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Magnesium in PDB 3mv1: E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium

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

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

Protein crystallography data

The structure of E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium, PDB code: 3mv1 was solved by M.L.Dugdale, M.Vance, M.L.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) 71.29 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 151.730, 161.520, 203.740, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 24.2

Other elements in 3mv1:

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

Sodium (Na) 16 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium atom in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium (pdb code 3mv1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium, PDB code: 3mv1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3mv1

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Magnesium binding site 1 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3001

b:25.4
occ:1.00
 OE1 1:GLU461 1.9 16.7 1.0
OE2 1:GLU416 2.1 19.5 1.0
O 1:HOH4076 2.1 19.1 1.0
ND1 1:HIS418 2.3 15.4 1.0
O 1:HOH4012 2.3 16.6 1.0
O 1:HOH4152 2.3 21.4 1.0
CD 1:GLU461 3.0 15.7 1.0
CE1 1:HIS418 3.2 14.8 1.0
CD 1:GLU416 3.2 18.8 1.0
CG 1:HIS418 3.3 16.6 1.0
CB 1:HIS418 3.6 15.7 1.0
OE2 1:GLU461 3.7 14.9 1.0
OE1 1:GLU416 3.7 19.1 1.0
CG 1:GLU461 4.0 16.8 1.0
CB 1:GLU461 4.0 15.3 1.0
OD1 1:ASN102 4.1 22.9 1.0
N 1:ASP201 4.2 22.5 1.0
CB 1:ASP201 4.3 22.3 1.0
O 1:ASP199 4.3 21.2 1.0
NE2 1:HIS418 4.3 14.9 1.0
ND2 1:ASN460 4.3 13.7 1.0
CD2 1:HIS418 4.4 13.8 1.0
CG 1:GLU416 4.4 17.2 1.0
O 1:HOH4937 4.5 29.3 1.0
O 1:HOH4869 4.5 33.7 1.0
O 1:HOH4936 4.5 20.6 1.0
O 1:ASN102 4.8 21.3 1.0
CA 1:ASP201 4.8 22.1 1.0
C 1:GLN200 4.9 23.1 1.0
CA 1:GLN200 4.9 22.2 1.0

Magnesium binding site 2 out of 12 in 3mv1

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Magnesium binding site 2 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3002

b:24.9
occ:1.00
 O 1:VAL21 2.2 23.8 1.0
NE2 1:GLN163 2.3 24.3 1.0
O 1:ASP15 2.3 29.9 1.0
O 1:ASN18 2.3 27.1 1.0
OD2 1:ASP193 2.4 30.8 1.0
OD1 1:ASP193 3.1 32.1 1.0
CG 1:ASP193 3.1 31.4 1.0
C 1:ASN18 3.2 28.5 1.0
CD 1:GLN163 3.3 27.2 1.0
C 1:VAL21 3.3 24.6 1.0
C 1:ASP15 3.5 30.4 1.0
OE1 1:GLN163 3.6 27.3 1.0
N 1:ASN18 3.7 28.3 1.0
CA 1:ASN18 3.9 29.3 1.0
OH 1:TYR161 4.0 25.6 1.0
CA 1:VAL21 4.1 24.5 1.0
CA 1:TRP16 4.1 28.6 1.0
N 1:PRO19 4.2 28.5 1.0
N 1:VAL21 4.2 24.8 1.0
CB 1:VAL21 4.2 25.2 1.0
CB 1:ASN18 4.3 31.1 1.0
N 1:TRP16 4.3 30.1 1.0
N 1:THR22 4.3 23.9 1.0
CE2 1:TYR161 4.3 25.6 1.0
C 1:TRP16 4.3 28.4 1.0
CA 1:PRO19 4.4 28.5 1.0
N 1:GLU17 4.4 27.1 1.0
CA 1:THR22 4.5 24.5 1.0
CB 1:ASP193 4.6 28.0 1.0
CA 1:ASP15 4.6 31.4 1.0
CG 1:GLN163 4.6 25.4 1.0
CZ 1:TYR161 4.7 24.8 1.0
CG1 1:VAL21 4.8 22.7 1.0
C 1:PRO19 4.8 27.8 1.0
C 1:GLU17 4.9 27.5 1.0
O 1:TRP16 4.9 28.0 1.0
CB 1:ASP15 4.9 33.0 1.0

