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Magnesium in PDB 3vdc: E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg, PDB code: 3vdc 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) 126.21 / 2.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.182, 161.055, 201.474, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.6

Other elements in 3vdc:

The structure of E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg 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) in Complex with Iptg (pdb code 3vdc). 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) in Complex with Iptg, PDB code: 3vdc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3vdc

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Magnesium binding site 1 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:53.6
occ:1.00
 OE1 A:GLU461 2.1 42.3 1.0
OE2 A:GLU416 2.1 52.6 1.0
O A:HOH4389 2.2 45.7 1.0
O A:HOH4428 2.3 62.9 1.0
O A:HOH4427 2.3 43.0 1.0
ND1 A:HIS418 2.4 46.4 1.0
CD A:GLU461 3.1 46.6 1.0
CD A:GLU416 3.2 46.0 1.0
CE1 A:HIS418 3.3 43.0 1.0
CG A:HIS418 3.4 42.5 1.0
CB A:HIS418 3.7 36.0 1.0
OE2 A:GLU461 3.8 45.5 1.0
OE1 A:GLU416 3.8 52.2 1.0
OD1 A:ASN102 4.1 41.8 1.0
CB A:ASP201 4.1 49.6 1.0
CG A:GLU461 4.1 35.8 1.0
CB A:GLU461 4.2 28.7 1.0
N A:ASP201 4.3 48.3 1.0
O A:HOH4121 4.3 54.8 1.0
O A:ASP199 4.4 43.6 1.0
CG A:GLU416 4.4 44.1 1.0
NE2 A:HIS418 4.5 47.8 1.0
CD2 A:HIS418 4.5 43.6 1.0
O A:HOH4122 4.5 30.6 1.0
O4 A:IPT2001 4.6 38.0 0.9
O3 A:IPT2001 4.7 42.0 0.9
C2 A:IPT2001 4.7 44.6 0.9
CA A:ASP201 4.8 48.5 1.0
O A:ASN102 4.8 53.2 1.0

Magnesium binding site 2 out of 8 in 3vdc

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Magnesium binding site 2 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:43.2
occ:1.00
 OD1 A:ASP193 2.1 41.2 1.0
OE1 A:GLN163 2.3 43.1 1.0
O A:ASN18 2.3 43.7 1.0
O A:ASP15 2.3 48.0 1.0
O A:VAL21 2.3 40.7 1.0
CG A:ASP193 2.9 41.6 1.0
OD2 A:ASP193 3.0 39.3 1.0
C A:ASN18 3.1 47.5 1.0
CD A:GLN163 3.2 40.6 1.0
C A:VAL21 3.5 40.5 1.0
C A:ASP15 3.5 50.4 1.0
NE2 A:GLN163 3.5 49.7 1.0
N A:ASN18 3.6 49.5 1.0
CA A:ASN18 3.8 48.5 1.0
N A:PRO19 4.0 48.3 1.0
CA A:TRP16 4.1 47.2 1.0
OH A:TYR161 4.1 34.4 1.0
N A:TRP16 4.2 48.0 1.0
CA A:VAL21 4.3 41.6 1.0
CA A:PRO19 4.3 48.2 1.0
CB A:ASN18 4.3 47.7 1.0
CB A:ASP193 4.3 40.0 1.0
C A:TRP16 4.3 47.5 1.0
N A:VAL21 4.4 44.0 1.0
CB A:VAL21 4.4 43.4 1.0
CE2 A:TYR161 4.5 37.3 1.0
N A:THR22 4.5 38.7 1.0
N A:GLU17 4.5 47.6 1.0
CG A:GLN163 4.5 37.4 1.0
CA A:ASP15 4.6 50.9 1.0
CA A:THR22 4.6 39.9 1.0
CZ A:TYR161 4.8 36.1 1.0
C A:GLU17 4.8 48.8 1.0
C A:PRO19 4.8 47.3 1.0
O A:TRP16 4.9 47.2 1.0
CG1 A:VAL21 4.9 39.2 1.0
CB A:ASP15 5.0 52.2 1.0

Magnesium binding site 3 out of 8 in 3vdc

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Magnesium binding site 3 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:46.8
occ:1.00
 OE2 B:GLU416 2.1 52.7 1.0
OE1 B:GLU461 2.1 43.5 1.0
O B:HOH4384 2.2 38.3 1.0
O B:HOH4012 2.3 35.7 1.0
O B:HOH4138 2.3 34.0 1.0
ND1 B:HIS418 2.4 43.1 1.0
CD B:GLU461 3.1 43.6 1.0
CD B:GLU416 3.3 51.9 1.0
CE1 B:HIS418 3.3 38.3 1.0
CG B:HIS418 3.4 41.0 1.0
CB B:HIS418 3.6 39.5 1.0
OE2 B:GLU461 3.7 41.0 1.0
OE1 B:GLU416 3.8 50.3 1.0
CG B:GLU461 4.1 35.4 1.0
CB B:GLU461 4.1 31.8 1.0
OD1 B:ASN102 4.1 45.8 1.0
O B:ASP199 4.2 49.0 1.0
CB B:ASP201 4.3 47.0 1.0
N B:ASP201 4.3 47.0 1.0
O B:HOH4139 4.4 47.1 1.0
CG B:GLU416 4.4 43.1 1.0
NE2 B:HIS418 4.5 43.7 1.0
CD2 B:HIS418 4.5 44.3 1.0
O B:HOH4140 4.6 39.2 1.0
O4 B:IPT2001 4.6 40.8 1.0
O3 B:IPT2001 4.6 49.5 1.0
O B:ASN102 4.7 51.3 1.0
CA B:ASP201 4.9 46.8 1.0
C2 B:IPT2001 4.9 47.0 1.0

