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Magnesium in PDB 3ii9: Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom

Enzymatic activity of Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom

All present enzymatic activity of Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom:
1.3.99.7;

Protein crystallography data

The structure of Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom, PDB code: 3ii9 was solved by R.F.Ismagilov, L.Li, W.B.Du, B.Staker, Accelerated Technologies Centerfor Gene To 3D Structure (Atcg3D), Seattle Structural Genomics Centerfor Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.23 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.966, 141.268, 84.012, 90.00, 112.26, 90.00
R / Rfree (%) 17 / 19.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom (pdb code 3ii9). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom, PDB code: 3ii9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3ii9

Go back to Magnesium Binding Sites List in 3ii9
Magnesium binding site 1 out of 4 in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom


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 Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg397

b:28.9
occ:1.00
 O A:HOH509 1.8 29.3 1.0
O A:HOH463 2.0 25.5 1.0
O A:HOH480 2.0 23.0 1.0
O A:HOH492 2.0 16.6 1.0
O A:HOH450 2.0 34.8 1.0
O A:HOH472 2.1 17.6 1.0
O A:HOH938 3.9 26.2 1.0
OD2 A:ASP177 4.0 12.3 1.0
OD1 A:ASP177 4.1 14.8 1.0
O A:ILE175 4.1 14.7 1.0
O A:HOH1041 4.3 34.7 1.0
NZ A:LYS200 4.4 29.7 1.0
O A:HOH437 4.4 23.1 1.0
CG A:ASP177 4.5 13.3 1.0
O A:HOH706 4.9 25.6 1.0
CD1 A:ILE133 4.9 14.8 1.0

Magnesium binding site 2 out of 4 in 3ii9

Go back to Magnesium Binding Sites List in 3ii9
Magnesium binding site 2 out of 4 in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom


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 Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg398

b:39.0
occ:1.00
 O C:LEU205 2.0 17.0 1.0
O C:HOH519 2.1 20.7 1.0
O C:HOH1036 2.1 14.5 1.0
O C:HOH1123 2.1 20.0 1.0
O C:HOH1007 2.2 25.4 1.0
C C:LEU205 3.2 17.2 1.0
CA C:SER206 3.9 18.4 1.0
N C:SER206 4.0 17.6 1.0
O C:CYS202 4.0 20.8 1.0
O C:HOH996 4.3 31.5 1.0
CA C:LEU205 4.3 17.5 1.0
O C:LYS200 4.4 23.9 1.0
CB C:SER206 4.4 18.9 1.0
O C:LYS203 4.5 20.8 1.0
N C:LEU205 4.5 17.5 1.0
CB C:LEU205 4.7 17.4 1.0
CG C:LEU205 5.0 19.3 1.0

Magnesium binding site 3 out of 4 in 3ii9

Go back to Magnesium Binding Sites List in 3ii9
Magnesium binding site 3 out of 4 in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom


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 Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg400

b:60.6
occ:1.00
 O C:HOH964 1.9 42.5 1.0
O C:HOH963 2.3 22.4 1.0
O C:HOH473 3.6 31.4 1.0
OD2 C:ASP9 3.9 23.5 1.0
O C:HOH981 4.1 40.3 1.0
OD1 C:ASP9 4.3 20.5 1.0
O C:HOH932 4.3 53.6 1.0
CG C:ASP9 4.5 18.2 1.0
ND1 C:HIS7 4.6 21.1 1.0
O C:HOH430 4.9 36.8 1.0

Magnesium binding site 4 out of 4 in 3ii9

Go back to Magnesium Binding Sites List in 3ii9
Magnesium binding site 4 out of 4 in the Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Glutaryl-Coa Dehydrogenase From Burkholderia Pseudomallei at 1.73 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg400

b:61.0
occ:1.00
 O D:HOH459 2.5 29.1 1.0
OD2 D:ASP9 4.0 24.4 1.0
O D:HOH845 4.4 69.2 1.0
O D:HOH435 4.4 27.2 1.0
OD1 D:ASP9 4.4 21.8 1.0
C1 D:PEG399 4.5 64.3 1.0
ND1 D:HIS7 4.6 21.9 1.0
CG D:ASP9 4.7 19.0 1.0
O1 D:PEG399 4.8 63.7 1.0
O2 D:PEG399 5.0 65.2 1.0

Reference:

L.Li, W.Du, R.Ismagilov. User-Loaded Slipchip For Equipment-Free Multiplexed Nanoliter-Scale Experiments. J.Am.Chem.Soc. V. 132 106 2010.
ISSN: ISSN 0002-7863
PubMed: 20000708
DOI: 10.1021/JA908555N
Page generated: Mon Dec 14 08:16:59 2020

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