Magnesium in PDB 3vd7: E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7 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) 44.78 / 2.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 128.460, 152.370, 135.110, 90.00, 104.25, 90.00
R / Rfree (%) 18.8 / 25

Other elements in 3vd7:

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

Sodium (Na) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole (pdb code 3vd7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole, PDB code: 3vd7:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 1 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:44.8
occ:1.00
O A:HOH4060 2.0 41.6 1.0
OE1 A:GLU461 2.1 35.1 1.0
O A:HOH4059 2.1 31.4 1.0
OE2 A:GLU416 2.3 34.4 1.0
O A:HOH4058 2.3 36.5 1.0
ND1 A:HIS418 2.4 30.9 1.0
CE1 A:HIS418 3.2 27.7 1.0
CD A:GLU461 3.3 38.5 1.0
CD A:GLU416 3.4 34.5 1.0
CG A:HIS418 3.4 28.9 1.0
CB A:HIS418 3.8 25.7 1.0
OD1 A:ASN102 3.9 53.8 1.0
OE1 A:GLU416 3.9 37.6 1.0
OE2 A:GLU461 4.1 44.7 1.0
CG A:GLU461 4.1 33.9 1.0
O4 A:GTZ2001 4.2 81.0 1.0
CB A:ASP201 4.2 46.5 1.0
N A:ASP201 4.3 42.3 1.0
O3 A:GTZ2001 4.3 68.3 1.0
NE2 A:HIS418 4.4 25.6 1.0
C2 A:GTZ2001 4.4 76.6 1.0
CB A:GLU461 4.4 32.5 1.0
O A:ASP199 4.5 32.4 1.0
CD2 A:HIS418 4.5 26.0 1.0
O A:ASN102 4.6 47.9 1.0
CG A:GLU416 4.6 28.8 1.0
CA A:ASP201 4.8 44.3 1.0
C3 A:GTZ2001 4.8 75.8 1.0
C1 A:GTZ2001 4.8 79.6 1.0
C A:GLN200 4.9 39.6 1.0

Magnesium binding site 2 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 2 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:31.0
occ:1.00
O B:HOH4092 1.9 56.1 1.0
OE1 B:GLU461 2.0 31.1 1.0
O B:HOH4077 2.2 27.0 1.0
OE2 B:GLU416 2.3 28.0 1.0
O B:HOH4002 2.5 23.1 1.0
ND1 B:HIS418 2.7 27.9 1.0
CD B:GLU461 3.3 30.6 1.0
CD B:GLU416 3.4 27.2 1.0
CE1 B:HIS418 3.5 30.0 1.0
CG B:HIS418 3.7 29.2 1.0
OD1 B:ASN102 3.8 48.0 1.0
CB B:ASP201 3.8 43.1 1.0
N B:ASP201 3.9 40.6 1.0
OE2 B:GLU461 4.0 34.1 1.0
CB B:HIS418 4.0 24.1 1.0
OE1 B:GLU416 4.0 27.2 1.0
O4 B:GTZ2001 4.1 67.3 1.0
O B:ASP199 4.1 37.6 1.0
O3 B:GTZ2001 4.2 60.2 1.0
CG B:GLU461 4.3 28.5 1.0
CA B:ASP201 4.4 42.0 1.0
C2 B:GTZ2001 4.5 74.7 1.0
CG B:GLU416 4.6 23.4 1.0
NE2 B:HIS418 4.7 30.5 1.0
O B:ASN102 4.7 38.8 1.0
C B:GLN200 4.7 38.0 1.0
C3 B:GTZ2001 4.8 71.5 1.0
CD2 B:HIS418 4.8 29.0 1.0
CA B:GLN200 4.8 39.1 1.0
CG B:ASN102 4.9 44.3 1.0
C1 B:GTZ2001 5.0 77.0 1.0
CG B:ASP201 5.0 45.7 1.0

Magnesium binding site 3 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 3 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:36.2
occ:1.00
OD2 B:ASP193 2.1 28.1 1.0
OE1 B:GLN163 2.3 36.5 1.0
O B:ASP15 2.3 35.6 1.0
O B:VAL21 2.3 30.6 1.0
O B:ASN18 2.7 32.6 1.0
CG B:ASP193 2.9 26.8 1.0
OD1 B:ASP193 3.1 30.2 1.0
CD B:GLN163 3.2 39.2 1.0
C B:ASP15 3.4 35.6 1.0
NE2 B:GLN163 3.4 32.4 1.0
C B:VAL21 3.5 29.3 1.0
C B:ASN18 3.5 32.2 1.0
OH B:TYR161 3.7 28.9 1.0
N B:ASN18 3.8 31.5 1.0
CA B:TRP16 3.8 30.1 1.0
C B:TRP16 4.1 29.5 1.0
CA B:ASN18 4.1 31.9 1.0
N B:TRP16 4.1 32.5 1.0
CE2 B:TYR161 4.2 30.3 1.0
CA B:VAL21 4.3 29.9 1.0
CB B:ASP193 4.4 24.0 1.0
N B:PRO19 4.4 31.6 1.0
CZ B:TYR161 4.4 25.6 1.0
N B:GLU17 4.4 31.4 1.0
CB B:VAL21 4.4 29.5 1.0
N B:THR22 4.4 27.7 1.0
O B:TRP16 4.5 31.5 1.0
N B:VAL21 4.5 31.0 1.0
CA B:THR22 4.6 23.7 1.0
CG B:GLN163 4.6 35.9 1.0
CA B:ASP15 4.6 35.8 1.0
CA B:PRO19 4.6 31.5 1.0
CB B:ASN18 4.6 32.2 1.0
CG1 B:VAL21 4.7 25.0 1.0
C B:GLU17 4.9 31.4 1.0
CB B:ASP15 5.0 34.9 1.0

