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Magnesium in PDB 3dyo: E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg, PDB code: 3dyo was solved by D.H.Juers, R.E.Huber, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 152.010, 162.520, 204.010, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 3dyo:

The structure of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg also contains other interesting chemical elements:

Sodium (Na) 18 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg (pdb code 3dyo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg, PDB code: 3dyo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 3dyo

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Magnesium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:17.1
occ:1.00
 OD1 A:ASN418 2.0 18.7 1.0
O A:HOH4013 2.0 14.8 1.0
OE2 A:GLU416 2.0 18.5 1.0
O A:HOH4153 2.1 15.6 1.0
O A:HOH4077 2.1 15.8 1.0
OE1 A:GLU461 2.1 19.3 1.0
CG A:ASN418 3.1 20.3 1.0
CD A:GLU461 3.1 28.1 1.0
CD A:GLU416 3.1 22.2 1.0
OE1 A:GLU416 3.5 18.2 1.0
CB A:ASN418 3.6 14.8 1.0
OE2 A:GLU461 3.9 30.5 1.0
CG A:GLU461 4.1 12.2 1.0
CB A:GLU461 4.1 14.2 1.0
N A:ASP201 4.1 19.3 1.0
CB A:ASP201 4.1 15.4 1.0
OD1 A:ASN102 4.2 18.2 1.0
O A:ASP199 4.2 18.4 1.0
O A:HOH4001 4.2 21.0 1.0
ND2 A:ASN418 4.2 12.7 1.0
ND2 A:ASN460 4.3 14.5 1.0
CG A:GLU416 4.3 14.4 1.0
O4 A:IPT2001 4.4 21.7 1.0
O A:ASN102 4.6 24.3 1.0
CA A:ASP201 4.7 16.4 1.0
CG2 A:VAL103 4.7 15.2 1.0
C2 A:IPT2001 4.8 26.7 1.0
O3 A:IPT2001 4.8 29.9 1.0
C A:GLN200 4.9 32.5 1.0
CA A:GLN200 5.0 17.1 1.0

Magnesium binding site 2 out of 14 in 3dyo

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Magnesium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:23.6
occ:1.00
 O A:ASN18 2.0 22.8 1.0
O A:ASP15 2.3 28.6 1.0
O A:VAL21 2.3 28.6 1.0
OE1 A:GLN163 2.3 28.2 1.0
OD2 A:ASP193 2.3 26.4 1.0
OD1 A:ASP193 2.9 25.4 1.0
C A:ASN18 2.9 22.4 1.0
CG A:ASP193 3.0 38.5 1.0
CD A:GLN163 3.2 40.8 1.0
C A:VAL21 3.4 22.5 1.0
N A:ASN18 3.5 29.2 1.0
C A:ASP15 3.5 31.5 1.0
NE2 A:GLN163 3.5 21.6 1.0
CA A:ASN18 3.7 30.9 1.0
N A:PRO19 3.9 26.8 1.0
CB A:ASN18 4.0 27.0 1.0
CA A:PRO19 4.1 26.6 1.0
OH A:TYR161 4.1 25.5 1.0
N A:VAL21 4.2 22.1 1.0
CA A:VAL21 4.2 21.3 1.0
CB A:VAL21 4.2 32.3 1.0
CA A:TRP16 4.2 27.2 1.0
N A:TRP16 4.2 27.9 1.0
C A:TRP16 4.3 24.3 1.0
N A:THR22 4.4 18.4 1.0
CB A:ASP193 4.4 25.2 1.0
N A:GLU17 4.4 23.2 1.0
CG A:GLN163 4.6 33.5 1.0
CE2 A:TYR161 4.6 34.2 1.0
CA A:ASP15 4.6 27.1 1.0
CA A:THR22 4.6 24.4 1.0
C A:PRO19 4.7 31.6 1.0
C A:GLU17 4.7 34.4 1.0
CG1 A:VAL21 4.7 24.1 1.0
N A:GLY20 4.8 32.0 1.0
O A:TRP16 4.9 28.9 1.0
CG A:ASN18 4.9 20.6 1.0
CZ A:TYR161 4.9 31.6 1.0

