.0
ND2 D:ASN460 4.1 13.5 1.0
CG D:GLU461 4.1 15.6 1.0
N D:ASP201 4.2 24.1 1.0
CB D:ASP201 4.2 22.9 1.0
NE2 D:HIS418 4.2 16.9 1.0
O4 D:2FG2001 4.2 18.5 1.0
O3 D:2FG2001 4.3 23.8 1.0
O D:ASP199 4.3 23.4 1.0
CD2 D:HIS418 4.3 20.2 1.0
CG D:GLU416 4.4 13.9 1.0
C2 D:2FG2001 4.5 23.8 1.0
CA D:ASP201 4.7 25.7 1.0
O D:ASN102 4.8 22.7 1.0
O D:HOH9001 4.8 16.5 1.0
C3 D:2FG2001 4.8 24.3 1.0
CA D:GLN200 4.9 15.6 1.0
F2 D:2FG2001 4.9 22.4 1.0
C D:GLN200 4.9 23.6 1.0

Magnesium binding site 8 out of 8 in 1jz2

Go back to Magnesium Binding Sites List in 1jz2
Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic)


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-Trapped 2-F-Galactosyl- Enzyme Intermediate (Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:26.6
occ:1.00
 O D:ASN18 2.1 20.5 1.0
O D:VAL21 2.3 20.5 1.0
OD2 D:ASP193 2.3 15.1 1.0
OE1 D:GLN163 2.3 34.2 1.0
O D:ASP15 2.5 29.3 1.0
OD1 D:ASP193 2.8 15.3 1.0
CG D:ASP193 2.9 29.2 1.0
C D:ASN18 3.0 25.5 1.0
CD D:GLN163 3.2 28.3 1.0
C D:VAL21 3.4 24.4 1.0
NE2 D:GLN163 3.4 21.6 1.0
N D:ASN18 3.6 30.6 1.0
C D:ASP15 3.7 27.5 1.0
CA D:ASN18 3.8 27.4 1.0
N D:PRO19 3.9 25.5 1.0
CA D:PRO19 4.0 34.0 1.0
N D:VAL21 4.1 16.6 1.0
CA D:VAL21 4.1 13.7 1.0
OH D:TYR161 4.2 30.1 1.0
CA D:TRP16 4.2 22.4 1.0
CB D:VAL21 4.3 18.6 1.0
CB D:ASN18 4.3 21.9 1.0
CB D:ASP193 4.4 18.4 1.0
N D:THR22 4.4 20.5 1.0
C D:TRP16 4.4 22.7 1.0
N D:TRP16 4.4 23.0 1.0
CA D:THR22 4.4 23.9 1.0
CG D:GLN163 4.5 20.6 1.0
N D:GLU17 4.5 25.0 1.0
C D:PRO19 4.5 31.0 1.0
CE2 D:TYR161 4.6 30.6 1.0
CA D:ASP15 4.8 29.7 1.0
CG1 D:VAL21 4.8 17.3 1.0
N D:GLY20 4.8 22.1 1.0
C D:GLU17 4.8 35.6 1.0
O D:TRP16 4.8 26.1 1.0
CG2 D:THR22 4.8 19.6 1.0
CZ D:TYR161 4.9 49.9 1.0

Reference:

D.H.Juers, T.D.Heightman, A.Vasella, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews. A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Mon Dec 14 06:12:09 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