Magnesium in PDB 3muz: E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Iptg

Enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Iptg

All present enzymatic activity of E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Iptg:
3.2.1.23;

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Iptg, PDB code: 3muz was solved by M.L.Dugdale, M.L.Vance, M.R.Driedger, A.Nibber, A.Tran, R.E.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.42 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.830, 163.280, 204.200, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 24.8

Other elements in 3muz:

The structure of E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Iptg also contains other interesting chemical elements:

Sodium (Na) 16 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 (R599A) in Complex with Iptg (pdb code 3muz). 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 (R599A) in Complex with Iptg, PDB code: 3muz:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 3muz

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Magnesium binding site 1 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3001

b:16.9
occ:1.00
 OE1 1:GLU461 2.0 17.6 1.0
OE2 1:GLU416 2.0 15.7 1.0
O 1:HOH4075 2.1 14.9 1.0
O 1:HOH4150 2.2 15.0 1.0
O 1:HOH4011 2.2 16.7 1.0
ND1 1:HIS418 2.3 15.8 1.0
CD 1:GLU461 3.1 19.6 1.0
CE1 1:HIS418 3.1 15.4 1.0
CD 1:GLU416 3.2 13.8 1.0
CG 1:HIS418 3.3 15.4 1.0
CB 1:HIS418 3.7 13.7 1.0
OE1 1:GLU416 3.7 14.6 1.0
OE2 1:GLU461 3.8 19.3 1.0
OD1 1:ASN102 4.1 14.2 1.0
CG 1:GLU461 4.1 17.8 1.0
CB 1:GLU461 4.1 15.8 1.0
N 1:ASP201 4.2 17.1 1.0
CB 1:ASP201 4.2 16.2 1.0
ND2 1:ASN460 4.3 11.7 1.0
NE2 1:HIS418 4.3 16.2 1.0
O 1:ASP199 4.3 16.3 1.0
CG 1:GLU416 4.4 14.2 1.0
CD2 1:HIS418 4.4 15.9 1.0
O 1:HOH4810 4.5 16.4 1.0
O4 1:IPT2001 4.5 17.9 0.9
O 1:HOH4811 4.6 31.4 1.0
O 1:ASN102 4.6 18.5 1.0
CA 1:ASP201 4.7 16.4 1.0
C2 1:IPT2001 4.8 21.9 0.9
C 1:GLN200 4.9 17.9 1.0
CA 1:GLN200 4.9 17.8 1.0
CG2 1:VAL103 5.0 18.8 1.0

Magnesium binding site 2 out of 14 in 3muz

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Magnesium binding site 2 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3002

b:24.2
occ:1.00
 O 1:ASN18 2.2 26.8 1.0
O 1:VAL21 2.2 24.6 1.0
OD2 1:ASP193 2.3 29.7 1.0
O 1:ASP15 2.3 26.4 1.0
OE1 1:GLN163 2.4 24.6 1.0
CG 1:ASP193 3.0 29.0 1.0
OD1 1:ASP193 3.1 26.9 1.0
C 1:ASN18 3.1 27.1 1.0
CD 1:GLN163 3.3 25.4 1.0
C 1:VAL21 3.3 24.7 1.0
C 1:ASP15 3.5 26.9 1.0
NE2 1:GLN163 3.5 23.1 1.0
N 1:ASN18 3.7 27.2 1.0
CA 1:ASN18 3.9 27.3 1.0
N 1:PRO19 4.0 28.3 1.0
CA 1:VAL21 4.0 24.7 1.0
N 1:VAL21 4.1 25.7 1.0
CB 1:VAL21 4.1 26.7 1.0
OH 1:TYR161 4.2 25.5 1.0
CB 1:ASN18 4.2 26.3 1.0
CA 1:TRP16 4.2 27.0 1.0
CA 1:PRO19 4.3 28.4 1.0
N 1:THR22 4.3 24.1 1.0
N 1:TRP16 4.3 26.9 1.0
CE2 1:TYR161 4.4 26.6 1.0
CB 1:ASP193 4.4 25.5 1.0
C 1:TRP16 4.4 26.4 1.0
N 1:GLU17 4.5 26.0 1.0
CA 1:THR22 4.5 24.0 1.0
CA 1:ASP15 4.6 28.0 1.0
CG 1:GLN163 4.6 24.9 1.0
CG1 1:VAL21 4.7 24.9 1.0
C 1:PRO19 4.7 28.8 1.0
CZ 1:TYR161 4.8 27.1 1.0
CB 1:ASP15 4.9 27.4 1.0
C 1:GLU17 4.9 27.7 1.0
N 1:GLY20 4.9 28.2 1.0
CG 1:ASN18 5.0 27.0 1.0