Magnesium binding site 3 out of 12 in 3mv1

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Magnesium binding site 3 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3004

b:49.9
occ:1.00
 O 1:HOH4600 2.3 46.7 1.0
O 1:HOH4559 2.3 52.3 1.0
O 1:HOH4256 2.4 28.9 1.0
O 1:HOH4810 2.4 50.1 1.0
O 1:HOH4362 2.6 23.7 1.0
OE1 1:GLN718 2.7 23.2 1.0
O 1:THR911 3.6 15.3 1.0
CD 1:GLN718 3.7 21.1 1.0
NE2 1:GLN718 4.0 20.1 1.0
O 1:HOH4247 4.0 40.3 1.0
NE2 1:HIS622 4.0 17.9 1.0
O 1:HOH4272 4.5 44.1 1.0
C 1:THR911 4.5 14.5 1.0
CA 1:THR911 4.7 13.6 1.0
N 1:GLN719 4.7 17.9 1.0
O 1:GLN719 4.7 20.3 1.0
CE1 1:HIS622 4.8 17.9 1.0
CB 1:THR911 4.8 13.5 1.0
O 1:HOH4078 4.8 14.8 1.0

Magnesium binding site 4 out of 12 in 3mv1

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Magnesium binding site 4 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3001

b:20.2
occ:1.00
 OE1 2:GLU461 2.0 10.0 1.0
OE2 2:GLU416 2.1 13.2 1.0
O 2:HOH4076 2.2 19.6 1.0
O 2:HOH4152 2.3 9.1 1.0
O 2:HOH4012 2.3 9.5 1.0
ND1 2:HIS418 2.4 11.8 1.0
CD 2:GLU461 3.1 12.3 1.0
CD 2:GLU416 3.2 12.9 1.0
CE1 2:HIS418 3.3 15.1 1.0
CG 2:HIS418 3.4 14.0 1.0
CB 2:HIS418 3.7 13.5 1.0
OE1 2:GLU416 3.7 11.7 1.0
OE2 2:GLU461 3.8 7.0 1.0
OD1 2:ASN102 4.0 18.9 1.0
N 2:ASP201 4.1 13.2 1.0
CB 2:ASP201 4.1 15.6 1.0
CG 2:GLU461 4.2 11.1 1.0
CB 2:GLU461 4.2 10.3 1.0
O 2:ASP199 4.2 13.5 1.0
ND2 2:ASN460 4.3 11.7 1.0
CG 2:GLU416 4.4 9.2 1.0
NE2 2:HIS418 4.5 14.9 1.0
O 2:HOH5086 4.5 35.2 1.0
CD2 2:HIS418 4.5 12.4 1.0
O 2:HOH5053 4.6 25.6 1.0
CA 2:ASP201 4.7 14.6 1.0
O 2:HOH5052 4.7 20.4 1.0
O 2:ASN102 4.7 17.2 1.0
C 2:GLN200 4.8 15.2 1.0
CA 2:GLN200 4.8 12.6 1.0
O 2:HOH5054 4.9 40.5 1.0

Magnesium binding site 5 out of 12 in 3mv1

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Magnesium binding site 5 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3002

b:15.6
occ:1.00
 O 2:VAL21 2.3 13.2 1.0
OD2 2:ASP193 2.3 13.7 1.0
NE2 2:GLN163 2.3 12.7 1.0
O 2:ASN18 2.3 15.3 1.0
O 2:ASP15 2.3 13.8 1.0
CG 2:ASP193 3.0 16.4 1.0
OD1 2:ASP193 3.0 15.7 1.0
C 2:ASN18 3.2 17.8 1.0
CD 2:GLN163 3.3 16.8 1.0
C 2:VAL21 3.4 16.4 1.0
OE1 2:GLN163 3.5 19.8 1.0
C 2:ASP15 3.5 16.6 1.0
N 2:ASN18 3.6 18.8 1.0
CA 2:ASN18 3.9 18.8 1.0
OH 2:TYR161 4.0 17.5 1.0
CA 2:TRP16 4.1 17.3 1.0
N 2:PRO19 4.1 17.4 1.0
CA 2:VAL21 4.2 16.3 1.0
CB 2:ASN18 4.3 18.2 1.0
N 2:TRP16 4.3 17.1 1.0
C 2:TRP16 4.3 18.8 1.0
N 2:VAL21 4.3 17.6 1.0
CB 2:VAL21 4.3 16.3 1.0
CA 2:PRO19 4.4 18.5 1.0
N 2:GLU17 4.4 18.2 1.0
CE2 2:TYR161 4.4 17.6 1.0
N 2:THR22 4.4 16.9 1.0
CB 2:ASP193 4.4 14.5 1.0
CA 2:THR22 4.6 17.2 1.0
CG 2:GLN163 4.6 15.2 1.0
CA 2:ASP15 4.6 17.6 1.0
CZ 2:TYR161 4.7 17.7 1.0
C 2:GLU17 4.8 19.9 1.0
C 2:PRO19 4.8 17.4 1.0
O 2:TRP16 4.8 17.7 1.0
CG1 2:VAL21 4.9 15.2 1.0

