Atomistry » Magnesium » PDB 3v4k-3vdb » 3vda
Atomistry »
  Magnesium »
    PDB 3v4k-3vdb »
      3vda »

Magnesium in PDB 3vda: E. Coli (Lacz) Beta-Galactosidase (N460T)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T)

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T):
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T), PDB code: 3vda 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) 46.05 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.596, 164.691, 203.245, 90.00, 90.00, 90.00
R / Rfree (%) 17.4 / 23.7

Other elements in 3vda:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) also contains other interesting chemical elements:

Sodium (Na) 10 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:39.6
occ:1.00
 O A:HOH4417 2.0 50.8 1.0
O A:HOH4402 2.0 37.2 1.0
OE1 A:GLU461 2.1 33.1 1.0
OE2 A:GLU416 2.1 32.7 1.0
O A:HOH4376 2.1 31.3 1.0
ND1 A:HIS418 2.4 37.3 1.0
CD A:GLU461 3.2 40.7 1.0
CD A:GLU416 3.2 36.5 1.0
CE1 A:HIS418 3.3 35.8 1.0
CG A:HIS418 3.4 34.6 1.0
CB A:HIS418 3.7 30.9 1.0
OE1 A:GLU416 3.8 42.7 1.0
OE2 A:GLU461 3.9 38.2 1.0
OD1 A:ASN102 4.2 47.7 1.0
CG A:GLU461 4.2 35.4 1.0
O A:ASP199 4.3 33.8 1.0
N A:ASP201 4.3 37.1 1.0
CB A:ASP201 4.3 38.5 1.0
CB A:GLU461 4.3 28.5 1.0
CG A:GLU416 4.4 35.2 1.0
O A:HOH4081 4.4 38.4 1.0
NE2 A:HIS418 4.4 38.7 1.0
CD2 A:HIS418 4.5 34.3 1.0
O A:ASN102 4.7 45.6 1.0
O A:HOH4301 4.7 54.0 1.0
CA A:ASP201 4.8 38.8 1.0
C A:GLN200 5.0 36.7 1.0

Magnesium binding site 2 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:39.1
occ:1.00
 OD2 A:ASP193 2.1 40.4 1.0
O A:ASN18 2.3 39.2 1.0
O A:VAL21 2.3 40.4 1.0
OE1 A:GLN163 2.3 41.7 1.0
O A:ASP15 2.3 42.4 1.0
CG A:ASP193 2.9 37.1 1.0
OD1 A:ASP193 3.1 40.4 1.0
C A:ASN18 3.2 40.4 1.0
CD A:GLN163 3.3 39.5 1.0
C A:VAL21 3.5 40.9 1.0
C A:ASP15 3.5 43.9 1.0
N A:ASN18 3.6 46.0 1.0
NE2 A:GLN163 3.7 38.9 1.0
CA A:ASN18 3.9 42.9 1.0
OH A:TYR161 4.1 38.6 1.0
N A:PRO19 4.1 40.2 1.0
CA A:TRP16 4.1 41.9 1.0
CB A:ASN18 4.2 41.9 1.0
N A:TRP16 4.2 43.1 1.0
CA A:VAL21 4.3 41.3 1.0
CA A:PRO19 4.3 40.4 1.0
C A:TRP16 4.3 43.9 1.0
CB A:ASP193 4.4 35.1 1.0
N A:VAL21 4.4 41.0 1.0
CB A:VAL21 4.4 42.5 1.0
N A:THR22 4.5 41.7 1.0
N A:GLU17 4.5 43.8 1.0
CE2 A:TYR161 4.5 37.6 1.0
CG A:GLN163 4.6 35.6 1.0
CA A:THR22 4.6 43.4 1.0
CA A:ASP15 4.6 43.8 1.0
CZ A:TYR161 4.8 37.4 1.0
C A:GLU17 4.8 46.6 1.0
CG1 A:VAL21 4.9 40.6 1.0
O A:TRP16 4.9 43.5 1.0
C A:PRO19 5.0 41.1 1.0

Magnesium binding site 3 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:39.8
occ:1.00
 OE2 B:GLU416 2.1 43.0 1.0
OE1 B:GLU461 2.1 45.7 1.0
O B:HOH4367 2.1 30.5 1.0
O B:HOH4394 2.1 30.0 1.0
O B:HOH4019 2.3 36.8 1.0
ND1 B:HIS418 2.4 43.6 1.0
CD B:GLU461 3.1 45.9 1.0
CE1 B:HIS418 3.2 40.6 1.0
CD B:GLU416 3.2 43.1 1.0
CG B:HIS418 3.5 38.9 1.0
OE1 B:GLU416 3.7 42.6 1.0
OE2 B:GLU461 3.8 43.5 1.0
CB B:HIS418 3.9 39.3 1.0
CB B:GLU461 4.1 34.2 1.0
CG B:GLU461 4.1 38.6 1.0
O B:HOH4401 4.4 53.1 1.0
OD1 B:ASN102 4.4 45.5 1.0
NE2 B:HIS418 4.4 41.8 1.0
CG B:GLU416 4.4 38.3 1.0
CB B:ASP201 4.5 35.6 1.0
O B:ASP199 4.5 41.3 1.0
CD2 B:HIS418 4.5 39.7 1.0
N B:ASP201 4.6 37.6 1.0
O B:ASN102 4.9 39.9 1.0

