Calcium in PDB 6al7: Crystal Structure HPIC1 F138S

The structure of Crystal Structure HPIC1 F138S, PDB code: 6al7 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)	46.20 / 1.69
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	62.053, 47.939, 174.256, 90.00, 97.19, 90.00
R / Rfree (%)	22.3 / 25.3

The binding sites of Calcium atom in the Crystal Structure HPIC1 F138S (pdb code 6al7). 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 F138S, PDB code: 6al7:
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 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:64.8 occ:1.00 O A:GLY149 2.3 27.7 1.0 O A:SER138 2.4 30.3 1.0 OD1 A:ASP175 2.4 33.0 1.0 OD1 A:ASN137 2.4 29.3 1.0 O A:LEU147 2.4 29.2 1.0 O A:HOH466 2.4 34.0 1.0 CG A:ASN137 3.5 32.2 1.0 C A:GLY149 3.5 34.6 1.0 C A:SER138 3.5 36.0 1.0 C A:LEU147 3.6 37.4 1.0 CG A:ASP175 3.6 38.2 1.0 N A:GLY149 3.7 36.1 1.0 N A:SER138 4.0 28.5 1.0 C A:ALA148 4.0 32.4 1.0 ND2 A:ASN137 4.0 35.0 1.0 CA A:GLY149 4.2 33.1 1.0 CA A:ALA148 4.2 34.9 1.0 C A:ASN137 4.2 30.5 1.0 CA A:SER138 4.3 29.6 1.0 OG A:SER138 4.3 39.4 1.0 N A:ALA148 4.3 36.5 1.0 OD2 A:ASP175 4.4 38.9 1.0 N A:GLY139 4.5 35.8 1.0 O A:HOH511 4.5 38.0 1.0 CB A:LEU147 4.5 34.5 1.0 O A:ASN137 4.5 33.3 1.0 CA A:GLY139 4.5 30.9 1.0 N A:PHE150 4.5 31.6 1.0 CB A:ASP175 4.6 36.2 1.0 CA A:LEU147 4.6 35.0 1.0 O A:ALA148 4.7 32.0 1.0 CB A:ASN137 4.7 30.1 1.0 CA A:PHE150 4.7 33.2 1.0 CA A:ASN137 4.7 31.3 1.0 CA A:ASP175 4.8 36.6 1.0 O A:GLY212 4.8 30.4 1.0 O A:PHE210 4.9 36.3 1.0 CB A:PHE210 4.9 33.8 1.0 CB A:SER138 5.0 36.5 1.0 CB A:PHE150 5.0 36.0 1.0

Calcium binding site 2 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.5 occ:1.00 OE2 A:GLU39 2.3 33.2 1.0 O A:GLY37 2.3 29.7 1.0 O A:ASN98 2.4 30.4 1.0 O A:GLU95 2.4 31.9 1.0 OD1 A:ASP216 2.4 34.4 1.0 OE1 A:GLU95 2.5 34.5 1.0 OD2 A:ASP216 2.9 33.0 1.0 CG A:ASP216 3.0 33.1 1.0 C A:GLY37 3.3 30.9 1.0 C A:GLU95 3.4 33.0 1.0 CD A:GLU39 3.4 33.1 1.0 C A:ASN98 3.5 29.3 1.0 CD A:GLU95 3.6 35.9 1.0 CA A:GLY37 3.7 32.9 1.0 N A:ASN98 3.9 32.1 1.0 CG A:GLU39 3.9 34.7 1.0 CB A:GLU95 4.0 31.7 1.0 CA A:GLU95 4.1 32.0 1.0 CA A:ASN98 4.2 29.1 1.0 N A:GLY96 4.3 33.8 1.0 N A:GLU95 4.4 33.5 1.0 CG A:GLU95 4.4 34.3 1.0 CA A:GLY96 4.4 31.1 1.0 CB A:ASP216 4.4 32.1 1.0 OE1 A:GLU39 4.4 32.8 1.0 OE2 A:GLU95 4.5 35.9 1.0 N A:PHE38 4.5 28.4 1.0 N A:ILE99 4.5 31.1 1.0 C A:GLY96 4.6 31.2 1.0 CB A:ASN98 4.6 28.7 1.0 N A:ARG97 4.6 31.2 1.0 CA A:ILE99 4.8 29.1 1.0 N A:GLU39 4.8 28.7 1.0 C A:ARG97 4.9 32.2 1.0 CB A:ALA93 4.9 32.5 1.0 C A:PHE38 4.9 30.9 1.0 N A:ASN217 4.9 32.9 1.0

Calcium binding site 3 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:74.0 occ:1.00 O A:HOH561 2.6 55.0 1.0 O A:HOH550 2.9 40.7 1.0 CB A:PHE178 4.2 29.2 1.0 OG1 A:THR180 4.2 32.8 1.0 O A:HOH402 4.3 44.2 1.0 O A:PHE178 4.3 31.8 1.0 CG A:ASP134 4.4 35.4 1.0 OD2 A:ASP134 4.4 36.8 1.0 OD1 A:ASP134 4.6 35.7 1.0 CB A:PRO94 4.6 35.8 1.0 C A:PHE178 4.6 32.7 1.0 OE1 A:GLN91 4.6 39.5 1.0 NE2 A:GLN91 4.8 40.9 1.0 CG A:PRO94 4.8 35.7 1.0 CB A:ASP134 4.8 32.0 1.0 CA A:LYS179 5.0 32.0 1.0

Calcium binding site 4 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:31.6 occ:1.00 OD1 B:ASP175 2.2 32.6 1.0 O B:GLY149 2.3 31.8 1.0 O B:SER138 2.3 32.7 1.0 OD1 B:ASN137 2.3 32.8 1.0 O B:LEU147 2.4 35.5 1.0 O B:HOH479 2.4 35.7 1.0 CG B:ASN137 3.4 30.0 1.0 C B:SER138 3.4 33.7 1.0 C B:GLY149 3.4 33.8 1.0 CG B:ASP175 3.5 35.0 1.0 C B:LEU147 3.6 38.4 1.0 N B:GLY149 3.7 35.5 1.0 N B:SER138 3.9 29.3 1.0 C B:ALA148 4.0 33.8 1.0 ND2 B:ASN137 4.0 31.8 1.0 C B:ASN137 4.1 30.8 1.0 CA B:GLY149 4.2 36.7 1.0 CA B:ALA148 4.2 35.5 1.0 OD2 B:ASP175 4.2 35.8 1.0 CA B:SER138 4.2 31.0 1.0 O B:ASN137 4.3 29.3 1.0 N B:ALA148 4.4 36.8 1.0 N B:GLY139 4.4 36.3 1.0 OG B:SER138 4.4 37.8 1.0 CB B:ASP175 4.5 35.4 1.0 N B:PHE150 4.5 34.5 1.0 CA B:ASN137 4.6 30.9 1.0 CB B:ASN137 4.6 28.8 1.0 CB B:LEU147 4.6 36.0 1.0 CA B:GLY139 4.6 32.5 1.0 O B:ALA148 4.6 37.5 1.0 CA B:LEU147 4.6 38.4 1.0 O B:HOH492 4.6 39.5 1.0 CA B:PHE150 4.7 33.4 1.0 CA B:ASP175 4.7 34.1 1.0 CB B:PHE150 4.9 30.9 1.0 CB B:SER138 5.0 34.1 1.0 CB B:PHE210 5.0 35.9 1.0

Calcium binding site 5 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:29.8 occ:1.00 OE2 B:GLU39 2.3 34.7 1.0 O B:GLY37 2.3 31.2 1.0 OE1 B:GLU95 2.4 34.6 1.0 O B:ASN98 2.4 30.6 1.0 OD1 B:ASP216 2.4 33.8 1.0 O B:GLU95 2.4 32.9 1.0 OD2 B:ASP216 2.8 32.2 1.0 CG B:ASP216 2.9 32.5 1.0 C B:GLY37 3.4 32.4 1.0 C B:GLU95 3.4 32.9 1.0 CD B:GLU39 3.4 36.3 1.0 C B:ASN98 3.5 32.8 1.0 CD B:GLU95 3.5 40.1 1.0 CA B:GLY37 3.7 36.0 1.0 N B:ASN98 3.9 32.3 1.0 CB B:GLU95 3.9 33.5 1.0 CG B:GLU39 4.0 36.0 1.0 CA B:GLU95 4.1 31.0 1.0 CA B:ASN98 4.2 29.6 1.0 CG B:GLU95 4.3 36.7 1.0 N B:GLY96 4.3 34.6 1.0 N B:GLU95 4.4 32.1 1.0 CB B:ASP216 4.4 29.7 1.0 OE2 B:GLU95 4.4 42.1 1.0 OE1 B:GLU39 4.5 35.2 1.0 CA B:GLY96 4.5 35.5 1.0 N B:ILE99 4.6 30.8 1.0 N B:PHE38 4.6 31.3 1.0 N B:ARG97 4.6 35.1 1.0 C B:GLY96 4.6 34.5 1.0 CB B:ASN98 4.6 29.3 1.0 CA B:ILE99 4.8 30.4 1.0 N B:GLU39 4.8 31.2 1.0 C B:ARG97 4.9 33.2 1.0 N B:ASN217 4.9 31.2 1.0 C B:PHE38 4.9 34.3 1.0 CB B:ALA93 4.9 35.9 1.0

Calcium binding site 6 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:58.5 occ:1.00 O D:ASN98 2.3 61.4 1.0 O D:GLY37 2.3 67.6 1.0 OE2 D:GLU39 2.3 65.5 1.0 OE1 D:GLU95 2.4 60.2 1.0 OD1 D:ASP216 2.4 57.4 1.0 O D:GLU95 2.5 72.5 1.0 CG D:ASP216 3.0 64.0 1.0 OD2 D:ASP216 3.0 64.6 1.0 C D:GLY37 3.3 66.8 1.0 C D:ASN98 3.4 66.9 1.0 CD D:GLU39 3.5 71.1 1.0 C D:GLU95 3.5 67.0 1.0 CD D:GLU95 3.6 66.7 1.0 CA D:GLY37 3.7 68.4 1.0 N D:ASN98 3.8 70.2 1.0 CG D:GLU39 4.0 69.7 1.0 CA D:ASN98 4.1 67.7 1.0 CB D:GLU95 4.2 65.2 1.0 CA D:GLU95 4.3 66.5 1.0 CB D:ASP216 4.4 63.9 1.0 OE2 D:GLU95 4.4 66.5 1.0 N D:GLY96 4.4 68.7 1.0 N D:GLU95 4.5 64.1 1.0 CG D:GLU95 4.5 64.1 1.0 OE1 D:GLU39 4.5 70.0 1.0 N D:ILE99 4.5 65.5 1.0 N D:PHE38 4.5 64.4 1.0 CA D:GLY96 4.5 66.7 1.0 CB D:ASN98 4.6 68.2 1.0 N D:ARG97 4.6 67.6 1.0 C D:GLY96 4.6 63.3 1.0 N D:GLU39 4.7 69.6 1.0 CA D:ILE99 4.8 63.3 1.0 C D:PHE38 4.8 69.2 1.0 CB D:ALA93 4.9 67.0 1.0 C D:ARG97 4.9 71.4 1.0 N D:ASN217 4.9 60.7 1.0

Calcium binding site 7 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:54.1 occ:1.00 OD1 D:ASP175 2.3 62.6 1.0 O D:LEU147 2.3 64.5 1.0 O D:SER138 2.3 60.5 1.0 O D:GLY149 2.3 56.3 1.0 O D:HOH413 2.4 67.2 1.0 OD1 D:ASN137 2.5 61.1 1.0 C D:GLY149 3.5 58.2 1.0 CG D:ASN137 3.5 58.3 1.0 C D:SER138 3.5 67.8 1.0 C D:LEU147 3.5 65.7 1.0 CG D:ASP175 3.5 63.0 1.0 N D:GLY149 3.6 61.2 1.0 N D:SER138 3.9 63.5 1.0 C D:ALA148 3.9 61.3 1.0 ND2 D:ASN137 4.0 58.8 1.0 OG D:SER138 4.2 61.7 1.0 CA D:GLY149 4.2 58.8 1.0 C D:ASN137 4.2 63.4 1.0 CA D:ALA148 4.2 62.5 1.0 CA D:SER138 4.3 66.7 1.0 OD2 D:ASP175 4.3 59.8 1.0 N D:ALA148 4.3 64.6 1.0 CB D:LEU147 4.4 64.7 1.0 CB D:ASP175 4.5 65.8 1.0 N D:GLY139 4.5 69.4 1.0 CA D:LEU147 4.5 66.0 1.0 N D:PHE150 4.5 55.7 1.0 O D:ALA148 4.5 59.2 1.0 O D:ASN137 4.6 60.9 1.0 CB D:ASN137 4.6 55.9 1.0 CA D:ASN137 4.6 59.9 1.0 CA D:GLY139 4.6 67.6 1.0 CA D:ASP175 4.7 66.8 1.0 CA D:PHE150 4.8 55.6 1.0 CB D:PHE210 4.8 59.0 1.0 CB D:SER138 4.9 64.7 1.0 O D:PHE210 4.9 55.1 1.0

Calcium binding site 8 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca301 b:55.6 occ:1.00 O E:GLY37 2.3 49.8 1.0 OE1 E:GLU95 2.3 63.5 1.0 O E:ASN98 2.4 54.2 1.0 OD1 E:ASP216 2.4 53.6 1.0 OE2 E:GLU39 2.4 50.8 1.0 O E:GLU95 2.5 67.5 1.0 OD2 E:ASP216 2.8 61.1 1.0 CG E:ASP216 2.9 61.0 1.0 C E:GLY37 3.3 54.0 1.0 C E:GLU95 3.4 69.2 1.0 CD E:GLU39 3.4 58.3 1.0 C E:ASN98 3.5 55.5 1.0 CD E:GLU95 3.5 65.4 1.0 CA E:GLY37 3.6 59.0 1.0 CB E:GLU95 3.9 65.0 1.0 CG E:GLU39 3.9 56.1 1.0 N E:ASN98 4.0 54.2 1.0 CA E:GLU95 4.0 67.6 1.0 CA E:ASN98 4.2 49.7 1.0 CG E:GLU95 4.3 65.6 1.0 N E:GLY96 4.3 66.0 1.0 N E:GLU95 4.3 68.8 1.0 CB E:ASP216 4.4 59.4 1.0 OE2 E:GLU95 4.4 65.9 1.0 OE1 E:GLU39 4.5 58.9 1.0 N E:PHE38 4.5 49.1 1.0 N E:ILE99 4.5 50.5 1.0 CA E:GLY96 4.5 63.7 1.0 C E:GLY96 4.6 59.9 1.0 N E:GLU39 4.7 55.6 1.0 CB E:ASN98 4.7 49.7 1.0 N E:ARG97 4.7 60.6 1.0 CA E:ILE99 4.7 52.6 1.0 C E:ARG97 4.9 52.7 1.0 C E:PHE38 4.9 55.6 1.0 N E:ASN217 4.9 64.9 1.0 CB E:ALA93 4.9 67.1 1.0

Calcium binding site 9 out of 9 in the Crystal Structure HPIC1 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 F138S within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca302 b:68.3 occ:1.00 OD1 E:ASN137 2.2 68.7 1.0 O E:GLY149 2.3 65.5 1.0 O E:SER138 2.4 70.5 1.0 O E:LEU147 2.5 70.4 1.0 OD2 E:ASP175 2.7 71.4 1.0 CG E:ASN137 3.3 67.8 1.0 C E:GLY149 3.4 68.7 1.0 C E:SER138 3.5 72.8 1.0 N E:GLY149 3.5 70.2 1.0 CG E:ASP175 3.5 72.7 1.0 C E:LEU147 3.8 71.2 1.0 N E:SER138 3.8 70.8 1.0 CB E:ASP175 3.9 72.9 1.0 ND2 E:ASN137 4.0 68.8 1.0 CA E:GLY149 4.0 69.5 1.0 C E:ASN137 4.1 70.5 1.0 C E:ALA148 4.2 69.7 1.0 CA E:SER138 4.2 72.5 1.0 CA E:ASP175 4.2 73.0 1.0 OG E:SER138 4.3 65.6 1.0 N E:PHE150 4.4 63.3 1.0 CA E:ALA148 4.4 72.6 1.0 N E:GLY139 4.5 74.9 1.0 CB E:ASN137 4.5 65.0 1.0 CA E:ASN137 4.5 67.6 1.0 O E:ASN137 4.5 72.3 1.0 N E:ALA148 4.5 71.6 1.0 OD1 E:ASP175 4.6 75.7 1.0 CB E:LEU147 4.7 70.5 1.0 CA E:PHE150 4.7 57.7 1.0 CA E:GLY139 4.8 73.9 1.0 CA E:LEU147 4.8 70.7 1.0 CB E:SER138 4.9 69.0 1.0 O E:ALA148 5.0 68.9 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