Magnesium binding site 4 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 4 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:35.7
occ:1.00
O C:HOH4075 1.8 33.0 1.0
OE1 C:GLU461 2.1 25.9 1.0
O C:HOH4003 2.2 25.9 1.0
OE2 C:GLU416 2.2 36.1 1.0
O C:HOH4076 2.3 33.8 1.0
ND1 C:HIS418 2.4 31.0 1.0
CD C:GLU461 3.2 26.7 1.0
CE1 C:HIS418 3.3 33.9 1.0
CG C:HIS418 3.4 31.8 1.0
CD C:GLU416 3.5 38.6 1.0
CB C:HIS418 3.6 31.1 1.0
CG C:GLU461 4.0 23.1 1.0
OD1 C:ASN102 4.1 39.4 1.0
OE1 C:GLU416 4.2 39.7 1.0
OE2 C:GLU461 4.2 30.9 1.0
O C:ASP199 4.2 31.8 1.0
CB C:GLU461 4.2 19.4 1.0
O C:ASN102 4.2 41.0 1.0
CB C:ASP201 4.3 33.9 1.0
N C:ASP201 4.3 35.7 1.0
O4 C:GTZ2001 4.4 60.9 1.0
NE2 C:HIS418 4.4 33.7 1.0
CD2 C:HIS418 4.5 36.0 1.0
CG C:GLU416 4.5 32.9 1.0
O3 C:GTZ2001 4.6 64.3 1.0
C2 C:GTZ2001 4.7 62.7 1.0
CA C:ASP201 4.8 34.1 1.0
C C:GLN200 4.9 32.3 1.0
CA C:GLN200 5.0 31.5 1.0

Magnesium binding site 5 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 5 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:31.9
occ:1.00
OD2 C:ASP193 2.1 32.9 1.0
OE1 C:GLN163 2.3 28.4 1.0
O C:VAL21 2.3 30.2 1.0
O C:ASP15 2.3 37.3 1.0
O C:ASN18 2.3 32.9 1.0
CG C:ASP193 3.1 28.4 1.0
C C:ASN18 3.2 30.8 1.0
CD C:GLN163 3.3 33.6 1.0
OD1 C:ASP193 3.4 37.4 1.0
C C:ASP15 3.4 37.9 1.0
C C:VAL21 3.5 29.3 1.0
N C:ASN18 3.7 30.2 1.0
NE2 C:GLN163 3.8 36.3 1.0
OH C:TYR161 3.8 40.3 1.0
CA C:ASN18 3.9 30.4 1.0
N C:PRO19 4.1 29.6 1.0
CA C:TRP16 4.1 34.0 1.0
CE2 C:TYR161 4.2 33.4 1.0
N C:TRP16 4.2 35.5 1.0
CA C:PRO19 4.2 31.0 1.0
C C:TRP16 4.3 32.4 1.0
CA C:VAL21 4.3 30.5 1.0
N C:THR22 4.4 28.1 1.0
CB C:ASP193 4.4 29.0 1.0
N C:VAL21 4.4 29.7 1.0
CB C:ASN18 4.4 29.6 1.0
CB C:VAL21 4.4 31.9 1.0
CA C:ASP15 4.5 39.6 1.0
CA C:THR22 4.5 29.9 1.0
CZ C:TYR161 4.5 33.0 1.0
N C:GLU17 4.5 30.5 1.0
CG C:GLN163 4.6 36.6 1.0
CG1 C:VAL21 4.7 32.2 1.0
O C:TRP16 4.8 31.9 1.0
CB C:ASP15 4.8 40.2 1.0
C C:PRO19 4.8 31.9 1.0
C C:GLU17 4.9 30.1 1.0

Magnesium binding site 6 out of 6 in 3vd7

Go back to Magnesium Binding Sites List in 3vd7
Magnesium binding site 6 out of 6 in the E. Coli (Lacz) Beta-Galactosidase (N460S) in Complex with Galactotetrazole


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) in Complex with Galactotetrazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg3001

b:37.1
occ:1.00
O D:HOH4122 1.8 29.5 1.0
OE1 D:GLU461 2.1 37.0 1.0
O D:HOH4121 2.1 43.6 1.0
O D:HOH4003 2.2 12.9 1.0
OE2 D:GLU416 2.3 21.6 1.0
ND1 D:HIS418 2.6 22.9 1.0
CD D:GLU461 3.3 32.7 1.0
CD D:GLU416 3.4 25.1 1.0
CE1 D:HIS418 3.4 19.3 1.0
CG D:HIS418 3.7 26.7 1.0
OE1 D:GLU416 3.8 25.7 1.0
CB D:ASP201 4.0 41.9 1.0
CB D:HIS418 4.0 26.4 1.0
OD1 D:ASN102 4.1 40.5 1.0
N D:ASP201 4.2 38.8 1.0
OE2 D:GLU461 4.2 36.2 1.0
C2 D:GTZ2001 4.2 82.4 1.0
CG D:GLU461 4.2 27.0 1.0
O D:ASN102 4.2 38.1 1.0
O3 D:GTZ2001 4.2 78.6 1.0
O D:ASP199 4.4 31.6 1.0
O4 D:GTZ2001 4.5 80.4 1.0
CB D:GLU461 4.5 24.9 1.0
NE2 D:HIS418 4.6 26.6 1.0
CA D:ASP201 4.6 39.4 1.0
CG D:GLU416 4.7 21.3 1.0
C1 D:GTZ2001 4.7 86.9 1.0
CD2 D:HIS418 4.8 27.3 1.0
C3 D:GTZ2001 4.8 80.6 1.0
C D:GLN200 4.9 37.7 1.0
N1 D:GTZ2001 5.0 90.9 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: Mon Dec 14 08:58:52 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