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Magnesium in PDB 3f0f: Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp

Enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp

All present enzymatic activity of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp:
4.6.1.12;

Protein crystallography data

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp, PDB code: 3f0f was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.078, 66.457, 131.465, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 24.6

Other elements in 3f0f:

The structure of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp (pdb code 3f0f). 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 Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp, PDB code: 3f0f:

Magnesium binding site 1 out of 1 in 3f0f

Go back to Magnesium Binding Sites List in 3f0f
Magnesium binding site 1 out of 1 in the Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Co-Crystal Structure of 2C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Burkholderia Pseudomallei with Hydrolyzed Cdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg164

b:43.5
occ:1.00
 O C:HOH217 2.3 32.2 1.0
O C:HOH165 2.5 34.9 1.0
O A:HOH201 2.6 31.2 1.0
O B:HOH166 3.2 33.3 1.0
O C:HOH176 3.5 37.5 1.0
O A:HOH167 3.6 32.4 1.0
OE1 B:GLU149 4.0 24.4 1.0
O B:HOH175 4.2 24.2 1.0
OE1 C:GLU149 4.2 23.8 1.0
O A:HOH168 4.3 29.5 1.0
OE2 B:GLU149 4.4 24.4 1.0
OE1 A:GLU149 4.4 25.1 1.0
O C:HOH178 4.4 31.8 1.0
OE2 C:GLU149 4.5 24.0 1.0
O C:HOH171 4.5 33.6 1.0
CD B:GLU149 4.6 24.6 1.0
OE2 A:GLU149 4.7 26.1 1.0
CD C:GLU149 4.8 24.4 1.0
CD A:GLU149 5.0 25.1 1.0

Reference:

L.Baugh, L.A.Gallagher, R.Patrapuvich, M.C.Clifton, A.S.Gardberg, T.E.Edwards, B.Armour, D.W.Begley, S.H.Dieterich, D.M.Dranow, J.Abendroth, J.W.Fairman, D.Fox, B.L.Staker, I.Phan, A.Gillespie, R.Choi, S.Nakazawa-Hewitt, M.T.Nguyen, A.Napuli, L.Barrett, G.W.Buchko, R.Stacy, P.J.Myler, L.J.Stewart, C.Manoil, W.C.Van Voorhis. Combining Functional and Structural Genomics to Sample the Essential Burkholderia Structome. Plos One V. 8 53851 2013.
ISSN: ESSN 1932-6203
PubMed: 23382856
DOI: 10.1371/JOURNAL.PONE.0053851
Page generated: Wed Aug 14 13:24:45 2024

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