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Magnesium in PDB 1f4a: E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- Orthorhombic)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- Orthorhombic)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- Orthorhombic):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- Orthorhombic), PDB code: 1f4a was solved by D.H.Juers, R.H.Jacobson, D.Wigley, X.J.Zhang, R.E.Huber, D.E.Tronrud, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 153.400, 173.400, 204.400, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- Orthorhombic) (pdb code 1f4a). 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 (Ncs Constrained Monomer- Orthorhombic), PDB code: 1f4a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1f4a

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:28.3
occ:1.00
 OE2 A:GLU461 1.9 58.4 1.0
O A:HOH4156 2.2 27.9 1.0
O A:HOH4014 2.4 29.4 1.0
ND1 A:HIS418 2.4 30.3 1.0
OE1 A:GLU416 2.8 6.3 1.0
CE1 A:HIS418 2.9 24.2 1.0
CD A:GLU461 3.0 47.7 1.0
ND2 A:ASN102 3.1 35.9 1.0
O A:HOH4568 3.6 57.4 1.0
CG A:HIS418 3.7 27.6 1.0
OE1 A:GLU461 3.7 7.8 1.0
CB A:ASP201 3.7 38.2 1.0
O A:HOH4001 3.8 54.1 1.0
CG A:GLU461 3.9 41.8 1.0
CD A:GLU416 3.9 44.2 1.0
N A:ASP201 4.1 26.1 1.0
NE2 A:HIS418 4.2 21.4 1.0
CB A:HIS418 4.3 21.7 1.0
O A:HOH4298 4.3 45.0 1.0
O A:ASN102 4.4 44.1 1.0
CG A:ASN102 4.4 48.3 1.0
CG2 A:VAL103 4.4 23.1 1.0
OE2 A:GLU416 4.5 6.7 1.0
CA A:ASP201 4.5 31.2 1.0
CD2 A:HIS418 4.6 26.8 1.0
C A:ASN102 4.8 42.1 1.0
CG A:ASP201 4.8 58.2 1.0
O A:ASP199 4.8 23.5 1.0
ND2 A:ASN460 4.8 29.4 1.0

Magnesium binding site 2 out of 8 in 1f4a

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:31.9
occ:1.00
 O A:VAL21 2.1 38.5 1.0
NE2 A:GLN163 2.2 21.3 1.0
OD2 A:ASP193 2.3 12.6 1.0
O A:ASN18 2.3 24.8 1.0
O A:ASP15 2.4 32.3 1.0
CD A:GLN163 3.0 30.8 1.0
C A:ASN18 3.1 32.4 1.0
CG A:ASP193 3.1 33.3 1.0
OE1 A:GLN163 3.2 28.4 1.0
OD1 A:ASP193 3.3 36.8 1.0
C A:VAL21 3.3 26.9 1.0
C A:ASP15 3.6 27.5 1.0
N A:ASN18 3.8 32.4 1.0
CA A:ASN18 3.9 27.1 1.0
N A:PRO19 3.9 29.5 1.0
OH A:TYR161 4.0 22.8 1.0
CE2 A:TYR161 4.1 18.6 1.0
CA A:VAL21 4.1 15.2 1.0
CA A:TRP16 4.1 21.3 1.0
N A:VAL21 4.2 22.8 1.0
CB A:VAL21 4.3 22.9 1.0
N A:TRP16 4.3 23.4 1.0
CA A:PRO19 4.3 27.1 1.0
N A:THR22 4.3 19.4 1.0
CG A:GLN163 4.3 15.0 1.0
CA A:THR22 4.4 18.6 1.0
C A:TRP16 4.5 25.3 1.0
CB A:ASP193 4.5 14.6 1.0
CZ A:TYR161 4.5 28.9 1.0
CB A:ASN18 4.5 27.1 1.0
CG1 A:VAL21 4.7 17.9 1.0
CA A:ASP15 4.7 24.6 1.0
N A:GLU17 4.7 20.4 1.0
C A:PRO19 4.8 28.2 1.0
CG2 A:THR22 4.9 18.9 1.0
CB A:ASP15 5.0 26.3 1.0
N A:GLY20 5.0 20.1 1.0

Magnesium binding site 3 out of 8 in 1f4a

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:28.3
occ:1.00
 OE2 B:GLU461 1.9 58.4 1.0
O B:HOH4198 2.2 27.9 1.0
O B:HOH4078 2.4 29.4 1.0
ND1 B:HIS418 2.4 30.3 1.0
OE1 B:GLU416 2.8 6.3 1.0
CE1 B:HIS418 2.9 24.2 1.0
CD B:GLU461 3.0 47.7 1.0
ND2 B:ASN102 3.1 35.9 1.0
O B:HOH4349 3.6 57.4 1.0
CG B:HIS418 3.7 27.6 1.0
OE1 B:GLU461 3.7 7.8 1.0
CB B:ASP201 3.7 38.2 1.0
O B:HOH4068 3.8 54.1 1.0
CG B:GLU461 3.9 41.8 1.0
CD B:GLU416 3.9 44.2 1.0
N B:ASP201 4.1 26.1 1.0
NE2 B:HIS418 4.2 21.4 1.0
CB B:HIS418 4.3 21.7 1.0
O B:HOH4275 4.3 45.0 1.0
O B:ASN102 4.4 44.1 1.0
CG B:ASN102 4.4 48.3 1.0
CG2 B:VAL103 4.4 23.1 1.0
OE2 B:GLU416 4.5 6.7 1.0
CA B:ASP201 4.5 31.2 1.0
CD2 B:HIS418 4.6 26.8 1.0
C B:ASN102 4.8 42.1 1.0
CG B:ASP201 4.8 58.2 1.0
O B:ASP199 4.8 23.5 1.0
ND2 B:ASN460 4.8 29.4 1.0

Magnesium binding site 4 out of 8 in 1f4a

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:31.9
occ:1.00
 O B:VAL21 2.1 38.5 1.0
NE2 B:GLN163 2.2 21.3 1.0
OD2 B:ASP193 2.3 12.6 1.0
O B:ASN18 2.3 24.8 1.0
O B:ASP15 2.4 32.3 1.0
CD B:GLN163 3.0 30.8 1.0
C B:ASN18 3.1 32.4 1.0
CG B:ASP193 3.1 33.3 1.0
OE1 B:GLN163 3.2 28.4 1.0
OD1 B:ASP193 3.3 36.8 1.0
C B:VAL21 3.3 26.9 1.0
C B:ASP15 3.6 27.5 1.0
N B:ASN18 3.8 32.4 1.0
CA B:ASN18 3.9 27.1 1.0
N B:PRO19 3.9 29.5 1.0
OH B:TYR161 4.0 22.8 1.0
CE2 B:TYR161 4.1 18.6 1.0
CA B:VAL21 4.1 15.2 1.0
CA B:TRP16 4.1 21.3 1.0
N B:VAL21 4.2 22.8 1.0
CB B:VAL21 4.3 22.9 1.0
N B:TRP16 4.3 23.4 1.0
CA B:PRO19 4.3 27.1 1.0
N B:THR22 4.3 19.4 1.0
CG B:GLN163 4.3 15.0 1.0
CA B:THR22 4.4 18.6 1.0
C B:TRP16 4.5 25.3 1.0
CB B:ASP193 4.5 14.6 1.0
CZ B:TYR161 4.5 28.9 1.0
CB B:ASN18 4.5 27.1 1.0
CG1 B:VAL21 4.7 17.9 1.0
CA B:ASP15 4.7 24.6 1.0
N B:GLU17 4.7 20.4 1.0
C B:PRO19 4.8 28.2 1.0
CG2 B:THR22 4.9 18.9 1.0
CB B:ASP15 5.0 26.3 1.0
N B:GLY20 5.0 20.1 1.0

Magnesium binding site 5 out of 8 in 1f4a

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:28.3
occ:1.00
 OE2 C:GLU461 1.9 58.4 1.0
O C:HOH4238 2.2 27.9 1.0
O C:HOH4118 2.4 29.4 1.0
ND1 C:HIS418 2.4 30.3 1.0
OE1 C:GLU416 2.8 6.3 1.0
CE1 C:HIS418 2.9 24.2 1.0
CD C:GLU461 3.0 47.7 1.0
ND2 C:ASN102 3.1 35.9 1.0
O C:HOH4389 3.6 57.4 1.0
CG C:HIS418 3.7 27.6 1.0
OE1 C:GLU461 3.7 7.8 1.0
CB C:ASP201 3.7 38.2 1.0
O C:HOH4108 3.8 54.1 1.0
CG C:GLU461 3.9 41.8 1.0
CD C:GLU416 3.9 44.2 1.0
N C:ASP201 4.1 26.1 1.0
NE2 C:HIS418 4.2 21.4 1.0
CB C:HIS418 4.3 21.7 1.0
O C:HOH4315 4.3 45.0 1.0
O C:ASN102 4.4 44.1 1.0
CG C:ASN102 4.4 48.3 1.0
CG2 C:VAL103 4.4 23.1 1.0
OE2 C:GLU416 4.5 6.7 1.0
CA C:ASP201 4.5 31.2 1.0
CD2 C:HIS418 4.6 26.8 1.0
C C:ASN102 4.8 42.1 1.0
CG C:ASP201 4.8 58.2 1.0
O C:ASP199 4.8 23.5 1.0
ND2 C:ASN460 4.8 29.4 1.0

Magnesium binding site 6 out of 8 in 1f4a

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:31.9
occ:1.00
 O C:VAL21 2.1 38.5 1.0
NE2 C:GLN163 2.2 21.3 1.0
OD2 C:ASP193 2.3 12.6 1.0
O C:ASN18 2.3 24.8 1.0
O C:ASP15 2.4 32.3 1.0
CD C:GLN163 3.0 30.8 1.0
C C:ASN18 3.1 32.4 1.0
CG C:ASP193 3.1 33.3 1.0
OE1 C:GLN163 3.2 28.4 1.0
OD1 C:ASP193 3.3 36.8 1.0
C C:VAL21 3.3 26.9 1.0
C C:ASP15 3.6 27.5 1.0
N C:ASN18 3.8 32.4 1.0
CA C:ASN18 3.9 27.1 1.0
N C:PRO19 3.9 29.5 1.0
OH C:TYR161 4.0 22.8 1.0
CE2 C:TYR161 4.1 18.6 1.0
CA C:VAL21 4.1 15.2 1.0
CA C:TRP16 4.1 21.3 1.0
N C:VAL21 4.2 22.8 1.0
CB C:VAL21 4.3 22.9 1.0
N C:TRP16 4.3 23.4 1.0
CA C:PRO19 4.3 27.1 1.0
N C:THR22 4.3 19.4 1.0
CG C:GLN163 4.3 15.0 1.0
CA C:THR22 4.4 18.6 1.0
C C:TRP16 4.5 25.3 1.0
CB C:ASP193 4.5 14.6 1.0
CZ C:TYR161 4.5 28.9 1.0
CB C:ASN18 4.5 27.1 1.0
CG1 C:VAL21 4.7 17.9 1.0
CA C:ASP15 4.7 24.6 1.0
N C:GLU17 4.7 20.4 1.0
C C:PRO19 4.8 28.2 1.0
CG2 C:THR22 4.9 18.9 1.0
CB C:ASP15 5.0 26.3 1.0
N C:GLY20 5.0 20.1 1.0

