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Magnesium in PDB 1mxg: Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose

Enzymatic activity of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose

All present enzymatic activity of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose:
3.2.1.1;

Protein crystallography data

The structure of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose, PDB code: 1mxg was solved by A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, M.Wilmanns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.480, 76.507, 136.455, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 17.2

Other elements in 1mxg:

The structure of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose (pdb code 1mxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose, PDB code: 1mxg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1mxg

Go back to Magnesium Binding Sites List in 1mxg
Magnesium binding site 1 out of 3 in the Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg439

b:11.9
occ:1.00
 O A:ILE292 2.0 12.1 1.0
O A:HOH510 2.0 17.0 1.0
OD1 A:ASP252 2.1 14.2 1.0
OD2 A:ASP256 2.1 13.1 1.0
O A:HOH512 2.1 17.9 1.0
O A:HOH507 2.1 17.6 1.0
CG A:ASP252 3.1 16.2 1.0
CG A:ASP256 3.1 15.0 1.0
C A:ILE292 3.2 11.8 1.0
OD2 A:ASP252 3.5 16.6 1.0
CB A:ASP256 3.6 14.3 1.0
CA A:ILE293 4.0 11.6 1.0
N A:ILE293 4.1 11.5 1.0
N A:TRP294 4.1 13.9 1.0
O A:HOH881 4.2 51.9 1.0
O A:HOH854 4.2 53.3 1.0
OD1 A:ASP256 4.2 15.1 1.0
CB A:ILE292 4.2 14.5 1.0
CA A:ILE292 4.2 11.6 1.0
O A:HOH692 4.3 34.6 1.0
O A:HOH669 4.3 34.8 1.0
CB A:ASP252 4.4 12.9 1.0
O A:HOH765 4.4 42.1 1.0
O A:HOH795 4.4 49.5 1.0
CG1 A:ILE292 4.6 14.5 1.0
C A:ILE293 4.6 12.8 1.0
O A:ASP252 4.8 13.9 1.0
CA A:ASP252 4.9 13.0 1.0

Magnesium binding site 2 out of 3 in 1mxg

Go back to Magnesium Binding Sites List in 1mxg
Magnesium binding site 2 out of 3 in the Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg440

b:18.0
occ:1.00
 OE2 A:GLU350 2.2 23.9 1.0
OD2 A:ASP347 2.2 21.6 1.0
O A:HOH566 2.2 26.6 1.0
OD1 A:ASP349 2.4 25.0 1.0
O A:HOH584 2.4 27.4 1.0
O A:HOH745 2.4 41.7 1.0
CG A:ASP347 2.8 19.6 1.0
OD1 A:ASP347 2.8 18.4 1.0
CD A:GLU350 3.2 20.3 1.0
CG A:ASP349 3.5 23.4 1.0
CG A:GLU350 3.5 19.1 1.0
OD2 A:ASP349 3.9 26.9 1.0
CB A:ASP347 4.2 16.3 1.0
CB A:GLU350 4.2 15.7 1.0
NH2 A:ARG377 4.3 22.0 1.0
O A:HOH673 4.3 37.3 1.0
ND2 A:ASN348 4.3 19.9 0.5
OE1 A:GLU350 4.3 21.4 1.0
N A:GLU350 4.5 14.4 1.0
O A:HOH798 4.6 50.4 1.0
N A:ASP349 4.6 16.3 1.0
OH A:TYR345 4.6 17.1 1.0
O A:HOH711 4.7 38.2 1.0
O A:HOH958 4.7 45.0 1.0
CB A:ASP349 4.7 19.4 1.0
C A:ASP349 4.8 16.4 1.0
CA A:ASP349 4.9 16.9 1.0
CE2 A:TYR345 5.0 15.4 1.0

Magnesium binding site 3 out of 3 in 1mxg

Go back to Magnesium Binding Sites List in 1mxg
Magnesium binding site 3 out of 3 in the Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Strucutre of A (Ca,Zn)-Dependent Alpha-Amylase From the Hyperthermophilic Archaeon Pyrococcus Woesei in Complex with Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg441

b:12.7
occ:1.00
 O A:HOH612 2.4 27.8 1.0
O A:HOH586 2.4 26.9 1.0
O A:GLY24 2.6 13.4 1.0
OE1 A:GLU80 2.6 18.2 1.0
O A:HOH582 2.6 24.3 1.0
OE2 A:GLU88 2.6 14.5 1.0
OE1 A:GLU88 2.6 13.2 1.0
OE2 A:GLU80 2.7 18.4 1.0
CD A:GLU88 3.0 12.5 1.0
CD A:GLU80 3.0 17.4 1.0
C A:GLY24 3.6 12.4 1.0
O A:HOH486 4.1 13.8 1.0
CA A:GLY24 4.2 12.2 1.0
O A:HOH887 4.3 58.5 1.0
CA A:GLY84 4.4 11.0 1.0
CG A:GLU88 4.5 11.6 1.0
N A:SER85 4.5 11.3 1.0
CG A:GLU80 4.5 12.6 1.0
O A:GLY23 4.6 14.7 1.0
OD2 A:ASP28 4.6 16.5 1.0
N A:ILE25 4.7 12.6 1.0
O A:HOH594 4.8 27.4 1.0
C A:GLY84 4.9 10.8 1.0
CA A:ILE25 5.0 13.2 1.0

Reference:

A.Linden, O.Mayans, W.Meyer-Klaucke, G.Antranikian, M.Wilmanns. Differential Regulation of A Hyperthermophilic Alpha-Amylase with A Novel (Ca,Zn) Two-Metal Center By Zinc J.Biol.Chem. V. 278 9875 2003.
ISSN: ISSN 0021-9258
PubMed: 12482867
DOI: 10.1074/JBC.M211339200
Page generated: Tue Aug 13 09:16:59 2024

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