Magnesium binding site 4 out of 8 in 3vdc

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Magnesium binding site 4 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:51.4
occ:1.00
 OD1 B:ASP193 2.1 52.2 1.0
O B:ASP15 2.3 53.5 1.0
O B:VAL21 2.3 45.0 1.0
O B:ASN18 2.3 50.0 1.0
OE1 B:GLN163 2.3 45.6 1.0
CG B:ASP193 2.9 50.5 1.0
OD2 B:ASP193 3.2 52.4 1.0
C B:ASN18 3.2 49.4 1.0
CD B:GLN163 3.3 45.9 1.0
C B:VAL21 3.5 43.4 1.0
C B:ASP15 3.5 54.4 1.0
N B:ASN18 3.5 47.8 1.0
NE2 B:GLN163 3.7 44.6 1.0
CA B:ASN18 3.8 48.7 1.0
OH B:TYR161 4.0 46.9 1.0
CA B:TRP16 4.1 51.2 1.0
CB B:ASN18 4.1 46.9 1.0
C B:TRP16 4.2 50.9 1.0
N B:TRP16 4.2 52.0 1.0
N B:PRO19 4.2 48.4 1.0
CE2 B:TYR161 4.2 48.1 1.0
CA B:VAL21 4.3 44.7 1.0
N B:GLU17 4.3 49.6 1.0
CB B:ASP193 4.3 46.2 1.0
N B:VAL21 4.4 42.9 1.0
CB B:VAL21 4.4 44.3 1.0
N B:THR22 4.5 42.3 1.0
CA B:PRO19 4.5 48.8 1.0
CG B:GLN163 4.6 46.0 1.0
CA B:ASP15 4.6 55.3 1.0
CZ B:TYR161 4.6 45.3 1.0
CA B:THR22 4.6 41.5 1.0
O B:TRP16 4.6 50.6 1.0
C B:GLU17 4.7 48.5 1.0
CG1 B:VAL21 4.9 40.7 1.0
CB B:ASP15 5.0 54.9 1.0

Magnesium binding site 5 out of 8 in 3vdc

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


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

b:52.4
occ:1.00
 O C:HOH4386 2.0 45.0 1.0
OE1 C:GLU461 2.1 50.6 1.0
OE2 C:GLU416 2.1 44.4 1.0
O C:HOH4141 2.1 37.5 1.0
ND1 C:HIS418 2.4 49.8 1.0
O C:HOH4036 2.4 35.0 1.0
CD C:GLU461 3.0 46.8 1.0
CD C:GLU416 3.2 43.5 1.0
CE1 C:HIS418 3.2 41.5 1.0
CG C:HIS418 3.4 45.8 1.0
OE2 C:GLU461 3.5 43.2 1.0
OE1 C:GLU416 3.7 45.3 1.0
CB C:HIS418 3.8 42.7 1.0
O C:HOH4098 4.2 41.6 1.0
OD1 C:ASN102 4.2 45.0 1.0
CG C:GLU461 4.2 41.5 1.0
CB C:ASP201 4.3 47.9 1.0
N C:ASP201 4.3 47.6 1.0
CB C:GLU461 4.3 35.8 1.0
O C:ASP199 4.3 42.3 1.0
O C:HOH4099 4.4 43.5 1.0
NE2 C:HIS418 4.4 45.4 1.0
CG C:GLU416 4.4 40.5 1.0
O3 C:IPT2001 4.5 45.5 1.0
CD2 C:HIS418 4.5 47.8 1.0
O4 C:IPT2001 4.6 49.0 1.0
C2 C:IPT2001 4.6 48.7 1.0
CA C:ASP201 4.9 47.1 1.0
O C:ASN102 4.9 49.1 1.0