Magnesium binding site 6 out of 12 in 3mv1

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Magnesium binding site 6 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
2:Mg3004

b:61.7
occ:1.00
 O 2:HOH4584 2.3 51.2 1.0
O 2:HOH4640 2.3 58.5 1.0
O 2:HOH4259 2.4 28.1 1.0
OE1 2:GLN718 2.4 22.0 1.0
O 2:HOH4828 2.5 35.7 1.0
O 2:THR911 3.4 17.9 1.0
CD 2:GLN718 3.5 23.2 1.0
NE2 2:HIS622 3.9 11.8 1.0
NE2 2:GLN718 4.0 22.3 1.0
O 2:HOH4275 4.1 65.1 1.0
N 2:GLN719 4.2 23.6 1.0
O 2:HOH4249 4.4 26.2 1.0
CE1 2:HIS622 4.4 13.5 1.0
C 2:THR911 4.5 16.4 1.0
O 2:GLN719 4.6 25.6 1.0
CA 2:GLN718 4.8 23.3 1.0
CG 2:GLN718 4.8 21.6 1.0
CB 2:GLN719 4.8 23.3 1.0
CA 2:THR911 4.9 15.3 1.0
CD2 2:HIS622 4.9 11.1 1.0
CA 2:GLN719 5.0 24.7 1.0

Magnesium binding site 7 out of 12 in 3mv1

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Magnesium binding site 7 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3001

b:16.8
occ:1.00
 OE1 3:GLU461 2.0 12.1 1.0
OE2 3:GLU416 2.1 14.6 1.0
O 3:HOH4154 2.1 12.4 1.0
ND1 3:HIS418 2.2 12.9 1.0
O 3:HOH4076 2.2 16.8 1.0
O 3:HOH4013 2.3 12.4 1.0
CD 3:GLU461 3.1 14.3 1.0
CE1 3:HIS418 3.1 14.0 1.0
CG 3:HIS418 3.2 12.3 1.0
CD 3:GLU416 3.2 14.0 1.0
CB 3:HIS418 3.5 10.6 1.0
OE2 3:GLU461 3.8 14.7 1.0
OE1 3:GLU416 3.8 15.5 1.0
CB 3:GLU461 4.0 11.1 1.0
OD1 3:ASN102 4.1 14.3 1.0
CG 3:GLU461 4.1 10.8 1.0
NE2 3:HIS418 4.2 13.2 1.0
N 3:ASP201 4.2 16.1 1.0
O 3:ASP199 4.3 12.7 1.0
CB 3:ASP201 4.3 15.8 1.0
CD2 3:HIS418 4.3 12.4 1.0
ND2 3:ASN460 4.4 12.9 1.0
CG 3:GLU416 4.4 11.8 1.0
O 3:HOH4899 4.5 40.7 1.0
O 3:HOH5032 4.7 29.6 1.0
O 3:HOH5031 4.7 21.0 1.0
O 3:ASN102 4.7 17.7 1.0
CA 3:ASP201 4.8 16.7 1.0
C 3:GLN200 4.9 15.5 1.0
CA 3:GLN200 4.9 14.2 1.0
CA 3:HIS418 5.0 12.6 1.0

Magnesium binding site 8 out of 12 in 3mv1

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Magnesium binding site 8 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3002

