Atomistry » Magnesium » PDB 3muz-3n82 » 3muz
Atomistry »
  Magnesium »
    PDB 3muz-3n82 »
      3muz »

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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Go back to Magnesium Binding Sites List in 3muz
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

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy