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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Mon Dec 14 08:26:53 2020

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