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Magnesium in PDB 4da1: Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site

Enzymatic activity of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site

All present enzymatic activity of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site:
3.1.3.16;

Protein crystallography data

The structure of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site, PDB code: 4da1 was solved by C.A.Brautigam, J.L.Chuang, D.T.Chuang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 2.38
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.276, 125.276, 61.660, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site (pdb code 4da1). 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 Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site, PDB code: 4da1:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4da1

Go back to Magnesium Binding Sites List in 4da1
Magnesium binding site 1 out of 3 in the Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg504

b:45.4
occ:1.00
 O A:HOH636 2.3 32.7 1.0
OD2 A:ASP127 2.3 33.8 1.0
OD1 A:ASP298 2.3 47.1 1.0
OD2 A:ASP337 2.3 44.1 1.0
O A:HOH601 2.4 35.6 1.0
O A:HOH638 2.4 38.1 1.0
CG A:ASP127 3.1 35.2 1.0
CG A:ASP298 3.3 46.7 1.0
CG A:ASP337 3.3 48.9 1.0
OD1 A:ASP127 3.3 37.6 1.0
OD1 A:ASP337 3.5 44.6 1.0
OD2 A:ASP298 3.6 52.3 1.0
O A:HOH620 3.7 38.4 1.0
MG A:MG505 3.7 43.1 1.0
O A:HOH604 3.9 44.5 1.0
O A:HOH603 4.0 30.7 1.0
O A:ASN338 4.3 34.3 1.0
N A:GLY299 4.3 33.5 1.0
O A:HOH602 4.3 31.9 1.0
OD1 A:ASP109 4.4 32.2 1.0
N A:ASP298 4.5 35.4 1.0
CB A:ASP127 4.5 29.6 1.0
CB A:ASP298 4.6 40.9 1.0
CB A:ASP337 4.6 43.4 1.0
O A:HOH663 4.6 58.3 1.0
CB A:THR297 4.8 35.4 1.0
CA A:ASP298 4.8 32.5 1.0
C A:ASP298 4.9 34.6 1.0
O A:HOH605 4.9 34.0 1.0
O A:HOH606 5.0 47.6 1.0

Magnesium binding site 2 out of 3 in 4da1

Go back to Magnesium Binding Sites List in 4da1
Magnesium binding site 2 out of 3 in the Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg505

b:43.1
occ:1.00
 O A:HOH636 2.1 32.7 1.0
O A:GLY128 2.2 37.7 1.0
O A:HOH602 2.3 31.9 1.0
OD1 A:ASP127 2.3 37.6 1.0
O A:HOH635 2.3 42.6 1.0
O A:HOH620 2.3 38.4 1.0
C A:GLY128 3.3 36.4 1.0
CG A:ASP127 3.4 35.2 1.0
MG A:MG504 3.7 45.4 1.0
O A:HOH605 3.8 34.0 1.0
OD2 A:ASP127 3.8 33.8 1.0
N A:GLY128 4.0 29.5 1.0
N A:HIS129 4.1 39.4 1.0
C A:ASP127 4.1 34.0 1.0
OE1 A:GLU108 4.1 47.2 1.0
CA A:HIS129 4.2 40.8 1.0
O A:HOH638 4.2 38.1 1.0
CA A:GLY128 4.2 34.2 1.0
CB A:GLU108 4.3 33.5 1.0
OD1 A:ASP109 4.3 32.2 1.0
CB A:HIS129 4.3 41.4 1.0
O A:HOH601 4.4 35.6 1.0
O A:ASP127 4.4 32.0 1.0
OD1 A:ASN338 4.4 45.1 1.0
CB A:ASP127 4.6 29.6 1.0
OD1 A:ASP337 4.6 44.6 1.0
CA A:ASP127 4.7 31.8 1.0
O A:HOH637 4.8 51.3 1.0
O A:HOH604 5.0 44.5 1.0

Magnesium binding site 3 out of 3 in 4da1

Go back to Magnesium Binding Sites List in 4da1
Magnesium binding site 3 out of 3 in the Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase with Mg (II) Ions at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg506

b:46.0
occ:1.00
 OD2 A:ASP112 2.3 43.5 1.0
O A:HOH614 2.3 48.2 1.0
O A:HOH615 2.3 46.2 1.0
O A:HOH613 2.3 45.0 1.0
OE1 A:GLU143 2.4 53.5 1.0
O A:HOH612 2.4 43.7 1.0
CD A:GLU143 3.1 52.1 1.0
OE2 A:GLU143 3.2 49.6 1.0
CG A:ASP112 3.2 43.2 1.0
OD1 A:ASP112 3.5 44.1 1.0
O A:HOH624 4.3 58.7 1.0
O A:HOH622 4.3 30.2 1.0
CE1 A:HIS139 4.4 40.3 1.0
O A:HIS139 4.4 40.9 1.0
O A:HOH616 4.4 37.3 1.0
CG A:GLU143 4.6 46.0 1.0
CB A:ASP112 4.6 33.8 1.0
ND1 A:HIS139 4.8 38.9 1.0
NE2 A:HIS139 4.9 46.7 1.0

Reference:

R.M.Wynn, J.Li, C.A.Brautigam, J.L.Chuang, D.T.Chuang. Structural and Biochemical Characterization of Human Mitochondrial Branched-Chain Alpha-Ketoacid Dehydrogenase Phosphatase. J.Biol.Chem. V. 287 9178 2012.
ISSN: ISSN 0021-9258
PubMed: 22291014
DOI: 10.1074/JBC.M111.314963
Page generated: Thu Aug 15 17:02:36 2024

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