Magnesium binding site 3 out of 14 in 3dyo

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Magnesium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3003

b:52.2
occ:1.00
 O A:HOH4621 2.2 37.9 1.0
OE1 A:GLN718 2.2 33.5 1.0
O A:HOH4366 2.3 33.3 1.0
O A:HOH4262 2.3 24.6 1.0
O A:HOH4573 2.6 30.1 1.0
CD A:GLN718 3.2 31.2 1.0
NE2 A:GLN718 3.5 23.5 1.0
O A:HOH4408 4.0 27.9 1.0
O A:HOH4277 4.1 39.1 1.0
O A:GLN719 4.2 17.5 1.0
O A:HOH4724 4.3 35.8 1.0
O A:THR911 4.3 18.8 1.0
NE2 A:HIS622 4.3 16.6 1.0
N A:GLN719 4.4 18.1 1.0
O A:HOH4252 4.6 18.3 1.0
O A:HOH4799 4.6 60.3 1.0
CG A:GLN718 4.6 15.0 1.0
O A:HOH4238 4.7 39.5 1.0
O A:HOH4079 4.9 15.9 1.0
CE1 A:HIS622 4.9 17.0 1.0

Magnesium binding site 4 out of 14 in 3dyo

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Magnesium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3012

b:40.6
occ:1.00
 O C:HOH4884 2.1 32.3 1.0
O C:HOH4007 2.1 47.2 1.0
O C:HOH4883 2.2 47.9 1.0
O C:HOH4888 2.2 30.5 1.0
O A:HOH4794 2.2 26.3 1.0
O A:HOH4791 2.5 43.9 1.0
OG A:SER236 4.2 18.9 1.0
OG C:SER236 4.2 19.3 1.0
O C:HOH4008 4.6 23.7 1.0
O A:HOH4759 4.6 22.4 1.0
CD C:ARG237 4.7 27.4 1.0
CD A:ARG237 4.8 25.6 1.0
ND2 C:ASN232 4.8 22.9 1.0
CG C:ARG237 4.9 36.2 1.0
ND2 A:ASN232 4.9 24.2 1.0
CG A:ARG237 4.9 23.3 1.0

Magnesium binding site 5 out of 14 in 3dyo

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Magnesium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:16.6
occ:1.00
 OE1 B:GLU461 2.0 13.5 1.0
OD1 B:ASN418 2.0 14.9 1.0
OE2 B:GLU416 2.1 16.4 1.0
O B:HOH4102 2.1 9.7 1.0
O B:HOH4179 2.2 13.8 1.0
O B:HOH4038 2.2 13.1 1.0
CD B:GLU461 3.1 25.5 1.0
CG B:ASN418 3.1 17.8 1.0
CD B:GLU416 3.2 11.4 1.0
CB B:ASN418 3.6 9.4 1.0
OE1 B:GLU416 3.6 12.8 1.0
OE2 B:GLU461 3.9 20.2 1.0
CB B:GLU461 4.0 9.9 1.0
CG B:GLU461 4.1 9.2 1.0
OD1 B:ASN102 4.2 17.4 1.0
N B:ASP201 4.2 11.2 1.0
O B:HOH4025 4.2 17.0 1.0
ND2 B:ASN460 4.2 12.8 1.0
CB B:ASP201 4.2 13.7 1.0
ND2 B:ASN418 4.3 13.3 1.0
O B:ASP199 4.3 17.7 1.0
CG B:GLU416 4.4 13.5 1.0
O4 B:IPT2001 4.5 19.9 1.0
O B:HOH4315 4.5 43.0 1.0
O B:ASN102 4.6 16.4 1.0
O3 B:IPT2001 4.7 18.7 1.0
CG2 B:VAL103 4.8 15.8 1.0
CA B:ASP201 4.8 10.5 1.0
C2 B:IPT2001 4.8 21.8 1.0
CA B:GLN200 4.9 11.8 1.0
C B:GLN200 4.9 14.0 1.0

Magnesium binding site 6 out of 14 in 3dyo

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Magnesium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:19.9
occ:1.00
 O B:VAL21 2.2 18.9 1.0
O B:ASP15 2.3 17.9 1.0
O B:ASN18 2.3 21.0 1.0
OD2 B:ASP193 2.4 15.6 1.0
OE1 B:GLN163 2.4 13.4 1.0
OD1 B:ASP193 2.9 19.4 1.0
CG B:ASP193 3.0 19.4 1.0
CD B:GLN163 3.2 30.7 1.0
C B:ASN18 3.2 18.3 1.0
NE2 B:GLN163 3.3 17.7 1.0
C B:VAL21 3.4 22.6 1.0
C B:ASP15 3.5 16.6 1.0
N B:ASN18 3.6 19.0 1.0
CA B:ASN18 3.9 18.3 1.0
OH B:TYR161 4.0 18.9 1.0
CA B:TRP16 4.0 19.0 1.0
N B:VAL21 4.1 20.7 1.0
CA B:VAL21 4.2 18.8 1.0
N B:PRO19 4.2 16.5 1.0
N B:TRP16 4.2 15.4 1.0
C B:TRP16 4.3 22.7 1.0
CB B:ASN18 4.3 18.2 1.0
CE2 B:TYR161 4.3 21.0 1.0
CB B:VAL21 4.3 20.9 1.0
N B:GLU17 4.4 18.8 1.0
CB B:ASP193 4.4 10.7 1.0
N B:THR22 4.5 16.3 1.0
CA B:PRO19 4.5 20.1 1.0
CA B:ASP15 4.6 14.2 1.0
CG B:GLN163 4.6 17.9 1.0
CZ B:TYR161 4.6 27.1 1.0
CA B:THR22 4.6 14.1 1.0
C B:GLU17 4.8 19.3 1.0
O B:TRP16 4.8 19.8 1.0
C B:PRO19 4.8 22.7 1.0
CG1 B:VAL21 4.9 22.3 1.0

Magnesium binding site 7 out of 14 in 3dyo

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Magnesium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3007

b:26.2
occ:1.00
 O B:HOH4967 1.9 31.9 1.0
O B:HOH4966 2.0 27.2 1.0
O B:HOH4986 2.1 29.6 1.0
O B:HOH4824 2.1 23.7 1.0
O B:HOH4969 2.3 29.9 1.0
O B:HOH4968 2.3 41.5 1.0
OE1 B:GLU369 3.8 23.5 1.0
OE2 B:GLU369 4.1 25.7 1.0
O B:HOH4958 4.2 27.8 1.0
CD B:GLU369 4.4 25.9 1.0
O B:HOH4937 4.4 30.7 1.0

Magnesium binding site 8 out of 14 in 3dyo

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Magnesium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) 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 (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3011

b:41.4
occ:1.00
 O D:HOH4849 2.1 33.0 1.0
O B:HOH4889 2.2 30.3 1.0
O D:HOH4852 2.2 30.6 1.0
O D:HOH4848 2.3 38.5 1.0
O B:HOH4888 2.5 54.3 1.0
O D:HOH4864 3.9 35.9 1.0
O B:HOH4906 3.9 35.8 1.0
OG D:SER236 4.1 21.9 1.0
OG B:SER236 4.2 19.8 1.0
CD B:ARG237 4.4 26.1 1.0
O D:HOH4017 4.4 26.6 1.0
O D:HOH4019 4.5 23.2 1.0
ND2 B:ASN232 4.7 22.4 1.0
ND2 D:ASN232 4.8 23.9 1.0
CG B:ARG237 4.8 19.2 1.0
CG D:ARG237 5.0 27.8 1.0
CD D:ARG237 5.0 28.1 1.0

