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Uranium in PDB 5vcr: Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide

Enzymatic activity of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide

All present enzymatic activity of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide:
2.4.1.143;

Protein crystallography data

The structure of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide, PDB code: 5vcr was solved by J.H.Sanders, R.Kadirvelraj, Z.A.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.40 / 1.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.670, 105.670, 171.950, 90.00, 90.00, 90.00
R / Rfree (%) 17.7 / 20.8

Other elements in 5vcr:

The structure of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Uranium Binding Sites:

The binding sites of Uranium atom in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide (pdb code 5vcr). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 4 binding sites of Uranium where determined in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide, PDB code: 5vcr:
Jump to Uranium binding site number: 1; 2; 3; 4;

Uranium binding site 1 out of 4 in 5vcr

Go back to Uranium Binding Sites List in 5vcr
Uranium binding site 1 out of 4 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 1 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U501

b:46.3
occ:0.80
U A:IUM501 0.0 46.3 0.8
O1 A:IUM501 1.8 0.1 0.8
O2 A:IUM501 1.8 0.8 0.8
OE1 A:GLU259 2.5 42.2 1.0
OD2 A:ASP261 2.7 47.0 1.0
OD1 A:ASP261 2.7 31.7 1.0
CG A:ASP261 3.0 40.1 1.0
CL A:CL504 3.5 51.9 0.5
CD A:GLU259 3.8 49.1 1.0
NE2 A:HIS374 4.0 58.4 1.0
NH2 A:ARG127 4.2 59.0 1.0
CD2 A:HIS374 4.3 50.9 1.0
CB A:GLU259 4.5 38.0 1.0
CB A:ASP261 4.5 37.8 1.0
OE2 A:GLU259 4.6 57.6 1.0
NE2 A:HIS262 4.8 38.4 1.0
CG A:GLU259 4.8 38.6 1.0

Uranium binding site 2 out of 4 in 5vcr

Go back to Uranium Binding Sites List in 5vcr
Uranium binding site 2 out of 4 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U502

b:58.0
occ:0.30
U A:IUM502 0.0 58.0 0.3
O1 A:IUM502 1.8 70.1 0.3
O2 A:IUM502 1.8 65.9 0.3
OE2 A:GLU159 2.7 64.9 1.0
O A:HOH604 3.5 61.2 1.0
NH2 A:ARG132 3.8 75.0 1.0
NE A:ARG132 3.8 77.7 1.0
CD A:GLU159 3.9 59.2 1.0
CZ A:ARG132 4.3 79.9 1.0
CG A:GLU159 4.4 51.6 1.0
CB A:PRO128 4.7 44.0 1.0
OE1 A:GLU159 4.9 61.8 1.0
CD A:ARG132 5.0 65.8 1.0

Uranium binding site 3 out of 4 in 5vcr

Go back to Uranium Binding Sites List in 5vcr
Uranium binding site 3 out of 4 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 3 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U502

b:25.1
occ:0.40
U B:IUM502 0.0 25.1 0.4
O1 B:IUM502 1.7 40.0 0.4
O2 B:IUM502 1.7 48.6 0.4
OE1 B:GLU259 2.4 42.9 1.0
OD2 B:ASP261 2.6 39.9 1.0
OD1 B:ASP261 2.8 32.0 1.0
CG B:ASP261 3.1 41.8 1.0
CD B:GLU259 3.6 52.7 1.0
CL B:CL504 3.8 60.0 0.4
NH2 B:ARG127 4.0 61.7 1.0
CB B:GLU259 4.4 37.8 1.0
OE2 B:GLU259 4.5 65.3 1.0
CE1 B:HIS374 4.5 54.2 1.0
CB B:ASP261 4.6 41.8 1.0
NE2 B:HIS374 4.6 56.9 1.0
CG B:GLU259 4.7 37.4 1.0
NE2 B:HIS262 4.7 34.2 1.0
NH1 B:ARG127 4.8 61.7 1.0
CZ B:ARG127 4.9 68.8 1.0

Uranium binding site 4 out of 4 in 5vcr

Go back to Uranium Binding Sites List in 5vcr
Uranium binding site 4 out of 4 in the Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 4 of Alpha-1,6-Mannosyl-Glycoprotein 2-Beta-N-Acetylglucosaminyltransferase with Bound Uranium Dioxide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U503

b:44.6
occ:0.30
U B:IUM503 0.0 44.6 0.3
O2 B:IUM503 1.8 29.0 0.3
O1 B:IUM503 1.8 23.3 0.3
OE1 B:GLU316 2.8 56.8 1.0
OE2 B:GLU316 2.9 70.3 1.0
CD B:GLU316 3.2 56.7 1.0
NZ B:LYS310 4.5 83.9 1.0
O B:HOH635 4.5 41.1 1.0
CG B:GLU316 4.7 38.8 1.0
CE B:LYS310 4.9 77.1 1.0
CD B:LYS310 4.9 72.6 1.0

Reference:

R.Kadirvelraj, J.Y.Yang, J.H.Sanders, L.Liu, A.Ramiah, P.K.Prabhakar, G.J.Boons, Z.A.Wood, K.W.Moremen. Humann-Acetylglucosaminyltransferase II Substrate Recognition Uses A Modular Architecture That Includes A Convergent Exosite. Proc. Natl. Acad. Sci. V. 115 4637 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29666272
DOI: 10.1073/PNAS.1716988115
Page generated: Wed Dec 16 02:29:58 2020

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