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Magnesium in PDB 2dkg: Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+)

Enzymatic activity of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+)

All present enzymatic activity of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+):
6.3.4.15;

Protein crystallography data

The structure of Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+), PDB code: 2dkg was solved by B.Bagautdinov, N.Kunishima, Riken Structural Genomics/Proteomicsinitiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.56 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.320, 82.721, 72.373, 90.00, 101.81, 90.00
R / Rfree (%) 18.9 / 22.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+) (pdb code 2dkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+), PDB code: 2dkg:

Magnesium binding site 1 out of 1 in 2dkg

Go back to Magnesium Binding Sites List in 2dkg
Magnesium binding site 1 out of 1 in the Crystal Structure of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+)


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 Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotinyl-5'-Amp, Pyrophosphate and Mg(2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:42.1
occ:1.00
 OP1 B:BT51301 2.3 32.0 1.0
OD2 A:ASP104 2.3 29.5 1.0
O1 A:POP4001 2.3 43.4 1.0
OD1 A:ASP104 2.4 29.1 1.0
OD1 A:ASN103 2.5 25.0 1.0
O5 A:POP4001 2.6 46.8 1.0
CG A:ASP104 2.7 28.1 1.0
O A:POP4001 3.0 46.2 1.0
P1 A:POP4001 3.1 44.6 1.0
CG A:ASN103 3.3 26.6 1.0
P2 A:POP4001 3.3 46.5 1.0
ND2 A:ASN103 3.5 25.6 1.0
P B:BT51301 3.8 31.1 1.0
NZ A:LYS111 4.0 28.4 1.0
O3 A:POP4001 4.1 44.5 1.0
CB A:ASP104 4.1 26.4 1.0
O2 A:POP4001 4.2 44.9 1.0
O5' B:BT51301 4.3 30.0 1.0
NZ A:LYS100 4.3 31.7 1.0
O6 A:POP4001 4.3 47.6 1.0
O4 A:POP4001 4.4 47.6 1.0
OCB B:BT51301 4.4 31.6 1.0
N A:ASP104 4.5 23.8 1.0
NH1 A:ARG48 4.5 39.9 1.0
OP2 B:BT51301 4.5 32.8 1.0
NH1 A:ARG51 4.6 44.2 1.0
C A:ASN103 4.6 25.0 1.0
CD A:ARG48 4.6 37.5 1.0
CE A:LYS111 4.7 27.8 1.0
CD A:PRO102 4.7 27.2 1.0
CB A:ASN103 4.7 25.3 1.0
OBB B:BT51301 4.7 29.9 1.0
N A:ASN103 4.7 28.2 1.0
CA A:ASP104 4.8 23.2 1.0
CA A:ASN103 4.9 26.4 1.0
CBB B:BT51301 4.9 30.1 1.0

Reference:

B.Bagautdinov, N.Kunishima. Ligand Structures of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 To Be Published.
Page generated: Tue Aug 13 22:30:28 2024

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