Magnesium binding site 6 out of 8 in 3vdc

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Magnesium binding site 6 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:49.9
occ:1.00
 OD1 C:ASP193 2.1 43.5 1.0
O C:ASP15 2.3 50.8 1.0
OE1 C:GLN163 2.3 40.4 1.0
O C:VAL21 2.3 48.1 1.0
O C:ASN18 2.3 52.0 1.0
CG C:ASP193 2.8 43.6 1.0
OD2 C:ASP193 2.9 49.3 1.0
CD C:GLN163 3.2 35.4 1.0
C C:ASN18 3.3 51.6 1.0
C C:ASP15 3.5 53.4 1.0
C C:VAL21 3.5 46.4 1.0
NE2 C:GLN163 3.5 37.4 1.0
N C:ASN18 3.7 49.2 1.0
OH C:TYR161 3.9 33.3 1.0
CA C:TRP16 4.0 50.5 1.0
CA C:ASN18 4.0 51.0 1.0
N C:TRP16 4.2 50.6 1.0
C C:TRP16 4.2 50.8 1.0
N C:PRO19 4.2 51.9 1.0
CB C:ASP193 4.2 41.8 1.0
CA C:VAL21 4.3 47.2 1.0
CA C:PRO19 4.4 52.2 1.0
N C:THR22 4.4 45.1 1.0
CB C:ASN18 4.4 50.7 1.0
N C:GLU17 4.5 50.4 1.0
CA C:THR22 4.5 46.0 1.0
CE2 C:TYR161 4.5 35.8 1.0
CB C:VAL21 4.5 46.4 1.0
N C:VAL21 4.5 50.0 1.0
CG C:GLN163 4.5 38.3 1.0
CA C:ASP15 4.6 54.7 1.0
CZ C:TYR161 4.7 36.6 1.0
O C:TRP16 4.7 50.1 1.0
CG1 C:VAL21 4.9 40.9 1.0
C C:GLU17 4.9 49.4 1.0
C C:PRO19 5.0 52.8 1.0

Magnesium binding site 7 out of 8 in 3vdc

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Magnesium binding site 7 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:54.1
occ:1.00
 OE1 D:GLU461 2.1 37.9 1.0
OE2 D:GLU416 2.1 54.3 1.0
O D:HOH4175 2.2 44.5 1.0
O D:HOH4040 2.3 46.6 1.0
ND1 D:HIS418 2.4 44.0 1.0
O D:HOH4017 2.4 38.8 1.0
CD D:GLU461 3.1 37.7 1.0
CD D:GLU416 3.2 50.1 1.0
CE1 D:HIS418 3.3 44.4 1.0
CG D:HIS418 3.4 42.5 1.0
CB D:HIS418 3.6 35.4 1.0
OE2 D:GLU461 3.7 37.1 1.0
OE1 D:GLU416 3.8 49.1 1.0
CG D:GLU461 4.1 32.8 1.0
CB D:GLU461 4.2 33.9 1.0
N D:ASP201 4.2 49.9 1.0
O D:ASP199 4.2 46.1 1.0
OD1 D:ASN102 4.2 46.4 1.0
CB D:ASP201 4.3 51.1 1.0
CG D:GLU416 4.4 44.5 1.0
NE2 D:HIS418 4.4 48.2 1.0
O D:HOH4197 4.5 31.4 1.0
O D:HOH4176 4.5 40.5 1.0
CD2 D:HIS418 4.5 38.5 1.0
O4 D:IPT2001 4.5 37.5 1.0
O D:ASN102 4.5 52.0 1.0
O3 D:IPT2001 4.7 45.8 1.0
CA D:ASP201 4.8 50.7 1.0
C2 D:IPT2001 4.8 44.3 1.0
C D:GLN200 4.9 49.3 1.0

Magnesium binding site 8 out of 8 in 3vdc

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Magnesium binding site 8 out of 8 in the E. Coli (Lacz) Beta-Galactosidase (N460T) in Complex with Iptg


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

b:45.0
occ:1.00
 OD1 D:ASP193 2.1 44.0 1.0
O D:ASP15 2.3 48.1 1.0
O D:ASN18 2.3 44.9 1.0
OE1 D:GLN163 2.3 48.5 1.0
O D:VAL21 2.3 41.2 1.0
CG D:ASP193 2.9 41.2 1.0
OD2 D:ASP193 3.0 51.1 1.0
C D:ASN18 3.2 47.2 1.0
CD D:GLN163 3.3 45.6 1.0
C D:ASP15 3.5 50.3 1.0
C D:VAL21 3.5 39.9 1.0
NE2 D:GLN163 3.6 42.9 1.0
N D:ASN18 3.6 50.0 1.0
CA D:ASN18 3.9 49.2 1.0
OH D:TYR161 3.9 43.4 1.0
CA D:TRP16 3.9 47.6 1.0
C D:TRP16 4.1 47.2 1.0
N D:TRP16 4.1 49.3 1.0
N D:PRO19 4.2 46.7 1.0
CB D:ASP193 4.3 40.6 1.0
CB D:ASN18 4.3 46.4 1.0
CA D:VAL21 4.3 40.2 1.0
N D:THR22 4.4 37.3 1.0
N D:VAL21 4.4 42.4 1.0
N D:GLU17 4.4 47.2 1.0
CE2 D:TYR161 4.5 41.9 1.0
CB D:VAL21 4.5 41.2 1.0
CA D:PRO19 4.5 47.4 1.0
O D:TRP16 4.6 42.9 1.0
CA D:THR22 4.6 37.5 1.0
CG D:GLN163 4.6 44.8 1.0
CA D:ASP15 4.6 52.1 1.0
CZ D:TYR161 4.7 42.5 1.0
CG1 D:VAL21 4.8 40.0 1.0
C D:GLU17 4.8 49.0 1.0
N D:ASP193 5.0 39.8 1.0
C D:PRO19 5.0 47.4 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 13:01:00 2024

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