Atomistry » Magnesium » PDB 3mfi-3mv0 » 3muy
Atomistry »
  Magnesium »
    PDB 3mfi-3mv0 »
      3muy »

Magnesium in PDB 3muy: E. Coli (Lacz) Beta-Galactosidase (R599A)

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (R599A)

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

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (R599A), PDB code: 3muy 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) 86.02 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.266, 167.237, 200.614, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.5

Other elements in 3muy:

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

Sodium (Na) 16 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 1 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:14.6
occ:1.00
 OE1 1:GLU461 2.0 15.6 1.0
OE2 1:GLU416 2.1 16.8 1.0
ND1 1:HIS418 2.1 12.4 1.0
O 1:HOH4156 2.1 6.5 1.0
O 1:HOH4078 2.2 16.5 1.0
O 1:HOH4014 2.3 9.3 1.0
CE1 1:HIS418 3.0 12.2 1.0
CD 1:GLU461 3.1 15.9 1.0
CG 1:HIS418 3.1 13.6 1.0
CD 1:GLU416 3.2 16.4 1.0
CB 1:HIS418 3.5 12.3 1.0
OE1 1:GLU416 3.8 18.6 1.0
OE2 1:GLU461 3.9 15.7 1.0
CB 1:GLU461 4.0 11.2 1.0
CG 1:GLU461 4.1 13.9 1.0
OD1 1:ASN102 4.1 22.1 1.0
NE2 1:HIS418 4.1 12.7 1.0
O 1:ASP199 4.1 16.7 1.0
N 1:ASP201 4.2 12.7 1.0
CD2 1:HIS418 4.2 11.9 1.0
CG 1:GLU416 4.2 15.4 1.0
CB 1:ASP201 4.3 13.2 1.0
ND2 1:ASN460 4.5 11.0 1.0
O 1:HOH7548 4.6 16.2 1.0
O 1:ASN102 4.6 16.3 1.0
O 1:HOH7504 4.7 39.2 1.0
CA 1:ASP201 4.8 13.4 1.0
O 1:HOH7549 4.8 10.4 1.0
C 1:GLN200 4.9 12.3 1.0
CA 1:GLN200 4.9 11.2 1.0
CA 1:HIS418 5.0 13.2 1.0

Magnesium binding site 2 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 2 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:23.2
occ:1.00
 O 1:VAL21 2.1 17.6 1.0
OE1 1:GLN163 2.2 9.9 1.0
O 1:ASP15 2.2 19.8 1.0
O 1:ASN18 2.3 18.5 1.0
OD2 1:ASP193 2.5 14.0 1.0
CD 1:GLN163 3.1 12.7 1.0
CG 1:ASP193 3.2 17.2 1.0
OD1 1:ASP193 3.2 19.4 1.0
C 1:VAL21 3.3 16.5 1.0
C 1:ASN18 3.3 17.4 1.0
C 1:ASP15 3.4 20.6 1.0
NE2 1:GLN163 3.6 12.3 1.0
N 1:ASN18 3.8 19.4 1.0
OH 1:TYR161 3.8 17.9 1.0
CE2 1:TYR161 4.0 17.5 1.0
CA 1:ASN18 4.0 17.9 1.0
CA 1:VAL21 4.1 15.5 1.0
CB 1:VAL21 4.2 14.0 1.0
CA 1:TRP16 4.2 18.6 1.0
N 1:VAL21 4.2 16.4 1.0
N 1:THR22 4.2 15.8 1.0
N 1:TRP16 4.3 19.1 1.0
N 1:PRO19 4.3 16.2 1.0
CB 1:ASN18 4.3 18.0 1.0
CG 1:GLN163 4.4 11.4 1.0
CA 1:THR22 4.4 15.1 1.0
CZ 1:TYR161 4.4 16.1 1.0
CA 1:ASP15 4.4 22.1 1.0
C 1:TRP16 4.4 18.7 1.0
N 1:GLU17 4.5 18.4 1.0
CA 1:PRO19 4.5 16.1 1.0
CG1 1:VAL21 4.6 12.3 1.0
CB 1:ASP193 4.6 15.7 1.0
CB 1:ASP15 4.7 21.8 1.0
C 1:PRO19 4.9 15.7 1.0
C 1:GLU17 5.0 20.1 1.0

Magnesium binding site 3 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 3 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
1:Mg3003

b:41.9
occ:1.00
 O 1:HOH7562 2.4 60.9 1.0
O 1:HOH4674 2.4 27.3 1.0
O 1:HOH5173 2.5 32.0 1.0
O 1:HOH5163 2.9 39.5 1.0
C1 1:DMS8406 3.7 59.3 1.0
O 1:HOH7530 4.2 41.4 1.0
S 1:DMS8406 4.3 60.5 1.0
O 1:HOH4736 4.5 35.5 1.0
OE2 1:GLU314 4.6 17.5 1.0
OE1 1:GLU314 4.6 16.5 1.0
O 1:DMS8406 4.9 60.0 1.0
O 1:HOH7017 4.9 33.2 1.0
O 1:HOH4706 4.9 17.3 1.0

Magnesium binding site 4 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 4 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:11.9
occ:1.00
 OE1 2:GLU461 1.9 12.4 1.0
O 2:HOH4078 2.1 3.5 1.0
O 2:HOH4014 2.3 11.6 1.0
ND1 2:HIS418 2.3 9.8 1.0
OE2 2:GLU416 2.3 10.8 1.0
O 2:HOH4156 2.4 17.9 1.0
CD 2:GLU461 2.9 11.1 1.0
CE1 2:HIS418 3.2 9.2 1.0
OE2 2:GLU461 3.4 10.5 1.0
CG 2:HIS418 3.4 12.7 1.0
CD 2:GLU416 3.5 11.6 1.0
CB 2:HIS418 3.7 12.7 1.0
OE1 2:GLU416 4.0 11.6 1.0
CG 2:GLU461 4.0 10.1 1.0
CB 2:GLU461 4.0 11.6 1.0
OD1 2:ASN102 4.1 18.9 1.0
ND2 2:ASN460 4.3 10.4 1.0
CB 2:ASP201 4.3 10.2 1.0
NE2 2:HIS418 4.3 9.2 1.0
N 2:ASP201 4.4 10.2 1.0
O 2:HOH7504 4.4 10.5 1.0
CD2 2:HIS418 4.5 10.8 1.0
O 2:HOH7564 4.5 38.8 1.0
O 2:ASP199 4.5 9.7 1.0
O 2:HOH4324 4.6 12.3 1.0
CG 2:GLU416 4.7 9.9 1.0
O 2:ASN102 4.9 16.8 1.0
CA 2:ASP201 4.9 11.1 1.0

Magnesium binding site 5 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 5 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:12.8
occ:1.00
 OD2 2:ASP193 2.2 12.1 1.0
NE2 2:GLN163 2.3 7.5 1.0
O 2:ASP15 2.3 15.9 1.0
O 2:ASN18 2.4 16.3 1.0
O 2:VAL21 2.4 16.6 1.0
CG 2:ASP193 2.9 10.8 1.0
OD1 2:ASP193 2.9 11.9 1.0
CD 2:GLN163 3.2 12.2 1.0
C 2:ASN18 3.2 17.4 1.0
OE1 2:GLN163 3.4 9.4 1.0
C 2:ASP15 3.5 18.7 1.0
C 2:VAL21 3.5 17.9 1.0
N 2:ASN18 3.7 18.6 1.0
CA 2:ASN18 3.9 17.3 1.0
OH 2:TYR161 4.0 14.5 1.0
CA 2:TRP16 4.1 17.1 1.0
N 2:PRO19 4.1 18.8 1.0
N 2:TRP16 4.3 17.5 1.0
C 2:TRP16 4.3 17.1 1.0
CB 2:ASP193 4.3 9.5 1.0
CE2 2:TYR161 4.3 12.6 1.0
CB 2:ASN18 4.4 16.5 1.0
N 2:GLU17 4.4 17.4 1.0
CA 2:VAL21 4.4 19.3 1.0
CA 2:PRO19 4.4 20.0 1.0
N 2:VAL21 4.4 21.0 1.0
N 2:THR22 4.5 18.3 1.0
CB 2:VAL21 4.5 19.3 1.0
CG 2:GLN163 4.6 10.0 1.0
CA 2:ASP15 4.6 20.3 1.0
CA 2:THR22 4.6 18.3 1.0
CZ 2:TYR161 4.6 12.3 1.0
C 2:GLU17 4.8 18.6 1.0
O 2:TRP16 4.8 17.2 1.0
C 2:PRO19 4.9 20.4 1.0
CB 2:ASP15 5.0 21.1 1.0