b:12.8
occ:1.00
 O 3:ASP15 2.2 17.2 1.0
NE2 3:GLN163 2.3 13.1 1.0
O 3:VAL21 2.3 16.2 1.0
OD2 3:ASP193 2.4 18.1 1.0
O 3:ASN18 2.4 18.6 1.0
CG 3:ASP193 3.1 18.8 1.0
OD1 3:ASP193 3.1 17.6 1.0
CD 3:GLN163 3.3 16.7 1.0
C 3:ASN18 3.3 19.2 1.0
C 3:ASP15 3.4 18.8 1.0
C 3:VAL21 3.4 16.6 1.0
OE1 3:GLN163 3.6 17.3 1.0
N 3:ASN18 3.7 18.3 1.0
OH 3:TYR161 3.9 13.1 1.0
CA 3:ASN18 3.9 19.2 1.0
CA 3:TRP16 4.0 17.0 1.0
N 3:TRP16 4.1 17.5 1.0
C 3:TRP16 4.2 16.8 1.0
CA 3:VAL21 4.2 16.2 1.0
N 3:PRO19 4.2 20.1 1.0
CE2 3:TYR161 4.3 13.5 1.0
CB 3:ASN18 4.3 20.4 1.0
CB 3:VAL21 4.3 18.7 1.0
N 3:VAL21 4.3 17.1 1.0
N 3:GLU17 4.3 16.7 1.0
N 3:THR22 4.4 15.5 1.0
CA 3:ASP15 4.5 20.2 1.0
CA 3:PRO19 4.5 20.2 1.0
CB 3:ASP193 4.5 16.5 1.0
CG 3:GLN163 4.6 15.4 1.0
CA 3:THR22 4.6 15.9 1.0
CZ 3:TYR161 4.6 11.2 1.0
O 3:TRP16 4.8 16.3 1.0
CG1 3:VAL21 4.8 18.6 1.0
C 3:GLU17 4.8 17.2 1.0
CB 3:ASP15 4.9 18.3 1.0
C 3:PRO19 4.9 20.6 1.0

Magnesium binding site 9 out of 12 in 3mv1

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Magnesium binding site 9 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
3:Mg3004

b:53.8
occ:1.00
 O 3:HOH4921 2.3 58.8 1.0
O 3:HOH4375 2.3 36.7 1.0
O 3:HOH4258 2.4 22.8 1.0
O 3:HOH4868 2.5 41.0 1.0
OE1 3:GLN718 2.5 26.6 1.0
O 3:HOH4638 2.6 42.6 1.0
CD 3:GLN718 3.6 24.0 1.0
O 3:THR911 3.7 17.1 1.0
NE2 3:GLN718 4.0 23.6 1.0
NE2 3:HIS622 4.1 9.2 1.0
O 3:HOH4248 4.3 37.5 1.0
O 3:GLN719 4.5 22.9 1.0
N 3:GLN719 4.6 20.3 1.0
C 3:THR911 4.7 16.0 1.0
O 3:HOH4426 4.7 41.8 1.0
CE1 3:HIS622 4.8 10.4 1.0
CA 3:THR911 4.9 15.4 1.0
CG 3:GLN718 4.9 21.8 1.0
O 3:HOH4078 4.9 14.5 1.0
CB 3:THR911 5.0 14.4 1.0

Magnesium binding site 10 out of 12 in 3mv1

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Magnesium binding site 10 out of 12 in the E.Coli (Lacz) Beta-Galactosidase (R599A) in Complex with Guanidinium


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 Guanidinium within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg3001

b:23.5
occ:1.00
 OE1 4:GLU461 2.0 17.8 1.0
O 4:HOH4076 2.1 20.8 1.0
OE2 4:GLU416 2.2 16.4 1.0
O 4:HOH4012 2.2 13.0 1.0
O 4:HOH4153 2.3 19.2 1.0
ND1 4:HIS418 2.4 18.9 1.0
CD 4:GLU461 3.2 18.8 1.0
CE1 4:HIS418 3.3 18.9 1.0
CD 4:GLU416 3.3 17.3 1.0
CG 4:HIS418 3.4 18.6 1.0
CB 4:HIS418 3.7 19.3 1.0
OE1 4:GLU416 3.8 20.0 1.0
OE2 4:GLU461 3.8 18.9 1.0
OD1 4:ASN102 3.9 27.3 1.0
CB 4:ASP201 4.1 24.0 1.0
N 4:ASP201 4.1 24.2 1.0
CG 4:GLU461 4.2 16.6 1.0
CB 4:GLU461 4.2 18.2 1.0
O 4:ASP199 4.2 22.2 1.0
ND2 4:ASN460 4.4 19.4 1.0
O 4:HOH4785 4.4 31.5 1.0
NE2 4:HIS418 4.4 19.4 1.0
O 4:HOH4838 4.5 39.9 1.0
CG 4:GLU416 4.5 16.3 1.0
CD2 4:HIS418 4.5 18.4 1.0
CA 4:ASP201 4.6 23.1 1.0
O 4:ASN102 4.7 25.4 1.0
C 4:GLN200 4.8 23.5 1.0
CA 4:GLN200 4.8 21.4 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 08:27:04 2020

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