Calcium in PDB 5l0t: Human POGLUT1 in Complex with Egf(+) and Udp

All present enzymatic activity of Human POGLUT1 in Complex with Egf(+) and Udp:
2.4.2.26;

The structure of Human POGLUT1 in Complex with Egf(+) and Udp, PDB code: 5l0t was solved by Z.Li, J.M.Rini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.98 / 1.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.660, 75.200, 82.950, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 17.3

The structure of Human POGLUT1 in Complex with Egf(+) and Udp also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Human POGLUT1 in Complex with Egf(+) and Udp (pdb code 5l0t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Human POGLUT1 in Complex with Egf(+) and Udp, PDB code: 5l0t:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Human POGLUT1 in Complex with Egf(+) and Udp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human POGLUT1 in Complex with Egf(+) and Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca405 b:27.2 occ:0.57 O A:HOH514 2.2 36.4 1.0 O A:HOH610 2.2 35.6 1.0 O A:HOH681 2.3 40.4 1.0 O A:HOH567 2.4 30.7 1.0 O A:GLN52 2.5 25.8 1.0 C A:GLN52 3.5 23.5 1.0 HA A:ASN53 3.8 22.3 1.0 HA A:GLN52 3.9 31.0 1.0 HB3 A:GLN52 4.0 35.0 1.0 HB2 A:ASP353 4.1 24.8 1.0 OE1 A:GLN351 4.2 35.2 1.0 CA A:GLN52 4.2 25.8 1.0 O A:HOH820 4.3 37.0 1.0 OD1 A:ASP354 4.4 25.4 1.0 N A:ASN53 4.4 18.4 1.0 O A:HOH793 4.5 44.2 1.0 HB2 A:GLN351 4.5 20.6 1.0 CA A:ASN53 4.6 18.6 1.0 OD2 A:ASP354 4.6 19.7 1.0 O A:HOH606 4.6 27.9 1.0 CB A:GLN52 4.6 29.1 1.0 HB3 A:ASP353 4.6 24.8 1.0 OE1 A:GLN52 4.6 56.3 1.0 CD A:GLN351 4.7 35.7 1.0 CG A:ASP354 4.8 25.6 1.0 CB A:ASP353 4.8 20.7 1.0 O A:HOH895 4.8 27.0 1.0 O A:ASN348 4.8 20.6 1.0

Calcium binding site 2 out of 3 in the Human POGLUT1 in Complex with Egf(+) and Udp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human POGLUT1 in Complex with Egf(+) and Udp within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca406 b:24.4 occ:0.57 OD1 A:ASP333 2.3 41.5 1.0 O A:HOH543 2.4 34.5 1.0 O A:HOH522 2.5 26.9 1.0 O A:HOH833 2.5 37.2 1.0 CG A:ASP333 3.5 40.8 1.0 HA A:ASP333 3.7 33.7 1.0 OD2 A:ASP332 4.1 24.5 1.0 OE1 A:GLN336 4.2 28.8 1.0 O A:HOH513 4.2 36.2 1.0 OD2 A:ASP333 4.2 46.3 1.0 O A:HOH733 4.3 41.2 1.0 CA A:ASP333 4.4 28.1 1.0 O A:HOH872 4.5 44.0 1.0 CB A:ASP333 4.5 31.1 1.0 N A:ASP333 4.7 24.1 1.0 O A:HOH690 4.8 51.6 1.0 O A:HOH594 4.8 29.2 1.0 HB3 A:ASP332 4.8 28.1 1.0 H A:ASP333 4.9 28.9 1.0 HB3 A:ASP333 4.9 37.3 1.0

Calcium binding site 3 out of 3 in the Human POGLUT1 in Complex with Egf(+) and Udp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human POGLUT1 in Complex with Egf(+) and Udp within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca100 b:33.2 occ:1.00 O B:HOH203 2.3 29.5 1.0 OD1 B:ASN18 2.3 32.3 1.0 O B:THR19 2.4 33.7 1.0 OE1 B:GLU4 2.4 34.4 1.0 O B:ILE2 2.5 41.6 1.0 O B:SER22 2.5 28.9 1.0 OD2 B:ASP1 2.5 46.6 1.0 H B:SER22 3.3 39.1 1.0 H B:THR19 3.3 36.2 1.0 CD B:GLU4 3.4 34.9 1.0 CG B:ASP1 3.4 49.4 1.0 CG B:ASN18 3.4 37.0 1.0 C B:SER22 3.5 30.2 1.0 N B:SER22 3.5 32.6 1.0 OD1 B:ASP1 3.5 52.4 1.0 OE2 B:GLU4 3.6 36.6 1.0 C B:THR19 3.6 38.0 1.0 HD21 B:ASN18 3.6 48.2 1.0 H B:GLU4 3.6 38.2 1.0 H B:GLY21 3.6 51.5 1.0 C B:ILE2 3.7 40.9 1.0 HA B:ASP3 3.8 44.0 1.0 N B:THR19 3.8 30.2 1.0 ND2 B:ASN18 3.9 40.1 1.0 CA B:SER22 3.9 32.7 1.0 HA B:SER22 4.0 39.3 1.0 N B:GLY21 4.0 42.9 1.0 C B:GLY21 4.1 42.4 1.0 HA B:ASN18 4.2 35.8 1.0 CA B:THR19 4.3 32.3 1.0 HA B:VAL20 4.4 44.9 1.0 HB B:ILE2 4.4 49.6 1.0 N B:GLU4 4.5 31.9 1.0 CA B:GLY21 4.5 42.7 1.0 H B:ILE2 4.5 63.4 1.0 CA B:ASP3 4.5 36.7 1.0 N B:ILE2 4.6 52.8 1.0 N B:ASP3 4.6 39.4 1.0 CB B:ASN18 4.6 32.7 1.0 N B:VAL20 4.6 39.7 1.0 C B:ASN18 4.6 31.3 1.0 HB3 B:TYR23 4.6 30.4 1.0 C B:VAL20 4.6 51.3 1.0 HB2 B:GLU4 4.6 34.4 1.0 CA B:ILE2 4.6 46.9 1.0 N B:TYR23 4.7 28.2 1.0 CA B:ASN18 4.7 29.9 1.0 HA2 B:GLY21 4.7 51.2 1.0 OG1 B:THR19 4.7 35.1 1.0 HD22 B:ASN18 4.8 48.2 1.0 CG B:GLU4 4.8 30.6 1.0 CA B:VAL20 4.8 37.4 1.0 CB B:ASP1 4.8 61.8 1.0 O B:GLY21 4.8 45.7 1.0 HA B:TYR23 4.8 31.6 1.0 O B:HOH229 4.9 43.8 1.0 HG22 B:ILE2 4.9 48.8 1.0 HB3 B:ASP1 5.0 74.2 1.0 C B:ASP1 5.0 56.0 1.0

Z.Li, M.Fischer, M.Satkunarajah, D.Zhou, S.G.Withers, J.M.Rini. Structural Basis of Notch O-Glucosylation and O-Xylosylation By Mammalian Protein-O-Glucosyltransferase 1 (POGLUT1). Nat Commun V. 8 185 2017.
ISSN: ESSN 2041-1723
PubMed: 28775322
DOI: 10.1038/S41467-017-00255-7