Magnesium binding site 9 out of 14 in 3dyo

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Magnesium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:15.6
occ:1.00
 OE1 C:GLU461 2.1 12.6 1.0
OD1 C:ASN418 2.1 16.5 1.0
O C:HOH4102 2.1 11.3 1.0
OE2 C:GLU416 2.1 16.4 1.0
O C:HOH4180 2.1 14.0 1.0
O C:HOH4038 2.2 12.1 1.0
CD C:GLU461 3.1 25.4 1.0
CG C:ASN418 3.1 18.3 1.0
CD C:GLU416 3.2 14.4 1.0
CB C:ASN418 3.6 11.6 1.0
OE1 C:GLU416 3.7 14.4 1.0
OE2 C:GLU461 3.9 21.9 1.0
CB C:GLU461 4.0 11.3 1.0
CB C:ASP201 4.1 12.1 1.0
CG C:GLU461 4.1 7.3 1.0
OD1 C:ASN102 4.2 16.2 1.0
O C:HOH4025 4.2 15.6 1.0
N C:ASP201 4.2 13.4 1.0
O C:ASP199 4.2 13.4 1.0
ND2 C:ASN418 4.3 16.5 1.0
ND2 C:ASN460 4.3 13.0 1.0
CG C:GLU416 4.4 12.4 1.0
O4 C:IPT2001 4.4 18.6 1.0
O C:ASN102 4.6 14.4 1.0
O C:HOH4318 4.6 35.6 1.0
CA C:ASP201 4.8 11.6 1.0
CA C:GLN200 4.8 11.8 1.0
CG2 C:VAL103 4.8 14.2 1.0
O3 C:IPT2001 4.9 21.8 1.0
C2 C:IPT2001 4.9 22.2 1.0
C C:GLN200 4.9 16.5 1.0

Magnesium binding site 10 out of 14 in 3dyo

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Magnesium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of E. Coli (Lacz) Beta-Galactosidase (H418N) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:18.4
occ:1.00
 O C:VAL21 2.2 16.0 1.0
OE1 C:GLN163 2.3 17.5 1.0
O C:ASP15 2.4 17.2 1.0
O C:ASN18 2.4 21.1 1.0
OD2 C:ASP193 2.5 17.7 1.0
OD1 C:ASP193 3.1 16.5 1.0
CG C:ASP193 3.1 19.3 1.0
CD C:GLN163 3.2 24.2 1.0
C C:ASN18 3.3 17.0 1.0
C C:VAL21 3.4 15.7 1.0
NE2 C:GLN163 3.5 16.0 1.0
C C:ASP15 3.6 23.7 1.0
N C:ASN18 3.7 20.3 1.0
CA C:ASN18 4.0 17.3 1.0
CA C:TRP16 4.1 16.9 1.0
OH C:TYR161 4.1 16.8 1.0
CA C:VAL21 4.1 14.7 1.0
CB C:VAL21 4.2 23.0 1.0
N C:PRO19 4.2 17.1 1.0
N C:VAL21 4.2 21.9 1.0
C C:TRP16 4.3 22.4 1.0
N C:TRP16 4.3 15.8 1.0
N C:THR22 4.4 14.7 1.0
CA C:PRO19 4.4 17.8 1.0
CE2 C:TYR161 4.4 17.9 1.0
CB C:ASN18 4.4 18.3 1.0
CA C:THR22 4.4 15.9 1.0
CG C:GLN163 4.5 16.3 1.0
N C:GLU17 4.5 15.6 1.0
CB C:ASP193 4.6 10.1 1.0
CA C:ASP15 4.6 15.7 1.0
CG1 C:VAL21 4.7 24.4 1.0
CZ C:TYR161 4.7 17.1 1.0
O C:TRP16 4.9 20.3 1.0
C C:PRO19 4.9 26.3 1.0
C C:GLU17 4.9 27.7 1.0
CB C:ASP15 4.9 14.5 1.0

Reference:

D.H.Juers, B.Rob, M.L.Dugdale, N.Rahimzadeh, C.Giang, M.Lee, B.W.Matthews, R.E.Huber. Direct and Indirect Roles of His-418 in Metal Binding and in the Activity of Beta-Galactosidase (E. Coli). Protein Sci. V. 18 1281 2009.
ISSN: ISSN 0961-8368
PubMed: 19472413
DOI: 10.1002/PRO.140
Page generated: Wed Aug 14 12:48:02 2024

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