Magnesium binding site 6 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 6 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:15.8
occ:1.00
 OE1 3:GLU461 1.9 3.6 1.0
OE2 3:GLU416 2.2 14.3 1.0
O 3:HOH4156 2.2 12.0 1.0
O 3:HOH4078 2.3 21.2 1.0
ND1 3:HIS418 2.3 14.2 1.0
O 3:HOH4014 2.3 13.9 1.0
CD 3:GLU461 3.0 7.6 1.0
CE1 3:HIS418 3.2 14.8 1.0
CD 3:GLU416 3.3 13.4 1.0
CG 3:HIS418 3.3 14.7 1.0
CB 3:HIS418 3.6 12.7 1.0
OE2 3:GLU461 3.8 6.2 1.0
OE1 3:GLU416 3.9 13.2 1.0
CG 3:GLU461 4.1 7.8 1.0
OD1 3:ASN102 4.1 18.5 1.0
CB 3:GLU461 4.1 8.7 1.0
N 3:ASP201 4.2 10.0 1.0
O 3:ASP199 4.2 8.0 1.0
CB 3:ASP201 4.3 11.9 1.0
NE2 3:HIS418 4.3 16.7 1.0
CG 3:GLU416 4.4 11.7 1.0
CD2 3:HIS418 4.4 15.4 1.0
ND2 3:ASN460 4.5 9.5 1.0
O 3:HOH7565 4.5 9.6 1.0
O 3:ASN102 4.5 14.0 1.0
O 3:HOH7567 4.6 49.2 1.0
CA 3:ASP201 4.8 11.1 1.0
O 3:HOH7566 4.8 30.2 1.0
C 3:GLN200 4.9 10.9 1.0
CA 3:GLN200 4.9 9.2 1.0

Magnesium binding site 7 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 7 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:17.1
occ:1.00
 O 3:VAL21 2.1 12.6 1.0
OD2 3:ASP193 2.3 15.9 1.0
O 3:ASN18 2.3 17.1 1.0
NE2 3:GLN163 2.4 8.4 1.0
O 3:ASP15 2.4 13.9 1.0
CG 3:ASP193 3.1 15.1 1.0
OD1 3:ASP193 3.1 15.2 1.0
C 3:ASN18 3.2 16.0 1.0
C 3:VAL21 3.2 14.5 1.0
CD 3:GLN163 3.3 13.2 1.0
OE1 3:GLN163 3.6 12.2 1.0
C 3:ASP15 3.6 15.8 1.0
N 3:ASN18 3.7 16.6 1.0
CA 3:ASN18 3.9 15.7 1.0
CA 3:VAL21 4.0 14.6 1.0
N 3:PRO19 4.0 15.7 1.0
OH 3:TYR161 4.1 14.6 1.0
N 3:VAL21 4.1 15.7 1.0
CB 3:VAL21 4.1 14.8 1.0
N 3:THR22 4.2 13.4 1.0
CA 3:PRO19 4.3 15.9 1.0
CA 3:TRP16 4.3 14.1 1.0
CB 3:ASN18 4.3 14.9 1.0
CA 3:THR22 4.4 13.6 1.0
CE2 3:TYR161 4.4 13.5 1.0
N 3:TRP16 4.4 14.6 1.0
N 3:GLU17 4.4 16.7 1.0
C 3:TRP16 4.4 16.1 1.0
CB 3:ASP193 4.5 14.8 1.0
CG 3:GLN163 4.6 12.6 1.0
CG1 3:VAL21 4.6 11.8 1.0
CA 3:ASP15 4.7 18.3 1.0
C 3:PRO19 4.7 16.1 1.0
CZ 3:TYR161 4.7 13.6 1.0
C 3:GLU17 4.9 17.8 1.0
N 3:GLY20 4.9 15.9 1.0

Magnesium binding site 8 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 8 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:7.9
occ:1.00
 OE1 4:GLU461 2.0 11.7 1.0
ND1 4:HIS418 2.1 14.4 1.0
O 4:HOH4156 2.1 12.1 1.0
O 4:HOH4078 2.2 13.7 1.0
OE2 4:GLU416 2.3 15.4 1.0
O 4:HOH4014 2.3 7.0 1.0
CE1 4:HIS418 3.0 14.9 1.0
CG 4:HIS418 3.1 13.8 1.0
CD 4:GLU461 3.2 14.4 1.0
CD 4:GLU416 3.3 15.7 1.0
CB 4:HIS418 3.5 11.8 1.0
OE1 4:GLU416 3.8 16.0 1.0
OE2 4:GLU461 3.9 12.3 1.0
CG 4:GLU461 4.1 13.3 1.0
CB 4:GLU461 4.1 10.8 1.0
NE2 4:HIS418 4.2 14.1 1.0
N 4:ASP201 4.2 12.1 1.0
CD2 4:HIS418 4.2 13.7 1.0
O 4:ASP199 4.2 9.0 1.0
OD1 4:ASN102 4.2 21.8 1.0
CB 4:ASP201 4.3 9.2 1.0
CG 4:GLU416 4.4 14.0 1.0
ND2 4:ASN460 4.4 10.7 1.0
O 4:HOH7555 4.6 44.1 1.0
O 4:ASN102 4.6 17.2 1.0
O 4:HOH7537 4.6 12.5 1.0
CA 4:ASP201 4.8 10.8 1.0
O 4:HOH7538 4.8 16.1 1.0
C 4:GLN200 4.9 11.8 1.0
CA 4:GLN200 4.9 10.9 1.0
CA 4:HIS418 4.9 11.7 1.0
CG2 4:VAL103 5.0 15.0 1.0

Magnesium binding site 9 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 9 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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

b:11.5
occ:1.00
 O 4:VAL21 2.2 14.5 1.0
NE2 4:GLN163 2.3 3.0 1.0
O 4:ASP15 2.3 17.8 1.0
OD2 4:ASP193 2.4 16.3 1.0
O 4:ASN18 2.5 15.3 1.0
CD 4:GLN163 3.0 8.4 1.0
CG 4:ASP193 3.1 14.5 1.0
OD1 4:ASP193 3.1 17.1 1.0
OE1 4:GLN163 3.2 7.9 1.0
C 4:VAL21 3.3 14.5 1.0
C 4:ASN18 3.5 16.3 1.0
C 4:ASP15 3.5 19.0 1.0
N 4:ASN18 3.9 17.7 1.0
OH 4:TYR161 4.1 21.6 1.0
CA 4:TRP16 4.1 17.1 1.0
CA 4:VAL21 4.2 14.6 1.0
N 4:THR22 4.2 14.3 1.0
CA 4:ASN18 4.2 17.1 1.0
CE2 4:TYR161 4.3 19.2 1.0
N 4:VAL21 4.3 14.3 1.0
N 4:PRO19 4.3 16.1 1.0
N 4:TRP16 4.3 17.5 1.0
CB 4:VAL21 4.3 14.6 1.0
CA 4:THR22 4.3 15.7 1.0
C 4:TRP16 4.4 16.6 1.0
CG 4:GLN163 4.4 8.5 1.0
CA 4:PRO19 4.5 16.2 1.0
CB 4:ASP193 4.5 13.4 1.0
N 4:GLU17 4.5 15.3 1.0
CA 4:ASP15 4.6 19.8 1.0
CZ 4:TYR161 4.7 19.0 1.0
CB 4:ASN18 4.7 19.5 1.0
CG1 4:VAL21 4.8 13.9 1.0
C 4:PRO19 4.9 16.6 1.0
CB 4:ASP15 4.9 20.7 1.0
O 4:TRP16 5.0 15.7 1.0

Magnesium binding site 10 out of 10 in 3muy

Go back to Magnesium Binding Sites List in 3muy
Magnesium binding site 10 out of 10 in the E. Coli (Lacz) Beta-Galactosidase (R599A)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
4:Mg3003

b:29.5
occ:1.00
 O 4:HOH4674 2.2 25.6 1.0
O 4:HOH7550 2.3 40.7 1.0
O 4:HOH5175 2.3 37.7 1.0
O 4:HOH7551 2.3 50.7 1.0
O 4:HOH4736 3.7 35.3 1.0
O 4:HOH5055 4.1 40.8 1.0
OE1 4:GLN266 4.2 35.8 1.0
OE2 4:GLU314 4.3 16.0 1.0
OE1 4:GLU314 4.5 16.8 1.0
OG 4:SER259 4.8 22.3 1.0
CD 4:GLU314 4.8 16.0 1.0
CZ2 4:TRP261 5.0 19.1 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 Beta-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
PubMed: 21102659
DOI: 10.1139/O10-144
Page generated: Wed Aug 14 19:26:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy