Magnesium in PDB 6hkv: Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers

The structure of Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers, PDB code: 6hkv was solved by N.H.Rustmeier, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.95 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	138.400, 145.705, 149.453, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.1

The structure of Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers (pdb code 6hkv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers, PDB code: 6hkv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:40.2 occ:1.00 O C:HOH727 2.2 38.5 1.0 O D:HOH730 2.4 42.7 1.0 O D:SER219 2.5 25.8 1.0 OE1 C:GLU49 2.5 35.0 1.0 O D:HOH643 2.5 25.0 1.0 O D:HOH515 2.8 48.2 1.0 C D:SER219 3.3 26.1 1.0 CD C:GLU49 3.4 38.0 1.0 O C:HOH749 3.4 32.8 1.0 OE2 C:GLU49 3.6 46.0 1.0 CA D:SER219 3.9 26.4 1.0 OH C:TYR291 4.0 27.3 1.0 N D:LYS220 4.1 24.9 1.0 CA D:LYS220 4.4 24.2 1.0 CG D:GLU222 4.4 39.5 1.0 O D:LYS220 4.6 24.7 1.0 O D:PRO218 4.6 23.6 1.0 O C:HOH587 4.6 35.7 1.0 CB D:SER219 4.8 28.5 1.0 CG C:GLU49 4.8 32.9 1.0 C D:LYS220 4.9 24.4 1.0

Magnesium binding site 2 out of 2 in the Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Trichodysplasia Spinulosa-Associated Polyomavirus (Tspyv) VP1 in Complex with Sialylated Precision Glycooligomers within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg402 b:37.2 occ:1.00 O G:HOH703 2.1 37.1 1.0 O F:HOH592 2.1 40.9 1.0 OE1 F:GLU49 2.4 30.9 1.0 O G:SER219 2.5 25.1 1.0 O G:HOH634 2.5 28.5 1.0 OE1 G:GLU222 2.6 49.3 1.0 CD F:GLU49 3.3 36.9 1.0 C G:SER219 3.3 23.5 1.0 CD G:GLU222 3.5 50.1 1.0 OE2 F:GLU49 3.5 35.5 1.0 O G:HOH508 3.6 26.3 1.0 OE2 G:GLU222 3.6 51.1 1.0 O G:HOH736 3.9 57.8 1.0 OH F:TYR291 3.9 26.6 1.0 O G:HOH650 3.9 52.3 1.0 CA G:SER219 3.9 24.0 1.0 O G:HOH517 4.1 43.9 1.0 N G:LYS220 4.3 23.0 1.0 CA G:LYS220 4.5 22.6 1.0 O G:PRO218 4.6 24.4 1.0 CG F:GLU49 4.7 31.1 1.0 CB G:SER219 4.7 24.9 1.0 O F:HOH533 4.7 30.5 1.0 O G:LYS220 4.7 20.2 1.0 CG G:GLU222 4.9 42.5 1.0 ND2 F:ASN293 5.0 33.4 1.0

M.Baier, N.H.Rustmeier, J.Harr, N.Cyrus, G.J.Reiss, A.Grafmuller, B.S.Blaum, T.Stehle, L.Hartmann. Divalent Sialylated Precision Glycooligomers Binding to Polyomaviruses and the Effect of Different Linkers. Macromol Biosci V. 19 00426 2019.
ISSN: ISSN 1616-5195
PubMed: 30884172
DOI: 10.1002/MABI.201800426