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Magnesium in PDB 2zyf: Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate

Enzymatic activity of Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate

All present enzymatic activity of Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate:
2.3.3.14;

Protein crystallography data

The structure of Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate, PDB code: 2zyf was solved by T.Okada, T.Tomita, T.Kuzuyama, M.Nishiyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.51 / 2.15
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 135.465, 135.465, 126.612, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 23.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate (pdb code 2zyf). 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 Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate, PDB code: 2zyf:

Magnesium binding site 1 out of 1 in 2zyf

Go back to Magnesium Binding Sites List in 2zyf
Magnesium binding site 1 out of 1 in the Crystal Structure of Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate


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 Homocitrate Synthase From Thermus Thermophilus Complexed with Magnesuim Ion and Alpha-Ketoglutarate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg384

b:37.3
occ:1.00
 O A:HOH501 2.1 40.5 1.0
O5 A:AKG383 2.1 57.2 1.0
NE2 A:HIS195 2.3 24.4 1.0
OE1 A:GLU13 2.4 29.4 1.0
NE2 A:HIS197 2.4 24.4 1.0
O1 A:AKG383 2.5 57.3 1.0
C2 A:AKG383 2.9 58.2 1.0
C1 A:AKG383 3.1 58.2 1.0
CD2 A:HIS197 3.1 21.4 1.0
CE1 A:HIS195 3.2 22.3 1.0
CD2 A:HIS195 3.3 23.1 1.0
CD A:GLU13 3.3 25.8 1.0
CE1 A:HIS197 3.6 22.0 1.0
OE2 A:GLU13 3.7 21.9 1.0
O A:HOH448 4.1 42.1 1.0
C3 A:AKG383 4.2 54.9 1.0
CG2 A:ILE231 4.3 15.0 1.0
NH2 A:ARG12 4.3 30.7 1.0
ND1 A:HIS195 4.3 24.0 1.0
O2 A:AKG383 4.3 57.2 1.0
C4 A:AKG383 4.3 54.9 1.0
NH1 A:ARG12 4.4 27.9 1.0
CG A:HIS195 4.4 23.1 1.0
CG A:HIS197 4.4 20.0 1.0
CG A:GLU13 4.5 25.0 1.0
ND1 A:HIS197 4.6 21.9 1.0
CZ A:ARG12 4.8 28.6 1.0

Reference:

T.Okada, T.Tomita, A.P.Wulandari, T.Kuzuyama, M.Nishiyama. Mechanism of Substrate Recognition and Insight Into Feedback Inhibition of Homocitrate Synthase From Thermus Thermophilus J.Biol.Chem. 2009.
ISSN: ESSN 1083-351X
PubMed: 19996101
DOI: 10.1074/JBC.M109.086330
Page generated: Sun Aug 10 17:07:29 2025

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