Magnesium binding site 4 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:46.7
occ:1.00
 OD2 B:ASP193 2.1 48.8 1.0
O B:ASN18 2.3 46.1 1.0
O B:VAL21 2.3 45.5 1.0
OE1 B:GLN163 2.3 41.8 1.0
O B:ASP15 2.3 47.7 1.0
CG B:ASP193 2.9 42.6 1.0
OD1 B:ASP193 3.1 51.2 1.0
CD B:GLN163 3.2 48.3 1.0
C B:ASN18 3.3 46.6 1.0
C B:VAL21 3.5 43.8 1.0
C B:ASP15 3.5 48.6 1.0
NE2 B:GLN163 3.6 53.0 1.0
N B:ASN18 3.7 48.0 1.0
CA B:ASN18 4.0 46.3 1.0
OH B:TYR161 4.0 35.4 1.0
CA B:TRP16 4.2 49.1 1.0
N B:PRO19 4.2 45.8 1.0
N B:TRP16 4.3 48.7 1.0
C B:TRP16 4.3 50.9 1.0
CA B:VAL21 4.3 45.2 1.0
CB B:ASP193 4.4 37.9 1.0
CE2 B:TYR161 4.4 43.1 1.0
N B:THR22 4.4 43.2 1.0
CA B:PRO19 4.4 45.9 1.0
N B:VAL21 4.5 45.3 1.0
N B:GLU17 4.5 48.6 1.0
CG B:GLN163 4.5 47.5 1.0
CB B:VAL21 4.5 45.3 1.0
CB B:ASN18 4.5 46.5 1.0
CA B:THR22 4.6 42.3 1.0
CA B:ASP15 4.6 48.9 1.0
CZ B:TYR161 4.7 42.5 1.0
O B:TRP16 4.8 52.6 1.0
C B:GLU17 4.9 49.0 1.0
CB B:ASP15 5.0 49.5 1.0
CG1 B:VAL21 5.0 45.9 1.0

Magnesium binding site 5 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 5 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:40.2
occ:1.00
 O C:HOH4364 2.0 36.6 1.0
OE1 C:GLU461 2.1 37.4 1.0
OE2 C:GLU416 2.1 41.1 1.0
O C:HOH4382 2.1 33.2 1.0
O C:HOH4314 2.1 37.0 1.0
ND1 C:HIS418 2.4 37.0 1.0
CD C:GLU416 3.2 38.3 1.0
CD C:GLU461 3.2 45.1 1.0
CE1 C:HIS418 3.3 39.5 1.0
CG C:HIS418 3.4 37.9 1.0
OE1 C:GLU416 3.7 40.1 1.0
CB C:HIS418 3.7 36.5 1.0
OE2 C:GLU461 4.0 43.5 1.0
OD1 C:ASN102 4.1 45.2 1.0
CB C:ASP201 4.2 39.9 1.0
O C:ASP199 4.2 35.8 1.0
CG C:GLU461 4.3 39.4 1.0
N C:ASP201 4.3 37.1 1.0
O C:ASN102 4.3 40.6 1.0
CB C:GLU461 4.4 34.6 1.0
NE2 C:HIS418 4.4 37.8 1.0
CG C:GLU416 4.5 39.2 1.0
CD2 C:HIS418 4.5 39.3 1.0
O C:HOH4067 4.6 33.5 1.0
O C:HOH4005 4.7 50.6 1.0
CA C:ASP201 4.8 38.7 1.0
C C:GLN200 4.9 35.9 1.0
CA C:GLN200 4.9 34.9 1.0

