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Magnesium in PDB 6fwz: Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac

Enzymatic activity of Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac

All present enzymatic activity of Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac:
2.7.8.15;

Protein crystallography data

The structure of Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac, PDB code: 6fwz was solved by A.C.W.Pike, Y.Y.Dong, A.Chu, A.Tessitore, S.Goubin, L.Dong, S.Mukhopadhyay, P.Mahajan, R.Chalk, G.Berridge, D.Wang, K.Kupinska, K.Belaya, D.Beeson, N.Burgess-Brown, A.M.Edwards, C.H.Arrowsmith, C.Bountra, E.P.Carpenter, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 3.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 102.459, 102.459, 238.209, 90.00, 90.00, 120.00
R / Rfree (%) 22.3 / 23.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac (pdb code 6fwz). 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 Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac, PDB code: 6fwz:

Magnesium binding site 1 out of 1 in 6fwz

Go back to Magnesium Binding Sites List in 6fwz
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac


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 Udp-N-Acetylglucosamine-Dolichyl-Phosphate N-Acetylglucosaminephosphotransferase (DPAGT1) (V264G Mutant) in Complex with Udp-Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg501

b:93.9
occ:1.00
 O1B A:UD1502 2.0 96.6 1.0
O A:HOH608 2.0 97.2 1.0
O A:HOH610 2.0 88.5 1.0
O1A A:UD1502 2.1 95.6 1.0
OD1 A:ASN185 2.2 0.1 1.0
OD1 A:ASP252 2.2 98.0 1.0
PA A:UD1502 3.2 96.5 1.0
PB A:UD1502 3.2 94.7 1.0
CG A:ASN185 3.3 0.6 1.0
CG A:ASP252 3.4 97.1 1.0
O3A A:UD1502 3.4 89.7 1.0
O A:HOH614 3.8 81.2 1.0
ND2 A:ASN185 3.9 0.8 1.0
O5' A:UD1502 4.1 91.0 1.0
OD2 A:ASP252 4.1 0.4 1.0
O6' A:UD1502 4.1 0.6 1.0
O5B A:UD1502 4.1 1.0 1.0
O A:ASN185 4.2 0.8 1.0
O2B A:UD1502 4.3 0.9 1.0
O1' A:UD1502 4.3 99.6 1.0
O2A A:UD1502 4.4 0.1 1.0
C1' A:UD1502 4.4 99.4 1.0
CA A:ASP252 4.5 90.2 1.0
CB A:ASP252 4.5 92.6 1.0
N A:ASP252 4.5 90.9 1.0
CB A:ASN185 4.6 0.4 1.0
O A:HOH616 4.7 86.0 1.0
SG A:CYS255 4.7 0.1 1.0
C5B A:UD1502 4.8 0.1 1.0
CA A:ASN185 4.8 0.1 1.0
C A:GLY251 4.9 92.4 1.0
C A:ASN185 5.0 0.6 1.0

Reference:

Y.Y.Dong, H.Wang, A.C.W.Pike, S.A.Cochrane, S.Hamedzadeh, F.J.Wyszynski, S.R.Bushell, S.F.Royer, D.A.Widdick, A.Sajid, H.I.Boshoff, Y.Park, R.Lucas, W.M.Liu, S.S.Lee, T.Machida, L.Minall, S.Mehmood, K.Belaya, W.W.Liu, A.Chu, L.Shrestha, S.M.M.Mukhopadhyay, C.Strain-Damerell, R.Chalk, N.A.Burgess-Brown, M.J.Bibb, C.E.Barry Iii, C.V.Robinson, D.Beeson, B.G.Davis, E.P.Carpenter. Structures of DPAGT1 Explain Glycosylation Disease Mechanisms and Advance Tb Antibiotic Design. Cell V. 175 1045 2018.
ISSN: ISSN 1097-4172
PubMed: 30388443
DOI: 10.1016/J.CELL.2018.10.037
Page generated: Tue Oct 1 00:54:41 2024

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