Magnesium binding site 3 out of 14 in 3muz

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Magnesium binding site 3 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3003

b:59.4
occ:1.00
 O 1:HOH4252 2.2 28.1 1.0
O 1:HOH4539 2.2 25.5 1.0
O 1:HOH4353 2.5 34.8 1.0
O 1:HOH4577 2.6 27.3 1.0
OE1 1:GLN718 2.7 27.8 1.0
CD 1:GLN718 3.7 25.9 1.0
NE2 1:GLN718 3.9 25.6 1.0
O 1:HOH5026 4.1 61.1 1.0
O 1:THR911 4.1 13.3 1.0
O 1:HOH4267 4.1 41.3 1.0
O 1:HOH5025 4.2 57.5 1.0
NE2 1:HIS622 4.4 16.4 1.0
O 1:HOH4243 4.6 19.9 1.0
O 1:HOH4659 4.6 24.1 1.0
O 1:GLN719 4.6 17.2 1.0
O 1:HOH4756 4.7 46.4 1.0
O 1:HOH4077 4.8 20.9 1.0
O 1:HOH4890 4.8 37.3 1.0
N 1:GLN719 4.9 15.9 1.0
CA 1:THR911 4.9 13.7 1.0
C 1:THR911 4.9 12.8 1.0
CB 1:THR911 5.0 13.8 1.0

Magnesium binding site 4 out of 14 in 3muz

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Magnesium binding site 4 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3004

b:43.4
occ:1.00
 O 3:HOH4984 2.1 38.5 1.0
O 1:HOH4962 2.1 33.1 1.0
O 3:HOH5090 2.3 33.0 1.0
O 1:HOH5056 2.4 52.1 1.0
O 3:HOH5004 2.5 47.4 1.0
O 3:HOH4931 2.6 34.4 1.0
OG 1:SER236 4.0 23.2 1.0
OG 3:SER236 4.3 19.1 1.0
O 3:HOH4932 4.4 44.6 1.0
CD 1:ARG237 4.6 26.7 1.0
CD 3:ARG237 4.6 24.4 1.0
O 1:HOH4526 4.7 27.9 1.0
O 3:HOH4961 4.7 27.1 1.0
CG 1:ARG237 4.8 24.1 1.0
CG 3:ARG237 4.8 22.3 1.0
ND2 1:ASN232 4.9 19.2 1.0
CB 1:SER236 4.9 19.3 1.0
ND2 3:ASN232 5.0 17.7 1.0

Magnesium binding site 5 out of 14 in 3muz

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Magnesium binding site 5 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3001

b:13.3
occ:1.00
 OE1 2:GLU461 2.0 10.1 1.0
OE2 2:GLU416 2.0 10.2 1.0
O 2:HOH4075 2.1 7.8 1.0
O 2:HOH4151 2.2 9.9 1.0
O 2:HOH4011 2.3 8.2 1.0
ND1 2:HIS418 2.3 11.9 1.0
CD 2:GLU461 3.1 11.0 1.0
CD 2:GLU416 3.1 7.8 1.0
CE1 2:HIS418 3.2 12.3 1.0
CG 2:HIS418 3.3 11.9 1.0
OE1 2:GLU416 3.6 7.5 1.0
CB 2:HIS418 3.7 9.6 1.0
OE2 2:GLU461 3.8 10.7 1.0
CG 2:GLU461 4.1 10.7 1.0
CB 2:GLU461 4.1 11.1 1.0
OD1 2:ASN102 4.1 13.4 1.0
CB 2:ASP201 4.2 11.9 1.0
N 2:ASP201 4.2 11.9 1.0
ND2 2:ASN460 4.3 9.9 1.0
O 2:ASP199 4.3 12.4 1.0
NE2 2:HIS418 4.4 12.9 1.0
O 2:HOH5011 4.4 16.7 1.0
CG 2:GLU416 4.4 8.6 1.0
O4 2:IPT2001 4.4 10.5 1.0
CD2 2:HIS418 4.4 11.7 1.0
O 2:HOH4950 4.5 23.9 1.0
O 2:ASN102 4.8 14.8 1.0
CA 2:ASP201 4.8 11.3 1.0
C2 2:IPT2001 4.8 16.7 1.0
O3 2:IPT2001 5.0 15.2 1.0
CA 2:GLN200 5.0 12.7 1.0
C 2:GLN200 5.0 12.9 1.0

Magnesium binding site 6 out of 14 in 3muz

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Magnesium binding site 6 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3002

b:15.8
occ:1.00
 NE2 2:GLN163 2.2 9.7 1.0
O 2:ASP15 2.3 12.8 1.0
OD2 2:ASP193 2.3 12.0 1.0
O 2:VAL21 2.3 15.0 1.0
O 2:ASN18 2.4 14.4 1.0
CG 2:ASP193 3.0 14.1 1.0
OD1 2:ASP193 3.0 15.5 1.0
CD 2:GLN163 3.2 15.4 1.0
C 2:ASN18 3.3 16.9 1.0
OE1 2:GLN163 3.4 18.4 1.0
C 2:VAL21 3.5 16.4 1.0
C 2:ASP15 3.5 14.4 1.0
N 2:ASN18 3.7 16.9 1.0
CA 2:TRP16 4.0 15.8 1.0
CA 2:ASN18 4.0 16.8 1.0
OH 2:TYR161 4.0 14.9 1.0
N 2:TRP16 4.2 13.3 1.0
C 2:TRP16 4.2 15.4 1.0
N 2:PRO19 4.2 17.7 1.0
CA 2:VAL21 4.3 17.4 1.0
CE2 2:TYR161 4.3 17.2 1.0
N 2:VAL21 4.3 18.0 1.0
CB 2:VAL21 4.4 17.8 1.0
CB 2:ASN18 4.4 16.4 1.0
N 2:GLU17 4.4 16.1 1.0
CB 2:ASP193 4.4 14.1 1.0
CA 2:PRO19 4.4 18.1 1.0
N 2:THR22 4.5 14.9 1.0
CG 2:GLN163 4.5 13.7 1.0
CA 2:ASP15 4.6 15.0 1.0
CA 2:THR22 4.6 15.4 1.0
CZ 2:TYR161 4.6 16.4 1.0
O 2:TRP16 4.7 16.0 1.0
CG1 2:VAL21 4.9 19.2 1.0
C 2:GLU17 4.9 16.9 1.0
C 2:PRO19 4.9 19.4 1.0
CB 2:ASP15 5.0 14.7 1.0

Magnesium binding site 7 out of 14 in 3muz

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Magnesium binding site 7 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3003

b:52.4
occ:1.00
 O 2:HOH4258 2.3 24.9 1.0
O 2:HOH4630 2.4 29.9 1.0
O 2:HOH4576 2.6 27.3 1.0
C2 2:DMS6030 2.8 64.8 1.0
OE1 2:GLN718 2.8 30.6 1.0
O 2:HOH4977 2.8 41.5 1.0
CD 2:GLN718 3.8 25.9 1.0
NE2 2:GLN718 4.0 25.9 1.0
O 2:THR911 4.0 13.7 1.0
O 2:HOH4274 4.1 36.7 1.0
S 2:DMS6030 4.3 65.6 1.0
NE2 2:HIS622 4.4 13.6 1.0
C1 2:DMS6030 4.4 65.1 1.0
O 2:HOH4248 4.5 19.1 1.0
O 2:HOH4804 4.6 27.4 1.0
O 2:HOH4404 4.6 29.3 1.0
O 2:GLN719 4.7 14.9 1.0
O 2:HOH4077 4.7 17.2 1.0
CA 2:THR911 4.9 13.1 1.0
C 2:THR911 4.9 13.2 1.0
O 2:HOH5068 4.9 81.6 1.0
N 2:GLN719 4.9 15.9 1.0
O 2:DMS6030 5.0 64.4 1.0
CB 2:THR911 5.0 14.9 1.0

Magnesium binding site 8 out of 14 in 3muz

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Magnesium binding site 8 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3004

b:34.6
occ:1.00
 O 2:HOH4776 2.2 30.9 1.0
O 2:HOH4996 2.2 25.7 1.0
O 2:HOH5072 2.3 32.0 1.0
O 2:HOH4987 2.5 37.5 1.0
O 2:HOH4961 2.6 40.4 1.0
O 2:HOH4998 2.6 45.7 1.0
OE1 2:GLU369 3.9 19.6 1.0
O 2:HOH4986 4.0 32.0 1.0
OE2 2:GLU369 4.1 23.5 1.0
O 2:HOH4925 4.4 33.7 1.0
O 2:HOH5051 4.4 40.8 1.0
CD 2:GLU369 4.5 21.1 1.0
O 2:HOH5008 4.7 44.2 1.0
O 2:HOH4900 4.7 67.2 1.0
C2 2:DMS6018 4.9 66.1 1.0
C1 2:DMS6018 4.9 65.9 1.0

Magnesium binding site 9 out of 14 in 3muz

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Magnesium binding site 9 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3001

b:13.9
occ:1.00
 OE2 3:GLU416 2.0 13.0 1.0
OE1 3:GLU461 2.1 9.5 1.0
O 3:HOH4153 2.1 8.1 1.0
O 3:HOH4012 2.2 7.9 1.0
O 3:HOH4075 2.2 6.7 1.0
ND1 3:HIS418 2.2 13.7 1.0
CD 3:GLU416 3.1 12.2 1.0
CE1 3:HIS418 3.1 12.1 1.0
CD 3:GLU461 3.2 12.7 1.0
CG 3:HIS418 3.3 11.9 1.0
OE1 3:GLU416 3.6 11.6 1.0
CB 3:HIS418 3.6 11.3 1.0
OE2 3:GLU461 4.0 12.2 1.0
CB 3:GLU461 4.1 12.1 1.0
OD1 3:ASN102 4.1 13.7 1.0
CG 3:GLU461 4.1 9.8 1.0
N 3:ASP201 4.2 11.2 1.0
CB 3:ASP201 4.2 10.8 1.0
O 3:ASP199 4.3 10.8 1.0
NE2 3:HIS418 4.3 14.0 1.0
ND2 3:ASN460 4.3 9.5 1.0
CG 3:GLU416 4.3 12.5 1.0
CD2 3:HIS418 4.4 11.4 1.0
O 3:HOH4910 4.5 12.8 1.0
O 3:HOH4911 4.6 23.8 1.0
O4 3:IPT2001 4.6 12.6 1.0
O 3:ASN102 4.8 12.9 1.0
CA 3:ASP201 4.8 11.4 1.0
C2 3:IPT2001 4.9 18.4 1.0
CA 3:GLN200 4.9 12.5 1.0
C 3:GLN200 4.9 12.5 1.0

Magnesium binding site 10 out of 14 in 3muz

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Magnesium binding site 10 out of 14 in the E.Coli (Lacz) Beta-Galactosidase (R599A) 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 (R599A) in Complex with Iptg within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3002

b:16.5
occ:1.00
 NE2 3:GLN163 2.2 11.3 1.0
O 3:ASP15 2.2 15.1 1.0
O 3:VAL21 2.3 13.0 1.0
OD2 3:ASP193 2.3 13.8 1.0
O 3:ASN18 2.5 18.3 1.0
CG 3:ASP193 3.0 15.3 1.0
OD1 3:ASP193 3.0 14.3 1.0
CD 3:GLN163 3.2 17.2 1.0
C 3:ASN18 3.4 17.0 1.0
C 3:ASP15 3.4 17.7 1.0
OE1 3:GLN163 3.4 17.6 1.0
C 3:VAL21 3.5 14.2 1.0
N 3:ASN18 3.8 17.5 1.0
OH 3:TYR161 3.9 13.2 1.0
CA 3:TRP16 4.0 17.1 1.0
CA 3:ASN18 4.0 17.4 1.0
N 3:TRP16 4.2 15.6 1.0
C 3:TRP16 4.3 16.0 1.0
CE2 3:TYR161 4.3 15.0 1.0
CA 3:VAL21 4.3 15.9 1.0
N 3:PRO19 4.3 16.7 1.0
CB 3:VAL21 4.3 17.4 1.0
N 3:VAL21 4.4 17.9 1.0
CB 3:ASN18 4.4 17.2 1.0
N 3:THR22 4.4 14.0 1.0
N 3:GLU17 4.4 15.2 1.0
CB 3:ASP193 4.5 14.3 1.0
CG 3:GLN163 4.5 15.8 1.0
CA 3:ASP15 4.5 17.6 1.0
CZ 3:TYR161 4.5 15.2 1.0
CA 3:THR22 4.6 14.8 1.0
CA 3:PRO19 4.6 17.4 1.0
O 3:TRP16 4.8 16.1 1.0
CG1 3:VAL21 4.8 17.4 1.0
CB 3:ASP15 4.9 17.3 1.0
C 3:GLU17 5.0 17.9 1.0

Reference:

M.L.Dugdale, M.L.Vance, R.W.Wheatley, M.R.Driedger, A.Nibber, A.Tran, R.E.Huber. Importance of Arg-599 of B-Galactosidase (Escherichia Coli) As An Anchor For the Open Conformations of Phe-601 and the Active-Site Loop Biochem.Cell Biol. V. 88 969 2010.
ISSN: ISSN 0829-8211
Page generated: Mon Dec 14 08:27:05 2020

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