Magnesium binding site 6 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:44.7
occ:1.00
 OD2 C:ASP193 2.1 38.5 1.0
O C:VAL21 2.3 45.2 1.0
O C:ASP15 2.3 47.2 1.0
OE1 C:GLN163 2.3 42.4 1.0
O C:ASN18 2.3 47.9 1.0
CG C:ASP193 2.8 39.0 1.0
OD1 C:ASP193 2.9 44.1 1.0
C C:ASN18 3.3 47.8 1.0
CD C:GLN163 3.3 37.3 1.0
C C:VAL21 3.5 44.7 1.0
C C:ASP15 3.5 48.2 1.0
N C:ASN18 3.7 47.1 1.0
NE2 C:GLN163 3.8 42.3 1.0
OH C:TYR161 3.9 41.2 1.0
CA C:ASN18 3.9 47.6 1.0
CA C:TRP16 4.1 45.0 1.0
N C:TRP16 4.2 45.4 1.0
N C:PRO19 4.3 47.8 1.0
CB C:ASP193 4.3 35.8 1.0
C C:TRP16 4.3 46.2 1.0
CA C:VAL21 4.3 45.5 1.0
CB C:ASN18 4.4 47.0 1.0
N C:THR22 4.4 45.3 1.0
N C:VAL21 4.5 49.3 1.0
N C:GLU17 4.5 45.9 1.0
CB C:VAL21 4.5 46.6 1.0
CA C:PRO19 4.5 47.6 1.0
CG C:GLN163 4.5 39.5 1.0
CA C:THR22 4.6 44.5 1.0
CA C:ASP15 4.6 48.4 1.0
CE2 C:TYR161 4.6 40.4 1.0
CZ C:TYR161 4.7 38.1 1.0
O C:TRP16 4.8 47.8 1.0
CG1 C:VAL21 4.8 42.0 1.0
C C:GLU17 4.9 44.7 1.0
CB C:ASP15 4.9 48.1 1.0

Magnesium binding site 7 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:39.7
occ:1.00
 O D:HOH4392 2.0 42.7 1.0
OE2 D:GLU416 2.1 41.0 1.0
OE1 D:GLU461 2.1 32.5 1.0
O D:HOH4263 2.2 28.8 1.0
O D:HOH4349 2.3 31.5 1.0
ND1 D:HIS418 2.4 38.3 1.0
CD D:GLU461 3.3 40.3 1.0
CD D:GLU416 3.3 39.5 1.0
CG D:HIS418 3.3 35.5 1.0
CE1 D:HIS418 3.3 38.2 1.0
CB D:HIS418 3.5 35.0 1.0
OE1 D:GLU416 3.8 47.0 1.0
OD1 D:ASN102 4.0 51.4 1.0
O D:ASP199 4.0 35.0 1.0
OE2 D:GLU461 4.1 35.8 1.0
N D:ASP201 4.1 37.6 1.0
CG D:GLU461 4.2 36.0 1.0
CB D:GLU461 4.3 32.6 1.0
CB D:ASP201 4.4 41.2 1.0
O D:ASN102 4.4 45.8 1.0
CG D:GLU416 4.4 35.6 1.0
NE2 D:HIS418 4.5 39.6 1.0
CD2 D:HIS418 4.5 34.1 1.0
CA D:ASP201 4.8 38.4 1.0
O D:HOH4069 4.8 41.8 1.0
C D:GLN200 4.9 38.8 1.0
CA D:GLN200 4.9 37.0 1.0
CG2 D:VAL103 5.0 42.9 1.0
CA D:HIS418 5.0 34.7 1.0

Magnesium binding site 8 out of 8 in 3vda

Go back to Magnesium Binding Sites List in 3vda
Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T)


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

b:45.8
occ:1.00
 OD2 D:ASP193 2.1 45.7 1.0
O D:VAL21 2.3 43.4 1.0
O D:ASN18 2.3 43.4 1.0
O D:ASP15 2.3 47.8 1.0
OE1 D:GLN163 2.7 40.9 1.0
CG D:ASP193 2.9 41.9 1.0
OD1 D:ASP193 3.1 46.1 1.0
C D:ASN18 3.2 42.6 1.0
CD D:GLN163 3.4 43.9 1.0
C D:VAL21 3.5 41.4 1.0
C D:ASP15 3.5 49.4 1.0
NE2 D:GLN163 3.6 40.3 1.0
N D:ASN18 3.8 43.9 1.0
CA D:ASN18 3.9 43.0 1.0
OH D:TYR161 4.0 36.3 1.0
CA D:TRP16 4.0 47.6 1.0
N D:PRO19 4.1 42.2 1.0
N D:TRP16 4.2 48.1 1.0
CB D:ASN18 4.2 42.6 1.0
C D:TRP16 4.3 46.6 1.0
CA D:VAL21 4.3 41.9 1.0
CA D:PRO19 4.3 42.6 1.0
CB D:ASP193 4.4 37.3 1.0
N D:VAL21 4.4 44.2 1.0
CB D:VAL21 4.5 42.8 1.0
N D:THR22 4.5 37.7 1.0
CE2 D:TYR161 4.5 38.9 1.0
N D:GLU17 4.6 46.7 1.0
CA D:THR22 4.6 37.0 1.0
CA D:ASP15 4.6 50.6 1.0
CG D:GLN163 4.6 43.0 1.0
O D:TRP16 4.7 44.5 1.0
CZ D:TYR161 4.8 38.9 1.0
C D:PRO19 4.9 43.9 1.0
CG1 D:VAL21 4.9 42.5 1.0
C D:GLU17 4.9 44.3 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 12:59:14 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy