Calcium in PDB 6al6: Crystal Structure HPIC1 in P42 Space Group

The structure of Crystal Structure HPIC1 in P42 Space Group, PDB code: 6al6 was solved by S.A.Newmister, S.Li, M.Garcia-Borras, J.N.Sanders, S.Yang, A.N.Lowell, F.Yu, J.L.Smith, R.M.Williams, K.N.Houk, D.H.Sherman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.76 / 2.09
Space group	P 42
Cell size a, b, c (Å), α, β, γ (°)	71.339, 71.339, 80.623, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.3

The binding sites of Calcium atom in the Crystal Structure HPIC1 in P42 Space Group (pdb code 6al6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure HPIC1 in P42 Space Group, PDB code: 6al6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:43.1 occ:1.00 O A:ASN98 2.3 37.6 1.0 OE2 A:GLU95 2.3 44.4 1.0 O A:GLU95 2.3 44.8 1.0 O A:GLY37 2.4 46.1 1.0 OE2 A:GLU39 2.4 46.3 1.0 OD1 A:ASP216 2.5 42.3 1.0 OD2 A:ASP216 2.6 46.6 1.0 CG A:ASP216 2.9 44.5 1.0 C A:GLY37 3.4 40.8 1.0 C A:GLU95 3.4 44.5 1.0 C A:ASN98 3.4 45.0 1.0 CD A:GLU95 3.5 48.9 1.0 CD A:GLU39 3.5 46.6 1.0 CA A:GLY37 3.8 42.5 1.0 N A:ASN98 3.8 44.4 1.0 CB A:GLU95 4.1 42.9 1.0 CG A:GLU39 4.1 42.6 1.0 CA A:ASN98 4.1 45.3 1.0 CA A:GLU95 4.2 44.8 1.0 OE1 A:GLU95 4.3 51.9 1.0 CB A:ASP216 4.3 40.4 1.0 N A:GLY96 4.3 44.7 1.0 CG A:GLU95 4.3 46.1 1.0 CA A:GLY96 4.4 44.6 1.0 N A:GLU95 4.4 44.2 1.0 OE1 A:GLU39 4.5 52.6 1.0 N A:ILE99 4.5 40.4 1.0 CB A:ASN98 4.6 44.2 1.0 N A:PHE38 4.6 35.6 1.0 C A:GLY96 4.6 43.2 1.0 N A:ARG97 4.7 42.5 1.0 CA A:ILE99 4.8 40.7 1.0 N A:ASN217 4.8 40.9 1.0 C A:ARG97 4.9 49.0 1.0 CB A:ALA93 4.9 42.6 1.0 N A:GLU39 4.9 46.1 1.0 C A:PHE38 4.9 44.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:50.8 occ:1.00 OD1 A:ASP175 2.1 55.6 1.0 O A:GLY149 2.2 48.0 1.0 OD1 A:ASN137 2.3 41.9 1.0 O A:PHE138 2.4 47.6 1.0 O A:LEU147 2.5 50.9 1.0 CG A:ASP175 3.2 54.4 1.0 CG A:ASN137 3.4 45.3 1.0 C A:GLY149 3.4 48.8 1.0 C A:PHE138 3.5 49.4 1.0 N A:GLY149 3.7 49.9 1.0 C A:LEU147 3.7 54.3 1.0 C A:ALA148 3.7 52.8 1.0 OD2 A:ASP175 3.8 59.9 1.0 ND2 A:ASN137 3.9 45.4 1.0 CA A:ALA148 4.0 53.2 1.0 N A:PHE138 4.1 48.0 1.0 CA A:GLY149 4.1 52.4 1.0 C A:ASN137 4.2 48.3 1.0 O A:ALA148 4.2 48.7 1.0 N A:ALA148 4.3 54.4 1.0 N A:GLY139 4.4 50.5 1.0 CB A:ASP175 4.4 54.0 1.0 CA A:PHE138 4.4 53.4 1.0 CA A:GLY139 4.5 51.6 1.0 N A:PHE150 4.5 46.0 1.0 O A:ASN137 4.5 52.6 1.0 CB A:ASN137 4.6 38.4 1.0 CA A:ASN137 4.6 45.3 1.0 O A:PHE210 4.7 50.3 1.0 CA A:PHE150 4.8 42.8 1.0 CA A:ASP175 4.8 47.5 1.0 CB A:PHE210 4.8 51.4 1.0 CA A:LEU147 4.8 55.0 1.0 CB A:LEU147 4.9 53.3 1.0 O A:GLY212 4.9 38.6 1.0 CD2 A:PHE138 5.0 48.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:74.3 occ:1.00 O A:TYR49 2.5 48.7 1.0 OD1 A:ASP48 2.6 50.0 1.0 CG A:ASP48 3.4 48.0 1.0 OD2 A:ASP48 3.6 47.4 1.0 C A:TYR49 3.6 46.0 1.0 N A:TYR49 4.0 43.4 1.0 CA A:TYR49 4.4 48.9 1.0 N A:THR50 4.5 42.0 1.0 CA A:THR50 4.7 38.5 1.0 CB A:ASP48 4.8 41.9 1.0

Calcium binding site 4 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:43.0 occ:1.00 OD1 B:ASP175 2.1 40.6 1.0 OD1 B:ASN137 2.3 37.7 1.0 O B:GLY149 2.3 42.9 1.0 O B:PHE138 2.4 42.0 1.0 O B:LEU147 2.5 48.3 1.0 CG B:ASN137 3.4 39.9 1.0 CG B:ASP175 3.4 40.0 1.0 C B:GLY149 3.5 40.4 1.0 C B:PHE138 3.6 38.5 1.0 N B:GLY149 3.7 46.0 1.0 C B:LEU147 3.7 48.2 1.0 C B:ALA148 3.9 45.4 1.0 ND2 B:ASN137 3.9 36.6 1.0 CA B:ALA148 4.1 46.6 1.0 OD2 B:ASP175 4.1 42.5 1.0 CA B:GLY149 4.2 42.7 1.0 C B:ASN137 4.2 35.1 1.0 N B:PHE138 4.2 38.4 1.0 O B:ASN137 4.4 37.2 1.0 N B:ALA148 4.4 44.9 1.0 CB B:ASP175 4.4 42.7 1.0 N B:GLY139 4.5 39.1 1.0 CA B:GLY139 4.5 43.1 1.0 CA B:PHE138 4.5 40.1 1.0 O B:ALA148 4.5 50.6 1.0 N B:PHE150 4.6 37.1 1.0 CB B:ASN137 4.6 31.6 1.0 CD1 B:PHE138 4.6 45.0 1.0 CA B:ASN137 4.7 35.1 1.0 O B:GLY212 4.7 37.6 1.0 CA B:PHE150 4.8 39.4 1.0 CB B:PHE210 4.8 46.5 1.0 CA B:LEU147 4.8 47.5 1.0 CB B:LEU147 4.8 48.6 1.0 CA B:ASP175 4.8 45.0 1.0 O B:PHE210 4.9 49.9 1.0 CE1 B:PHE138 5.0 45.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:33.9 occ:1.00 O B:ASN98 2.2 28.4 1.0 OE2 B:GLU95 2.3 39.0 1.0 O B:GLU95 2.4 30.6 1.0 OE2 B:GLU39 2.4 43.4 1.0 O B:GLY37 2.5 36.8 1.0 OD1 B:ASP216 2.5 42.2 1.0 OD2 B:ASP216 2.7 35.9 1.0 CG B:ASP216 2.9 41.0 1.0 C B:ASN98 3.4 36.4 1.0 C B:GLU95 3.4 37.7 1.0 CD B:GLU95 3.5 42.7 1.0 C B:GLY37 3.5 37.1 1.0 CD B:GLU39 3.6 43.8 1.0 N B:ASN98 3.8 30.2 1.0 CA B:GLY37 3.9 36.6 1.0 CA B:ASN98 4.1 37.4 1.0 CB B:GLU95 4.1 36.4 1.0 CG B:GLU39 4.2 42.7 1.0 CA B:GLU95 4.2 33.9 1.0 OE1 B:GLU95 4.2 44.4 1.0 N B:GLY96 4.4 33.9 1.0 CB B:ASP216 4.4 32.2 1.0 CG B:GLU95 4.4 35.9 1.0 N B:ILE99 4.4 32.9 1.0 CA B:GLY96 4.4 34.5 1.0 N B:GLU95 4.4 34.5 1.0 CB B:ASN98 4.5 35.1 1.0 C B:GLY96 4.6 36.3 1.0 OE1 B:GLU39 4.6 43.9 1.0 N B:ARG97 4.6 32.0 1.0 CA B:ILE99 4.7 34.3 1.0 N B:PHE38 4.7 36.8 1.0 CB B:ALA93 4.8 35.8 1.0 C B:ARG97 4.8 35.3 1.0 N B:GLU39 4.9 37.9 1.0 N B:ASN217 4.9 31.9 1.0 C B:PHE38 5.0 36.0 1.0

Calcium binding site 6 out of 6 in the Crystal Structure HPIC1 in P42 Space Group


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure HPIC1 in P42 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:30.4 occ:0.50 O B:PHE178 2.2 31.2 1.0 O B:HOH449 2.3 32.2 0.5 O B:HOH403 2.4 28.4 1.0 O B:HOH419 2.5 31.2 1.0 C B:PHE178 3.4 28.9 1.0 N B:PHE178 4.2 32.3 1.0 CA B:PHE178 4.3 26.2 1.0 N B:LYS179 4.3 28.2 1.0 CA B:LYS179 4.3 27.2 1.0 OE1 B:GLN91 4.4 31.8 1.0 OE2 B:GLU177 4.5 42.4 1.0 CG B:LYS179 4.6 39.1 1.0 CB B:PHE178 4.6 31.5 1.0

S.A.Newmister, S.Li, M.Garcia-Borras, J.N.Sanders, S.Yang, A.N.Lowell, F.Yu, J.L.Smith, R.M.Williams, K.N.Houk, D.H.Sherman. Structural Basis of the Cope Rearrangement and Cyclization in Hapalindole Biogenesis. Nat. Chem. Biol. V. 14 345 2018.
ISSN: ESSN 1552-4469
PubMed: 29531360
DOI: 10.1038/S41589-018-0003-X