Atomistry » Magnesium » PDB 1jx2-1k9m » 1jyn
Atomistry »
  Magnesium »
    PDB 1jx2-1k9m »
      1jyn »

Magnesium in PDB 1jyn: E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose

Enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose

All present enzymatic activity of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose:
3.2.1.23;

Protein crystallography data

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose, PDB code: 1jyn was solved by D.H.Juers, B.W.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 149.550, 168.630, 200.880, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 21.9

Other elements in 1jyn:

The structure of E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose also contains other interesting chemical elements:

Sodium (Na) 15 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 (E537Q) in Complex with Lactose (pdb code 1jyn). 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 (E537Q) in Complex with Lactose, PDB code: 1jyn:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 1 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3001

b:10.3
occ:1.00
 OE2 A:GLU416 2.0 8.9 1.0
O A:HOH8521 2.1 7.0 1.0
ND1 A:HIS418 2.1 11.0 1.0
OE1 A:GLU461 2.2 10.6 1.0
O A:HOH8662 2.2 5.2 1.0
O A:HOH8585 2.2 7.5 1.0
CE1 A:HIS418 3.1 9.4 1.0
CD A:GLU416 3.1 13.0 1.0
CD A:GLU461 3.2 11.3 1.0
CG A:HIS418 3.3 14.1 1.0
OE1 A:GLU416 3.6 8.5 1.0
CB A:HIS418 3.7 6.6 1.0
CB A:GLU461 3.9 6.6 1.0
OE2 A:GLU461 4.0 9.6 1.0
CG A:GLU461 4.1 2.5 1.0
O A:HOH8508 4.1 9.2 1.0
OD1 A:ASN102 4.1 11.3 1.0
N A:ASP201 4.2 11.2 1.0
CB A:ASP201 4.2 10.5 1.0
ND2 A:ASN460 4.3 8.6 1.0
NE2 A:HIS418 4.3 8.8 1.0
O4 A:LAT2001 4.3 9.8 0.9
O A:ASP199 4.3 11.2 1.0
CG A:GLU416 4.4 6.8 1.0
CD2 A:HIS418 4.4 8.7 1.0
O3 A:LAT2001 4.4 8.3 0.9
O A:ASN102 4.7 10.3 1.0
CA A:ASP201 4.8 9.3 1.0
CA A:GLN200 4.8 4.2 1.0
C A:GLN200 4.8 9.0 1.0
CG2 A:VAL103 5.0 9.8 1.0

Magnesium binding site 2 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 2 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3002

b:12.7
occ:1.00
 O A:ASP15 2.2 12.4 1.0
O A:ASN18 2.3 11.3 1.0
OE1 A:GLN163 2.3 9.1 1.0
O A:VAL21 2.3 12.8 1.0
OD2 A:ASP193 2.4 11.0 1.0
OD1 A:ASP193 3.0 11.8 1.0
CG A:ASP193 3.1 12.9 1.0
C A:ASN18 3.2 10.1 1.0
CD A:GLN163 3.2 15.3 1.0
C A:ASP15 3.4 14.1 1.0
C A:VAL21 3.5 15.0 1.0
NE2 A:GLN163 3.5 11.0 1.0
N A:ASN18 3.6 17.9 1.0
CA A:ASN18 3.9 12.6 1.0
CA A:TRP16 3.9 9.5 1.0
OH A:TYR161 4.0 9.8 1.0
N A:PRO19 4.1 12.8 1.0
N A:TRP16 4.1 10.2 1.0
CB A:ASN18 4.2 15.3 1.0
C A:TRP16 4.2 14.4 1.0
CA A:VAL21 4.3 10.7 1.0
N A:VAL21 4.3 9.4 1.0
CE2 A:TYR161 4.4 10.4 1.0
CA A:PRO19 4.4 12.7 1.0
N A:GLU17 4.4 12.8 1.0
CB A:VAL21 4.4 8.7 1.0
N A:THR22 4.5 6.4 1.0
CB A:ASP193 4.5 7.5 1.0
CG A:GLN163 4.5 13.4 1.0
CA A:ASP15 4.6 8.0 1.0
CA A:THR22 4.6 8.3 1.0
CZ A:TYR161 4.6 11.9 1.0
O A:TRP16 4.8 12.9 1.0
C A:GLU17 4.8 18.4 1.0
C A:PRO19 4.9 12.9 1.0
CG1 A:VAL21 4.9 9.8 1.0
CB A:ASP15 4.9 13.1 1.0

Magnesium binding site 3 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 3 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3005

b:31.6
occ:1.00
 O A:HOH9341 2.0 23.6 1.0
O A:HOH9424 2.0 29.6 1.0
O A:HOH9149 2.1 25.5 1.0
O A:HOH9342 2.1 36.8 1.0
C2 A:DMS8406 3.1 42.5 1.0
O A:HOH9333 3.4 43.6 1.0
C1 A:DMS8406 3.9 59.5 1.0
OE1 A:GLU314 4.1 12.2 1.0
OE2 A:GLU314 4.1 15.0 1.0
O A:HOH9204 4.3 17.1 1.0
S A:DMS8406 4.4 61.1 1.0
O A:HOH9461 4.4 17.2 1.0
CD A:GLU314 4.6 19.1 1.0
O A:HOH9195 4.9 27.0 1.0

Magnesium binding site 4 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 4 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg3105

b:77.3
occ:1.00
 O A:HOH9107 1.4 35.4 1.0
O A:HOH8995 2.4 31.7 1.0
O A:HOH9501 2.6 0.0 1.0
O A:ASN597 2.7 12.6 1.0
O A:HOH8951 2.8 18.3 1.0
O A:HOH9240 3.5 32.3 1.0
O A:HOH8728 3.6 22.3 1.0
C A:ASN597 3.9 19.2 1.0
OE2 A:GLU797 4.0 46.0 1.0
N A:ASN597 4.2 13.2 1.0
NH1 A:ARG800 4.2 49.4 1.0
OE1 A:GLU797 4.2 40.8 1.0
OD1 A:ASP598 4.3 16.1 1.0
O A:HOH8954 4.4 24.9 1.0
CD A:GLU797 4.5 34.9 1.0
O A:HOH9304 4.6 35.7 1.0
O A:HOH9517 4.6 43.3 1.0
O A:HOH8834 4.6 27.4 1.0
CA A:ASN597 4.7 9.2 1.0
CA A:ASP598 4.7 10.3 1.0
N A:ASP598 4.7 9.5 1.0
CG A:ASP598 4.8 20.3 1.0
CB A:PRO596 4.9 15.5 1.0

Magnesium binding site 5 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 5 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3001

b:8.9
occ:1.00
 O B:HOH8699 2.0 6.8 1.0
OE2 B:GLU416 2.0 8.0 1.0
OE1 B:GLU461 2.0 8.4 1.0
O B:HOH8775 2.1 8.0 1.0
ND1 B:HIS418 2.1 7.0 1.0
O B:HOH8635 2.2 7.8 1.0
CD B:GLU461 3.0 7.7 1.0
CE1 B:HIS418 3.0 3.9 1.0
CD B:GLU416 3.2 7.7 1.0
CG B:HIS418 3.3 7.4 1.0
OE1 B:GLU416 3.6 9.3 1.0
CB B:HIS418 3.6 8.1 1.0
OE2 B:GLU461 3.8 11.1 1.0
CB B:GLU461 4.0 8.3 1.0
CG B:GLU461 4.0 8.1 1.0
O B:HOH8622 4.1 10.1 1.0
OD1 B:ASN102 4.1 10.3 1.0
CB B:ASP201 4.3 4.6 1.0
NE2 B:HIS418 4.3 6.6 1.0
N B:ASP201 4.3 9.2 1.0
ND2 B:ASN460 4.3 7.2 1.0
O B:ASP199 4.3 9.4 1.0
CG B:GLU416 4.4 3.7 1.0
CD2 B:HIS418 4.4 4.7 1.0
O3 B:LAT2001 4.4 5.1 0.9
O4 B:LAT2001 4.4 5.7 0.9
O B:ASN102 4.7 10.5 1.0
CA B:GLN200 4.8 5.2 1.0
CA B:ASP201 4.9 5.6 1.0
C2 B:LAT2001 4.9 4.3 0.9
C B:GLN200 5.0 9.9 1.0

Magnesium binding site 6 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 6 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg3002

b:13.5
occ:1.00
 OE1 B:GLN163 2.2 10.8 1.0
O B:VAL21 2.3 12.5 1.0
OD2 B:ASP193 2.3 7.7 1.0
O B:ASP15 2.3 12.7 1.0
O B:ASN18 2.4 14.3 1.0
OD1 B:ASP193 3.1 14.2 1.0
CG B:ASP193 3.1 17.2 1.0
CD B:GLN163 3.1 12.5 1.0
C B:ASN18 3.3 10.8 1.0
NE2 B:GLN163 3.4 11.2 1.0
C B:VAL21 3.5 12.8 1.0
C B:ASP15 3.5 12.8 1.0
N B:ASN18 3.8 18.8 1.0
OH B:TYR161 4.0 11.4 1.0
CA B:ASN18 4.0 15.4 1.0
CA B:TRP16 4.0 7.7 1.0
N B:PRO19 4.2 11.2 1.0
N B:TRP16 4.2 9.6 1.0
CA B:VAL21 4.2 10.9 1.0
N B:VAL21 4.3 10.6 1.0
CB B:ASN18 4.3 9.9 1.0
C B:TRP16 4.3 15.2 1.0
CE2 B:TYR161 4.3 6.3 1.0
CB B:VAL21 4.3 14.1 1.0
CA B:PRO19 4.4 15.3 1.0
N B:GLU17 4.4 11.0 1.0
CG B:GLN163 4.5 6.8 1.0
N B:THR22 4.5 9.4 1.0
CB B:ASP193 4.5 5.6 1.0
CA B:THR22 4.6 8.9 1.0
CZ B:TYR161 4.6 11.2 1.0
CA B:ASP15 4.7 15.5 1.0
C B:PRO19 4.8 20.2 1.0
O B:TRP16 4.8 10.7 1.0
CG1 B:VAL21 4.9 16.6 1.0
C B:GLU17 4.9 15.1 1.0

Magnesium binding site 7 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 7 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3001

b:10.6
occ:1.00
 OE2 C:GLU416 2.0 10.9 1.0
OE1 C:GLU461 2.1 6.1 1.0
O C:HOH8785 2.1 6.3 1.0
O C:HOH8708 2.1 7.0 1.0
O C:HOH8644 2.2 7.1 1.0
ND1 C:HIS418 2.2 8.9 1.0
CD C:GLU461 3.0 14.8 1.0
CE1 C:HIS418 3.1 10.4 1.0
CD C:GLU416 3.2 15.4 1.0
CG C:HIS418 3.3 6.8 1.0
OE1 C:GLU416 3.5 8.2 1.0
CB C:HIS418 3.6 6.8 1.0
OE2 C:GLU461 3.9 11.1 1.0
CB C:GLU461 4.0 4.5 1.0
CG C:GLU461 4.0 7.1 1.0
O C:HOH8631 4.2 6.6 1.0
OD1 C:ASN102 4.2 11.7 1.0
N C:ASP201 4.2 7.9 1.0
ND2 C:ASN460 4.2 8.8 1.0
CB C:ASP201 4.3 5.5 1.0
O C:ASP199 4.3 7.4 1.0
NE2 C:HIS418 4.3 8.3 1.0
O4 C:LAT2001 4.4 7.6 0.9
CG C:GLU416 4.4 3.0 1.0
CD2 C:HIS418 4.4 9.1 1.0
O3 C:LAT2001 4.4 7.8 0.9
O C:ASN102 4.8 9.0 1.0
CA C:ASP201 4.8 3.8 1.0
CA C:GLN200 4.9 11.2 1.0
C2 C:LAT2001 4.9 5.2 0.9
CG2 C:VAL103 4.9 12.2 1.0
C C:GLN200 4.9 15.4 1.0

Magnesium binding site 8 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 8 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3002

b:9.9
occ:1.00
 O C:VAL21 2.2 8.6 1.0
O C:ASP15 2.3 12.6 1.0
O C:ASN18 2.3 11.8 1.0
OE1 C:GLN163 2.4 9.8 1.0
OD2 C:ASP193 2.4 11.4 1.0
OD1 C:ASP193 3.1 12.4 1.0
CG C:ASP193 3.1 13.3 1.0
CD C:GLN163 3.2 8.1 1.0
C C:ASN18 3.3 11.2 1.0
C C:VAL21 3.4 9.2 1.0
C C:ASP15 3.5 14.1 1.0
NE2 C:GLN163 3.5 8.9 1.0
N C:ASN18 3.8 12.8 1.0
OH C:TYR161 3.9 10.3 1.0
CA C:ASN18 4.0 14.1 1.0
CA C:TRP16 4.1 16.5 1.0
CA C:VAL21 4.2 9.9 1.0
N C:VAL21 4.2 8.8 1.0
N C:TRP16 4.2 10.3 1.0
N C:PRO19 4.2 16.9 1.0
CB C:ASN18 4.2 13.1 1.0
CE2 C:TYR161 4.3 8.2 1.0
C C:TRP16 4.3 11.3 1.0
N C:THR22 4.4 5.6 1.0
CB C:VAL21 4.4 8.6 1.0
CA C:PRO19 4.4 11.0 1.0
CA C:THR22 4.5 9.7 1.0
N C:GLU17 4.5 14.1 1.0
CG C:GLN163 4.5 8.8 1.0
CB C:ASP193 4.6 5.8 1.0
CZ C:TYR161 4.6 9.0 1.0
CA C:ASP15 4.7 10.7 1.0
O C:TRP16 4.8 12.3 1.0
C C:PRO19 4.9 14.5 1.0
C C:GLU17 4.9 20.9 1.0
CB C:ASP15 5.0 9.7 1.0
CG1 C:VAL21 5.0 12.0 1.0

Magnesium binding site 9 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 9 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3004

b:37.1
occ:1.00
 O C:HOH9557 2.4 34.9 1.0
O C:HOH9559 2.4 27.3 1.0
O C:HOH9571 2.5 38.4 1.0
OE1 C:GLN49 2.9 0.0 1.0
CD C:GLN49 3.5 0.0 1.0
CG C:GLN49 4.0 35.5 1.0
O C:HOH9601 4.2 45.0 1.0
OE2 C:GLU41 4.2 14.7 1.0
NE2 C:GLN49 4.2 79.4 1.0
O C:HOH9333 4.3 15.8 1.0
O C:HOH9455 4.7 19.1 1.0
O C:HOH9486 4.7 22.4 1.0

Magnesium binding site 10 out of 14 in 1jyn

Go back to Magnesium Binding Sites List in 1jyn
Magnesium binding site 10 out of 14 in the E. Coli (Lacz) Beta-Galactosidase (E537Q) in Complex with Lactose


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 (E537Q) in Complex with Lactose within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3006

b:27.0
occ:1.00
 O C:HOH9561 1.7 30.6 1.0
O C:HOH9591 1.8 30.0 1.0
O C:HOH9521 2.2 22.4 1.0
O C:HOH9580 4.2 29.6 1.0
O C:HOH9459 4.2 22.7 1.0
O C:ALA179 4.3 18.7 1.0
O C:GLU181 4.3 16.0 1.0
CD C:ARG178 4.5 35.7 1.0
CG C:ARG178 4.6 42.7 1.0
N C:GLU181 4.6 14.8 1.0
CB C:GLU181 5.0 12.8 1.0

Reference:

D.H.Juers, T.D.Heightman, A.Vasella, J.D.Mccarter, L.Mackenzie, S.G.Withers, B.W.Matthews. A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase Biochemistry V. 40 14781 2001.
ISSN: ISSN 0006-2960
PubMed: 11732897
DOI: 10.1021/BI011727I
Page generated: Tue Aug 13 06:52:41 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy