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Magnesium in PDB 3vd5: E. Coli (Lacz) Beta-Galactosidase (N460S)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S)

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S), PDB code: 3vd5 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) 54.58 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 126.299, 150.745, 131.086, 90.00, 104.06, 90.00
R / Rfree (%) 20.3 / 27.6

Other elements in 3vd5:

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

Sodium (Na) 11 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460S) (pdb code 3vd5). 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 (N460S), PDB code: 3vd5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3vd5

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:51.6
occ:1.00
 O A:HOH4195 2.0 44.3 1.0
OE2 A:GLU416 2.1 46.0 1.0
OE1 A:GLU461 2.1 46.8 1.0
O A:HOH4194 2.1 35.5 1.0
ND1 A:HIS418 2.4 46.2 1.0
O A:HOH4041 2.8 35.2 1.0
CD A:GLU461 2.9 43.5 1.0
CD A:GLU416 3.3 38.0 1.0
CE1 A:HIS418 3.3 46.2 1.0
OE2 A:GLU461 3.3 43.9 1.0
CG A:HIS418 3.4 43.7 1.0
CB A:HIS418 3.6 38.7 1.0
OD1 A:ASN102 3.8 46.1 1.0
OE1 A:GLU416 3.8 47.0 1.0
CB A:ASP201 4.0 43.0 1.0
CG A:GLU461 4.0 41.3 1.0
CB A:GLU461 4.1 38.6 1.0
N A:ASP201 4.1 39.3 1.0
O A:ASP199 4.3 36.3 1.0
CG A:GLU416 4.4 33.8 1.0
O A:HOH4105 4.4 46.8 1.0
NE2 A:HIS418 4.5 49.2 1.0
CD2 A:HIS418 4.5 44.8 1.0
CA A:ASP201 4.6 40.6 1.0
O A:ASN102 4.9 44.1 1.0
C A:GLN200 4.9 36.7 1.0
CA A:GLN200 5.0 34.4 1.0
CG2 A:VAL103 5.0 37.1 1.0

Magnesium binding site 2 out of 8 in 3vd5

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:43.2
occ:1.00
 OD2 A:ASP193 2.1 41.5 1.0
O A:ASP15 2.3 43.7 1.0
O A:ASN18 2.3 40.4 1.0
OE1 A:GLN163 2.3 44.1 1.0
O A:VAL21 2.3 42.3 1.0
CG A:ASP193 3.0 37.6 1.0
C A:ASN18 3.2 41.9 1.0
OD1 A:ASP193 3.2 37.5 1.0
CD A:GLN163 3.2 33.1 1.0
C A:VAL21 3.4 38.1 1.0
C A:ASP15 3.5 44.8 1.0
NE2 A:GLN163 3.5 36.4 1.0
N A:ASN18 3.7 45.8 1.0
CA A:ASN18 3.9 42.4 1.0
OH A:TYR161 3.9 44.8 1.0
N A:PRO19 4.1 41.3 1.0
CA A:TRP16 4.1 41.8 1.0
CA A:VAL21 4.2 36.8 1.0
N A:TRP16 4.2 44.8 1.0
C A:TRP16 4.2 40.4 1.0
CB A:VAL21 4.3 34.6 1.0
CA A:PRO19 4.3 41.5 1.0
CB A:ASN18 4.3 44.0 1.0
CE2 A:TYR161 4.3 37.4 1.0
N A:VAL21 4.3 37.2 1.0
CB A:ASP193 4.4 34.1 1.0
N A:THR22 4.4 36.5 1.0
CA A:THR22 4.5 36.8 1.0
CA A:ASP15 4.5 44.6 1.0
CG A:GLN163 4.5 36.6 1.0
N A:GLU17 4.5 41.4 1.0
CZ A:TYR161 4.6 37.6 1.0
O A:TRP16 4.6 40.6 1.0
CG1 A:VAL21 4.8 30.2 1.0
C A:PRO19 4.8 42.8 1.0
C A:GLU17 4.9 44.0 1.0

Magnesium binding site 3 out of 8 in 3vd5

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:42.6
occ:1.00
 O C:HOH4171 2.0 43.9 1.0
OE2 C:GLU416 2.1 33.9 1.0
OE1 C:GLU461 2.1 45.7 1.0
O C:HOH4109 2.3 48.1 1.0
ND1 C:HIS418 2.4 48.1 1.0
O C:HOH4017 2.4 30.0 1.0
CD C:GLU461 3.0 48.1 1.0
CD C:GLU416 3.2 36.3 1.0
CE1 C:HIS418 3.3 48.2 1.0
CG C:HIS418 3.4 48.6 1.0
OE2 C:GLU461 3.5 53.4 1.0
CB C:HIS418 3.7 43.5 1.0
OE1 C:GLU416 3.7 31.3 1.0
CG C:GLU461 4.1 48.5 1.0
CB C:GLU461 4.1 44.8 1.0
CB C:ASP201 4.3 56.3 1.0
CG C:GLU416 4.3 38.8 1.0
OD1 C:ASN102 4.4 52.2 1.0
O C:ASP199 4.4 48.4 1.0
N C:ASP201 4.4 52.5 1.0
NE2 C:HIS418 4.4 50.5 1.0
CD2 C:HIS418 4.5 51.1 1.0
O C:ASN102 4.6 52.0 1.0
CA C:ASP201 4.9 55.2 1.0

Magnesium binding site 4 out of 8 in 3vd5

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:54.5
occ:1.00
 OD2 C:ASP193 2.1 54.6 1.0
O C:ASN18 2.3 54.5 1.0
O C:VAL21 2.3 52.9 1.0
O C:ASP15 2.3 56.9 1.0
OE1 C:GLN163 2.3 62.9 1.0
CG C:ASP193 3.1 54.4 1.0
CD C:GLN163 3.3 63.5 1.0
C C:ASN18 3.3 55.3 1.0
C C:VAL21 3.5 51.3 1.0
C C:ASP15 3.5 56.9 1.0
OD1 C:ASP193 3.5 57.4 1.0
NE2 C:GLN163 3.7 64.8 1.0
N C:ASN18 3.8 55.9 1.0
OH C:TYR161 3.8 50.2 1.0
CA C:ASN18 4.0 55.7 1.0
CA C:TRP16 4.3 55.9 1.0
N C:TRP16 4.3 56.3 1.0
CA C:VAL21 4.3 51.4 1.0
CE2 C:TYR161 4.3 49.1 1.0
CB C:ASN18 4.4 55.1 1.0
CB C:VAL21 4.4 50.5 1.0
N C:PRO19 4.4 55.9 1.0
N C:VAL21 4.4 51.2 1.0
N C:THR22 4.4 52.2 1.0
CB C:ASP193 4.5 50.4 1.0
CA C:ASP15 4.5 57.5 1.0
C C:TRP16 4.5 54.4 1.0
CA C:THR22 4.5 53.1 1.0
CZ C:TYR161 4.6 51.4 1.0
N C:GLU17 4.6 54.8 1.0
CG C:GLN163 4.6 59.3 1.0
CA C:PRO19 4.7 56.9 1.0
CG1 C:VAL21 4.8 51.6 1.0
CB C:ASP15 4.9 56.2 1.0

Magnesium binding site 5 out of 8 in 3vd5

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Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:39.1
occ:1.00
 O D:HOH4231 1.9 52.4 1.0
OE2 D:GLU416 2.1 38.3 1.0
OE1 D:GLU461 2.1 47.0 1.0
O D:HOH4232 2.3 54.0 1.0
O D:HOH4134 2.3 33.3 1.0
ND1 D:HIS418 2.4 38.9 1.0
CD D:GLU461 2.9 50.7 1.0
CD D:GLU416 3.2 36.8 1.0
CE1 D:HIS418 3.3 32.2 1.0
OE2 D:GLU461 3.3 51.0 1.0
CG D:HIS418 3.4 36.5 1.0
OE1 D:GLU416 3.7 37.1 1.0
CB D:HIS418 3.8 36.9 1.0
CG D:GLU461 4.0 42.7 1.0
CB D:ASP201 4.0 46.3 1.0
CB D:GLU461 4.1 35.7 1.0
N D:ASP201 4.1 44.7 1.0
OD1 D:ASN102 4.3 56.5 1.0
O D:ASN102 4.3 51.6 1.0
NE2 D:HIS418 4.4 35.6 1.0
CG D:GLU416 4.4 34.7 1.0
O D:ASP199 4.4 42.3 1.0
CD2 D:HIS418 4.5 26.4 1.0
CA D:ASP201 4.6 45.5 1.0
O D:HOH4081 4.8 39.7 1.0
C D:GLN200 4.9 42.3 1.0
CA D:GLN200 5.0 41.4 1.0
CG2 D:VAL103 5.0 42.5 1.0

Magnesium binding site 6 out of 8 in 3vd5

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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

b:42.4
occ:1.00
 OD2 D:ASP193 2.1 44.1 1.0
O D:ASN18 2.3 41.9 1.0
O D:ASP15 2.3 44.0 1.0
OE1 D:GLN163 2.3 34.8 1.0
O D:VAL21 2.3 39.2 1.0
CG D:ASP193 2.8 44.3 1.0
OD1 D:ASP193 2.9 44.6 1.0
C D:ASN18 3.1 40.6 1.0
CD D:GLN163 3.2 33.1 1.0
C D:ASP15 3.5 42.8 1.0
C D:VAL21 3.5 35.9 1.0
N D:ASN18 3.5 41.8 1.0
NE2 D:GLN163 3.6 36.5 1.0
CA D:ASN18 3.8 39.5 1.0
CA D:TRP16 4.0 41.3 1.0
N D:PRO19 4.1 38.7 1.0
C D:TRP16 4.2 40.8 1.0
N D:TRP16 4.2 43.4 1.0
CB D:ASN18 4.2 40.7 1.0
CA D:VAL21 4.3 35.0 1.0
OH D:TYR161 4.3 30.5 1.0
CB D:ASP193 4.3 40.5 1.0
N D:GLU17 4.3 39.7 1.0
CA D:PRO19 4.3 37.1 1.0
N D:VAL21 4.3 37.7 1.0
CB D:VAL21 4.3 35.2 1.0
N D:THR22 4.5 33.7 1.0
CG D:GLN163 4.5 32.7 1.0
CA D:ASP15 4.6 41.8 1.0
CA D:THR22 4.6 35.3 1.0
CE2 D:TYR161 4.6 32.1 1.0
O D:TRP16 4.7 39.1 1.0
C D:GLU17 4.7 42.9 1.0
C D:PRO19 4.9 35.9 1.0
CG1 D:VAL21 4.9 31.9 1.0
CZ D:TYR161 4.9 31.7 1.0

Magnesium binding site 7 out of 8 in 3vd5

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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 (N460S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:50.7
occ:1.00
 OE2 B:GLU416 2.1 48.0 1.0
OE1 B:GLU461 2.1 52.9 1.0
O B:HOH4211 2.1 39.0 1.0
O B:HOH4027 2.2 42.8 1.0
ND1 B:HIS418 2.4 48.6 1.0
O B:HOH4111 2.5 24.3 1.0
CD B:GLU461 3.2 48.0 1.0
CD B:GLU416 3.3 45.1 1.0
CE1 B:HIS418 3.3 46.9 1.0
CG B:HIS418 3.3 51.4 1.0
CB B:HIS418 3.6 48.6 1.0
OE2 B:GLU461 3.8 48.1 1.0
OE1 B:GLU416 4.0 47.3 1.0
OD1 B:ASN102 4.1 55.5 1.0
N B:ASP201 4.2 58.6 1.0
CB B:ASP201 4.2 58.8 1.0
O B:ASP199 4.2 53.1 1.0
CG B:GLU461 4.3 41.7 1.0
CG B:GLU416 4.3 43.0 1.0
CB B:GLU461 4.4 44.3 1.0
O B:ASN102 4.4 57.5 1.0
NE2 B:HIS418 4.4 49.8 1.0
O B:HOH4005 4.5 44.2 1.0
CD2 B:HIS418 4.5 49.8 1.0
O B:HOH4014 4.6 51.3 1.0
CA B:ASP201 4.7 58.5 1.0
C B:GLN200 4.8 55.8 1.0
CA B:GLN200 5.0 55.6 1.0

Magnesium binding site 8 out of 8 in 3vd5

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460S)


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 (N460S) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:56.1
occ:1.00
 OD2 B:ASP193 2.1 63.1 1.0
O B:VAL21 2.3 50.5 1.0
O B:ASP15 2.3 55.9 1.0
OE1 B:GLN163 2.3 52.2 1.0
O B:ASN18 2.3 55.9 1.0
CG B:ASP193 2.9 57.6 1.0
OD1 B:ASP193 3.1 61.3 1.0
C B:ASN18 3.2 55.0 1.0
CD B:GLN163 3.3 52.1 1.0
C B:VAL21 3.5 47.9 1.0
C B:ASP15 3.5 56.5 1.0
NE2 B:GLN163 3.7 50.5 1.0
N B:ASN18 3.7 55.1 1.0
OH B:TYR161 3.9 40.1 1.0
CA B:ASN18 3.9 54.6 1.0
N B:PRO19 4.1 53.4 1.0
CA B:TRP16 4.2 53.9 1.0
CB B:ASN18 4.2 56.3 1.0
N B:TRP16 4.3 55.2 1.0
CA B:VAL21 4.3 48.7 1.0
CB B:VAL21 4.3 47.6 1.0
CB B:ASP193 4.3 51.4 1.0
CE2 B:TYR161 4.3 43.2 1.0
CA B:PRO19 4.4 52.0 1.0
N B:VAL21 4.4 51.8 1.0
C B:TRP16 4.4 53.5 1.0
N B:THR22 4.4 46.6 1.0
CA B:ASP15 4.5 58.8 1.0
N B:GLU17 4.5 55.0 1.0
CA B:THR22 4.6 45.8 1.0
CG B:GLN163 4.6 49.5 1.0
CZ B:TYR161 4.6 42.7 1.0
CG1 B:VAL21 4.7 46.4 1.0
C B:PRO19 4.8 51.3 1.0
C B:GLU17 4.9 56.1 1.0
O B:TRP16 4.9 52.7 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 12:55:24 2024

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