Magnesium binding site 7 out of 8 in 1f4a

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:28.3
occ:1.00
 OE2 D:GLU461 1.9 58.4 1.0
O D:HOH4156 2.2 27.9 1.0
O D:HOH4014 2.4 29.4 1.0
ND1 D:HIS418 2.4 30.3 1.0
OE1 D:GLU416 2.8 6.3 1.0
CE1 D:HIS418 2.9 24.2 1.0
CD D:GLU461 3.0 47.7 1.0
ND2 D:ASN102 3.1 35.9 1.0
O D:HOH4568 3.6 57.4 1.0
CG D:HIS418 3.7 27.6 1.0
OE1 D:GLU461 3.7 7.8 1.0
CB D:ASP201 3.7 38.2 1.0
O D:HOH4001 3.8 54.1 1.0
CG D:GLU461 3.9 41.8 1.0
CD D:GLU416 3.9 44.2 1.0
N D:ASP201 4.1 26.1 1.0
NE2 D:HIS418 4.2 21.4 1.0
CB D:HIS418 4.3 21.7 1.0
O D:HOH4298 4.3 45.0 1.0
O D:ASN102 4.4 44.1 1.0
CG D:ASN102 4.4 48.3 1.0
CG2 D:VAL103 4.4 23.1 1.0
OE2 D:GLU416 4.5 6.7 1.0
CA D:ASP201 4.5 31.2 1.0
CD2 D:HIS418 4.6 26.8 1.0
C D:ASN102 4.8 42.1 1.0
CG D:ASP201 4.8 58.2 1.0
O D:ASP199 4.8 23.5 1.0
ND2 D:ASN460 4.8 29.4 1.0

Magnesium binding site 8 out of 8 in 1f4a

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (Ncs Constrained Monomer- 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 (Ncs Constrained Monomer- Orthorhombic) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3002

b:31.9
occ:1.00
 O D:VAL21 2.1 38.5 1.0
NE2 D:GLN163 2.2 21.3 1.0
OD2 D:ASP193 2.3 12.6 1.0
O D:ASN18 2.3 24.8 1.0
O D:ASP15 2.4 32.3 1.0
CD D:GLN163 3.0 30.8 1.0
C D:ASN18 3.1 32.4 1.0
CG D:ASP193 3.1 33.3 1.0
OE1 D:GLN163 3.2 28.4 1.0
OD1 D:ASP193 3.3 36.8 1.0
C D:VAL21 3.3 26.9 1.0
C D:ASP15 3.6 27.5 1.0
N D:ASN18 3.8 32.4 1.0
CA D:ASN18 3.9 27.1 1.0
N D:PRO19 3.9 29.5 1.0
OH D:TYR161 4.0 22.8 1.0
CE2 D:TYR161 4.1 18.6 1.0
CA D:VAL21 4.1 15.2 1.0
CA D:TRP16 4.1 21.3 1.0
N D:VAL21 4.2 22.8 1.0
CB D:VAL21 4.3 22.9 1.0
N D:TRP16 4.3 23.4 1.0
CA D:PRO19 4.3 27.1 1.0
N D:THR22 4.3 19.4 1.0
CG D:GLN163 4.3 15.0 1.0
CA D:THR22 4.4 18.6 1.0
C D:TRP16 4.5 25.3 1.0
CB D:ASP193 4.5 14.6 1.0
CZ D:TYR161 4.5 28.9 1.0
CB D:ASN18 4.5 27.1 1.0
CG1 D:VAL21 4.7 17.9 1.0
CA D:ASP15 4.7 24.6 1.0
N D:GLU17 4.7 20.4 1.0
C D:PRO19 4.8 28.2 1.0
CG2 D:THR22 4.9 18.9 1.0
CB D:ASP15 5.0 26.3 1.0
N D:GLY20 5.0 20.1 1.0

Reference:

D.H.Juers, R.H.Jacobson, D.Wigley, X.J.Zhang, R.E.Huber, D.E.Tronrud, B.W.Matthews. High Resolution Refinement of Beta-Galactosidase in A New Crystal Form Reveals Multiple Metal-Binding Sites and Provides A Structural Basis For Alpha-Complementation. Protein Sci. V. 9 1685 2000.
ISSN: ISSN 0961-8368
PubMed: 11045615
Page generated: Tue Aug 13 03:06:55 2024

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