Calcium in PDB 6al8: Crystal Structure HPIC1 Y101F/F138S

The structure of Crystal Structure HPIC1 Y101F/F138S, PDB code: 6al8 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)	47.50 / 1.64
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	61.990, 47.951, 174.765, 90.00, 97.05, 90.00
R / Rfree (%)	22.3 / 25.4

The binding sites of Calcium atom in the Crystal Structure HPIC1 Y101F/F138S (pdb code 6al8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure HPIC1 Y101F/F138S, PDB code: 6al8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:65.5 occ:1.00 O A:HOH548 3.2 35.3 1.0 OG1 A:THR180 3.9 28.5 1.0 CB A:PHE178 4.0 27.9 1.0 CG A:ASP134 4.0 30.9 1.0 O A:PHE178 4.1 30.4 1.0 OD1 A:ASP134 4.1 29.7 1.0 O A:HOH420 4.1 41.1 1.0 OD2 A:ASP134 4.2 32.8 1.0 C A:PHE178 4.2 29.7 1.0 CB A:ASP134 4.5 26.8 1.0 CA A:LYS179 4.5 26.2 1.0 N A:LYS179 4.5 26.3 1.0 C A:LYS179 4.6 27.9 1.0 N A:THR180 4.6 28.1 1.0 CB A:PRO94 4.6 28.5 1.0 O A:HOH546 4.7 35.5 1.0 CG A:PRO94 4.7 28.9 1.0 CA A:PHE178 4.8 26.8 1.0 OE1 A:GLN91 4.8 37.7 1.0

Calcium binding site 2 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:26.2 occ:1.00 OE2 A:GLU39 2.3 23.4 1.0 OE1 A:GLU95 2.3 27.1 1.0 O A:GLU95 2.3 28.0 1.0 O A:GLY37 2.3 27.1 1.0 O A:ASN98 2.4 26.4 1.0 OD1 A:ASP216 2.4 26.6 1.0 OD2 A:ASP216 2.9 26.2 1.0 CG A:ASP216 3.0 27.4 1.0 C A:GLY37 3.3 26.4 1.0 C A:GLU95 3.3 27.5 1.0 CD A:GLU39 3.4 30.3 1.0 C A:ASN98 3.5 24.2 1.0 CD A:GLU95 3.5 29.9 1.0 CA A:GLY37 3.7 29.8 1.0 N A:ASN98 3.9 27.4 1.0 CG A:GLU39 3.9 29.4 1.0 CB A:GLU95 4.0 26.9 1.0 CA A:GLU95 4.1 24.6 1.0 CA A:ASN98 4.2 23.2 1.0 N A:GLY96 4.3 29.1 1.0 CG A:GLU95 4.3 29.6 1.0 OE2 A:GLU95 4.4 35.4 1.0 N A:GLU95 4.4 29.7 1.0 OE1 A:GLU39 4.4 31.1 1.0 CA A:GLY96 4.4 27.6 1.0 CB A:ASP216 4.5 26.7 1.0 C A:GLY96 4.6 27.7 1.0 N A:ILE99 4.6 22.5 1.0 N A:PHE38 4.6 26.0 1.0 CB A:ASN98 4.6 23.5 1.0 N A:ARG97 4.6 27.3 1.0 N A:GLU39 4.8 25.9 1.0 CA A:ILE99 4.8 22.7 1.0 C A:ARG97 4.9 29.1 1.0 CB A:ALA93 4.9 29.3 1.0 C A:PHE38 4.9 25.4 1.0 N A:ASN217 4.9 25.2 1.0

Calcium binding site 3 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:27.3 occ:1.00 O A:HOH539 2.3 26.0 1.0 OD1 A:ASP175 2.3 26.2 1.0 O A:SER138 2.3 29.7 1.0 OD1 A:ASN137 2.3 26.5 1.0 O A:LEU147 2.4 28.6 1.0 O A:GLY149 2.4 27.8 1.0 CG A:ASN137 3.4 27.7 1.0 C A:SER138 3.5 29.3 1.0 C A:GLY149 3.5 27.1 1.0 CG A:ASP175 3.5 28.9 1.0 C A:LEU147 3.5 31.8 1.0 N A:GLY149 3.6 26.9 1.0 C A:ALA148 3.9 28.4 1.0 N A:SER138 3.9 23.8 1.0 ND2 A:ASN137 4.0 27.5 1.0 CA A:ALA148 4.1 28.9 1.0 CA A:GLY149 4.2 27.1 1.0 C A:ASN137 4.2 26.1 1.0 OD2 A:ASP175 4.3 36.5 1.0 CA A:SER138 4.3 26.1 1.0 N A:ALA148 4.3 29.4 1.0 OG A:SER138 4.4 34.6 1.0 N A:GLY139 4.5 30.0 1.0 O A:HOH507 4.5 33.6 1.0 CB A:ASP175 4.5 30.8 1.0 O A:ASN137 4.5 30.7 1.0 N A:PHE150 4.6 26.1 1.0 O A:ALA148 4.6 28.4 1.0 CB A:LEU147 4.6 32.7 1.0 CA A:LEU147 4.6 30.5 1.0 CA A:GLY139 4.6 26.5 1.0 CB A:ASN137 4.6 26.9 1.0 CA A:ASN137 4.7 26.3 1.0 CA A:PHE150 4.7 31.0 1.0 CA A:ASP175 4.7 30.2 1.0 CB A:PHE210 4.9 27.1 1.0 O A:GLY212 4.9 27.9 1.0 O A:PHE210 5.0 29.8 1.0 CB A:SER138 5.0 30.5 1.0

Calcium binding site 4 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:28.1 occ:1.00 OD1 B:ASP175 2.2 28.7 1.0 O B:SER138 2.3 25.3 1.0 OD1 B:ASN137 2.3 24.9 1.0 O B:GLY149 2.3 26.5 1.0 O B:LEU147 2.4 28.0 1.0 O B:HOH495 2.4 29.4 1.0 CG B:ASN137 3.4 27.4 1.0 C B:SER138 3.4 27.4 1.0 C B:GLY149 3.5 29.8 1.0 CG B:ASP175 3.5 30.0 1.0 C B:LEU147 3.6 33.3 1.0 N B:GLY149 3.6 30.5 1.0 N B:SER138 3.9 23.4 1.0 C B:ALA148 3.9 31.4 1.0 ND2 B:ASN137 4.0 25.7 1.0 C B:ASN137 4.1 25.0 1.0 CA B:GLY149 4.2 30.4 1.0 CA B:ALA148 4.2 31.1 1.0 OD2 B:ASP175 4.2 37.6 1.0 CA B:SER138 4.3 24.0 1.0 O B:ASN137 4.3 25.5 1.0 N B:ALA148 4.3 30.7 1.0 OG B:SER138 4.4 30.6 1.0 N B:GLY139 4.4 31.2 1.0 CB B:ASP175 4.4 31.0 1.0 N B:PHE150 4.5 28.7 1.0 CB B:LEU147 4.6 34.6 1.0 O B:ALA148 4.6 32.5 1.0 CA B:GLY139 4.6 28.1 1.0 CB B:ASN137 4.6 27.1 1.0 CA B:LEU147 4.6 34.0 1.0 CA B:ASN137 4.6 23.1 1.0 CA B:ASP175 4.7 28.0 1.0 O B:HOH524 4.7 36.1 1.0 CA B:PHE150 4.7 27.4 1.0 CB B:PHE210 4.9 28.5 1.0 CB B:SER138 5.0 30.2 1.0 CB B:PHE150 5.0 30.6 1.0

Calcium binding site 5 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:26.8 occ:1.00 OD1 B:ASP216 2.3 24.2 1.0 O B:GLY37 2.3 25.9 1.0 OE1 B:GLU95 2.4 28.2 1.0 O B:ASN98 2.4 26.1 1.0 OE1 B:GLU39 2.4 26.3 1.0 O B:GLU95 2.4 26.2 1.0 OD2 B:ASP216 2.8 26.7 1.0 CG B:ASP216 2.9 28.4 1.0 C B:GLY37 3.3 24.7 1.0 C B:GLU95 3.4 27.1 1.0 CD B:GLU39 3.5 32.6 1.0 C B:ASN98 3.5 27.9 1.0 CD B:GLU95 3.5 33.5 1.0 CA B:GLY37 3.7 30.0 1.0 CB B:GLU95 3.9 31.0 1.0 N B:ASN98 3.9 28.4 1.0 CG B:GLU39 4.1 30.4 1.0 CA B:GLU95 4.1 27.5 1.0 CA B:ASN98 4.2 23.3 1.0 N B:GLY96 4.3 30.9 1.0 CG B:GLU95 4.3 34.8 1.0 N B:GLU95 4.4 29.7 1.0 CB B:ASP216 4.4 24.1 1.0 OE2 B:GLU95 4.4 39.5 1.0 CA B:GLY96 4.4 29.4 1.0 OE2 B:GLU39 4.5 30.9 1.0 N B:PHE38 4.6 26.8 1.0 C B:GLY96 4.6 27.0 1.0 N B:ILE99 4.6 25.0 1.0 N B:ARG97 4.6 29.5 1.0 CB B:ASN98 4.7 24.1 1.0 CA B:ILE99 4.8 23.7 1.0 N B:GLU39 4.9 27.5 1.0 N B:ASN217 4.9 27.9 1.0 C B:ARG97 4.9 29.1 1.0 CB B:ALA93 4.9 29.2 1.0 C B:PHE38 4.9 27.9 1.0

Calcium binding site 6 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


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 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:49.4 occ:1.00 O D:ASN98 2.2 50.3 1.0 O D:GLY37 2.3 53.6 1.0 OE2 D:GLU39 2.4 53.8 1.0 OD1 D:ASP216 2.4 48.3 1.0 OE1 D:GLU95 2.5 50.4 1.0 O D:GLU95 2.5 57.6 1.0 OD2 D:ASP216 2.8 54.8 1.0 CG D:ASP216 2.8 53.1 1.0 C D:ASN98 3.3 53.7 1.0 C D:GLY37 3.4 55.4 1.0 CD D:GLU39 3.5 58.8 1.0 C D:GLU95 3.5 55.9 1.0 CD D:GLU95 3.7 55.0 1.0 N D:ASN98 3.7 58.1 1.0 CA D:GLY37 3.8 55.3 1.0 CG D:GLU39 4.0 55.9 1.0 CB D:GLU95 4.0 54.4 1.0 CA D:ASN98 4.1 53.3 1.0 CB D:ASP216 4.1 54.3 1.0 CA D:GLU95 4.2 56.9 1.0 N D:GLU95 4.4 53.1 1.0 N D:ILE99 4.4 50.9 1.0 CG D:GLU95 4.5 55.8 1.0 N D:GLY96 4.5 58.6 1.0 N D:ARG97 4.5 54.5 1.0 OE1 D:GLU39 4.5 58.0 1.0 N D:PHE38 4.5 53.9 1.0 OE2 D:GLU95 4.6 58.3 1.0 CB D:ASN98 4.6 55.5 1.0 N D:GLU39 4.6 59.0 1.0 CB D:ALA93 4.6 57.5 1.0 CA D:GLY96 4.7 54.7 1.0 C D:GLY96 4.7 51.9 1.0 CA D:ILE99 4.7 51.6 1.0 C D:PHE38 4.8 57.5 1.0 C D:ARG97 4.8 57.8 1.0 N D:ASN217 4.9 48.3 1.0 CB D:PHE38 5.0 53.1 1.0 CA D:PHE38 5.0 56.4 1.0

Calcium binding site 7 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure HPIC1 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:47.3 occ:1.00 OD1 D:ASP175 2.3 49.5 1.0 O D:SER138 2.3 49.9 1.0 O D:GLY149 2.3 49.5 1.0 O D:LEU147 2.4 54.6 1.0 OD1 D:ASN137 2.4 47.7 1.0 O D:HOH417 2.5 45.5 1.0 C D:SER138 3.4 51.2 1.0 CG D:ASN137 3.4 48.5 1.0 C D:LEU147 3.5 55.8 1.0 C D:GLY149 3.5 50.0 1.0 CG D:ASP175 3.5 50.5 1.0 N D:GLY149 3.7 53.9 1.0 N D:SER138 3.9 48.2 1.0 C D:ALA148 4.0 53.0 1.0 C D:ASN137 4.0 49.6 1.0 ND2 D:ASN137 4.1 48.7 1.0 CA D:ALA148 4.1 51.6 1.0 CA D:GLY149 4.2 50.3 1.0 N D:ALA148 4.2 54.2 1.0 CA D:SER138 4.3 49.8 1.0 O D:ASN137 4.3 49.0 1.0 N D:GLY139 4.3 54.9 1.0 CB D:LEU147 4.4 54.0 1.0 OG D:SER138 4.4 46.0 1.0 OD2 D:ASP175 4.4 51.6 1.0 CA D:GLY139 4.4 54.6 1.0 CB D:ASP175 4.4 53.2 1.0 CA D:LEU147 4.5 55.4 1.0 N D:PHE150 4.6 47.2 1.0 CA D:ASN137 4.6 45.2 1.0 CB D:ASN137 4.6 47.3 1.0 CA D:ASP175 4.6 54.0 1.0 O D:ALA148 4.7 52.5 1.0 CA D:PHE150 4.7 46.1 1.0 CB D:PHE210 4.8 50.7 1.0 CB D:SER138 5.0 49.0 1.0 O D:GLY212 5.0 43.2 1.0

Calcium binding site 8 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure HPIC1 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:42.0 occ:1.00 O E:GLY37 2.1 38.8 1.0 OE2 E:GLU39 2.4 45.2 1.0 O E:GLU95 2.4 49.1 1.0 OE1 E:GLU95 2.5 51.7 1.0 O E:ASN98 2.5 43.0 1.0 OD1 E:ASP216 2.5 40.8 1.0 C E:GLY37 3.2 43.5 1.0 CG E:ASP216 3.2 41.4 1.0 OD2 E:ASP216 3.2 43.7 1.0 C E:GLU95 3.4 48.9 1.0 CD E:GLU39 3.5 47.3 1.0 C E:ASN98 3.6 42.9 1.0 CA E:GLY37 3.6 44.2 1.0 CD E:GLU95 3.6 49.9 1.0 CG E:GLU39 3.9 43.9 1.0 CB E:GLU95 4.0 47.7 1.0 N E:ASN98 4.0 43.3 1.0 CA E:GLU95 4.1 47.6 1.0 N E:GLY96 4.2 49.7 1.0 CA E:ASN98 4.2 36.6 1.0 N E:PHE38 4.4 44.3 1.0 CG E:GLU95 4.4 51.3 1.0 CA E:GLY96 4.4 45.3 1.0 N E:GLU95 4.5 45.2 1.0 OE2 E:GLU95 4.5 47.4 1.0 CB E:ASN98 4.6 37.7 1.0 OE1 E:GLU39 4.6 48.0 1.0 N E:ILE99 4.6 38.8 1.0 N E:GLU39 4.6 45.2 1.0 CB E:ASP216 4.6 42.5 1.0 C E:GLY96 4.7 45.8 1.0 N E:ARG97 4.7 46.6 1.0 C E:PHE38 4.7 45.5 1.0 CB E:ALA93 4.8 50.1 1.0 CA E:ILE99 4.9 39.4 1.0 N E:ASN217 4.9 46.4 1.0 CA E:PHE38 4.9 42.8 1.0 CB E:PHE38 4.9 38.2 1.0 C E:ARG97 5.0 38.4 1.0

Calcium binding site 9 out of 9 in the Crystal Structure HPIC1 Y101F/F138S


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure HPIC1 Y101F/F138S within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:45.2 occ:1.00 OD1 E:ASN137 2.2 47.0 1.0 O E:HOH401 2.3 47.8 1.0 OD1 E:ASP175 2.3 49.2 1.0 O E:SER138 2.4 48.7 1.0 O E:GLY149 2.4 46.3 1.0 O E:LEU147 2.4 46.4 1.0 O E:HOH420 2.5 45.5 1.0 CG E:ASN137 3.2 46.5 1.0 C E:SER138 3.4 47.3 1.0 C E:GLY149 3.5 50.2 1.0 CG E:ASP175 3.5 49.8 1.0 C E:LEU147 3.6 49.7 1.0 N E:GLY149 3.6 47.2 1.0 N E:SER138 3.8 43.8 1.0 ND2 E:ASN137 3.8 45.9 1.0 C E:ASN137 3.9 43.3 1.0 C E:ALA148 3.9 46.8 1.0 CA E:ALA148 4.1 49.2 1.0 CA E:GLY149 4.2 47.4 1.0 CA E:SER138 4.2 45.9 1.0 O E:ASN137 4.2 46.4 1.0 CB E:ASP175 4.3 48.4 1.0 N E:ALA148 4.3 47.1 1.0 OG E:SER138 4.3 43.8 1.0 CB E:ASN137 4.3 41.7 1.0 CA E:ASN137 4.3 45.0 1.0 N E:GLY139 4.4 49.4 1.0 CA E:ASP175 4.5 50.9 1.0 OD2 E:ASP175 4.5 52.3 1.0 CA E:GLY139 4.6 47.7 1.0 N E:PHE150 4.6 45.3 1.0 O E:ALA148 4.6 47.0 1.0 CA E:LEU147 4.7 47.8 1.0 CB E:LEU147 4.7 49.3 1.0 CA E:PHE150 4.9 43.0 1.0 CB E:SER138 4.9 43.0 1.0 CD1 E:PHE150 5.0 43.6 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