Magnesium in PDB 6w2l: Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp

Enzymatic activity of Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp

All present enzymatic activity of Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp:
2.5.1.87;

Protein crystallography data

The structure of Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp, PDB code: 6w2l was solved by B.H.Edani, Y.Ha, W.C.Sessa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.92 / 2.31
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 185.670, 185.670, 113.351, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 25.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp (pdb code 6w2l). 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 Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp, PDB code: 6w2l:

Magnesium binding site 1 out of 1 in 6w2l

Go back to Magnesium Binding Sites List in 6w2l
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp


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 Human Dehydrodolichyl Diphosphate Synthase (Ngbr/Dhdds) in Complex with Mg and Ipp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:65.9
occ:1.00
 O1A A:IPE403 2.3 66.6 1.0
O A:HOH506 2.3 71.6 1.0
O3B A:IPE402 2.3 59.5 1.0
O2A A:IPE402 2.4 65.1 1.0
OD1 A:ASP34 2.9 65.4 1.0
O1B A:IPE402 3.0 64.5 1.0
PB A:IPE402 3.1 65.5 1.0
O A:HOH514 3.2 60.5 1.0
PA A:IPE403 3.5 63.3 1.0
O2A A:IPE403 3.7 66.5 1.0
PA A:IPE402 3.8 62.2 1.0
NH2 A:ARG85 3.8 63.7 1.0
NH2 B:ARG290 3.8 67.7 1.0
O3B A:IPE403 3.9 63.1 1.0
CG A:ASP34 3.9 65.7 1.0
O3A A:IPE402 3.9 65.6 1.0
NE B:ARG290 4.1 75.7 1.0
NH2 A:ARG38 4.2 59.5 1.0
OD2 A:ASP34 4.2 75.5 1.0
O2B A:IPE403 4.3 56.1 1.0
NH2 A:ARG37 4.3 70.0 1.0
O3A A:IPE403 4.4 61.9 1.0
PB A:IPE403 4.4 67.9 1.0
CZ B:ARG290 4.5 67.6 1.0
O2B A:IPE402 4.6 62.2 1.0
O1 A:IPE402 4.7 63.4 1.0
O1A A:IPE402 4.8 68.7 1.0
O1 A:IPE403 4.8 60.2 1.0
CZ A:ARG85 5.0 68.3 1.0

Reference:

B.H.Edani, K.A.Grabinska, R.Zhang, E.J.Park, B.Siciliano, L.Surmacz, Y.Ha, W.C.Sessa. Structural Elucidation of Thecis-Prenyltransferase Ngbr/Dhdds Complex Reveals Insights in Regulation of Protein Glycosylation. Proc.Natl.Acad.Sci.Usa V. 117 20794 2020.
ISSN: ESSN 1091-6490
PubMed: 32817466
DOI: 10.1073/PNAS.2008381117
Page generated: Tue Dec 15 01:31:25 2020

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