Calcium in PDB 5yvp: Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau

The structure of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau, PDB code: 5yvp was solved by X.Y.Hu, W.D.Liu, C.C.Chen, R.T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.24 / 2.05
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	86.758, 255.893, 34.912, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 25.5

The binding sites of Calcium atom in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau (pdb code 5yvp). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau, PDB code: 5yvp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:31.3 occ:1.00 O A:ASN98 2.4 32.6 1.0 O A:GLY37 2.4 31.7 1.0 OE1 A:GLU95 2.4 32.5 1.0 OE2 A:GLU39 2.4 32.9 1.0 O A:GLU95 2.4 36.1 1.0 OD1 A:ASP216 2.4 30.5 1.0 OD2 A:ASP216 2.6 32.8 1.0 CG A:ASP216 2.8 33.0 1.0 C A:GLU95 3.4 35.2 1.0 C A:GLY37 3.4 30.1 1.0 C A:ASN98 3.5 31.4 1.0 CD A:GLU39 3.5 34.4 1.0 CD A:GLU95 3.6 35.7 1.0 CA A:GLY37 3.8 27.8 1.0 N A:ASN98 3.9 30.4 1.0 CG A:GLU39 4.1 29.0 1.0 CB A:GLU95 4.1 29.8 1.0 CA A:GLU95 4.2 32.2 1.0 CA A:ASN98 4.2 31.2 1.0 N A:GLY96 4.3 35.8 1.0 CB A:ASP216 4.3 31.3 1.0 N A:GLU95 4.4 31.9 1.0 CA A:GLY96 4.4 36.3 1.0 OE2 A:GLU95 4.4 36.3 1.0 CG A:GLU95 4.5 36.0 1.0 N A:ILE99 4.6 32.0 1.0 OE1 A:GLU39 4.6 35.0 1.0 C A:GLY96 4.6 37.8 1.0 N A:PHE38 4.6 28.7 1.0 N A:ARG97 4.7 34.9 1.0 CB A:ASN98 4.7 31.3 1.0 CB A:ALA93 4.7 38.6 1.0 CA A:ILE99 4.8 29.2 1.0 N A:ASN217 4.8 27.3 1.0 C A:ARG97 4.9 38.1 1.0 N A:GLU39 4.9 29.4 1.0 C A:PHE38 5.0 29.8 1.0

Calcium binding site 2 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:0.7 occ:1.00 O A:PHE147 2.2 41.0 1.0 O A:LEU138 2.3 47.5 1.0 O A:GLY149 2.4 45.2 1.0 OD1 A:ASN137 2.4 31.7 1.0 OE1 A:GLU175 2.7 52.2 1.0 O A:HOH416 3.3 36.7 1.0 N A:GLY149 3.4 41.5 1.0 C A:PHE147 3.4 45.2 1.0 C A:GLY149 3.4 54.6 1.0 C A:LEU138 3.4 44.2 1.0 CG A:ASN137 3.4 34.1 1.0 CD A:GLU175 3.5 50.3 1.0 OE2 A:GLU175 3.6 54.1 1.0 C A:ALA148 3.7 40.5 1.0 CA A:ALA148 3.8 38.9 1.0 ND2 A:ASN137 3.9 34.7 1.0 CA A:GLY149 4.0 49.5 1.0 N A:LEU138 4.0 35.3 1.0 N A:ALA148 4.1 41.0 1.0 CA A:LEU138 4.2 41.7 1.0 CD2 A:PHE210 4.4 39.5 1.0 C A:ASN137 4.4 33.3 1.0 N A:ALA139 4.4 45.5 1.0 O A:ALA148 4.4 43.5 1.0 CB A:LEU138 4.5 47.2 1.0 CB A:PHE210 4.5 36.3 1.0 CA A:PHE147 4.5 48.2 1.0 N A:PHE150 4.6 73.5 1.0 CA A:ALA139 4.6 44.7 1.0 CB A:PHE147 4.6 48.0 1.0 CB A:ASN137 4.7 30.5 1.0 CA A:ASN137 4.9 28.9 1.0 O A:ASN137 4.9 31.4 1.0 CG A:PHE210 4.9 36.4 1.0 CG A:GLU175 4.9 48.1 1.0 CA A:PHE150 4.9 47.5 1.0

Calcium binding site 3 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:36.9 occ:1.00 O B:ASN98 2.3 31.4 1.0 O B:GLY37 2.4 32.3 1.0 OE2 B:GLU39 2.4 42.8 1.0 OE2 B:GLU95 2.5 53.1 1.0 O B:GLU95 2.5 45.2 1.0 OD1 B:ASP216 2.5 38.1 1.0 OD2 B:ASP216 2.7 40.7 1.0 CG B:ASP216 2.9 37.5 1.0 CD B:GLU95 3.2 51.8 1.0 CG B:GLU95 3.4 49.3 1.0 C B:GLY37 3.4 30.4 1.0 C B:ASN98 3.5 33.6 1.0 C B:GLU95 3.5 48.7 1.0 CD B:GLU39 3.6 44.5 1.0 CA B:GLY37 3.8 31.4 1.0 N B:ASN98 3.9 38.1 1.0 CG B:GLU39 4.2 42.6 1.0 CA B:ASN98 4.2 36.5 1.0 CA B:GLU95 4.3 44.5 1.0 OE1 B:GLU95 4.4 53.1 1.0 N B:GLU95 4.4 44.4 1.0 CB B:ASP216 4.4 33.6 1.0 CB B:GLU95 4.4 45.3 1.0 N B:GLY96 4.4 51.9 1.0 N B:ILE99 4.5 32.6 1.0 CA B:GLY96 4.5 47.5 1.0 N B:PHE38 4.6 32.2 1.0 OE1 B:GLU39 4.6 42.9 1.0 C B:GLY96 4.7 46.1 1.0 CB B:ASN98 4.7 38.4 1.0 N B:ARG97 4.7 46.5 1.0 CA B:ILE99 4.7 36.5 1.0 CB B:ALA93 4.8 39.6 1.0 N B:GLU39 4.8 39.6 1.0 C B:ARG97 4.9 40.0 1.0 C B:PHE38 4.9 35.8 1.0 N B:ASN217 4.9 38.1 1.0

Calcium binding site 4 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:59.4 occ:1.00 O B:LEU138 2.2 52.9 1.0 O B:GLY149 2.3 42.2 1.0 O B:PHE147 2.3 43.4 1.0 OD1 B:ASN137 2.4 38.9 1.0 OE1 B:GLU175 2.4 57.0 1.0 CD B:GLU175 3.2 56.0 1.0 N B:GLY149 3.3 41.5 1.0 C B:GLY149 3.3 36.6 1.0 OE2 B:GLU175 3.4 58.4 1.0 C B:LEU138 3.4 52.3 1.0 CG B:ASN137 3.4 37.3 1.0 C B:PHE147 3.5 40.2 1.0 O B:HOH416 3.6 36.5 1.0 C B:ALA148 3.7 40.1 1.0 ND2 B:ASN137 3.8 35.6 1.0 CA B:ALA148 3.8 39.8 1.0 CA B:GLY149 3.9 34.7 1.0 N B:LEU138 4.0 42.1 1.0 N B:ALA148 4.1 36.0 1.0 CA B:LEU138 4.1 49.3 1.0 N B:ALA139 4.4 52.8 1.0 C B:ASN137 4.4 35.7 1.0 O B:ALA148 4.5 42.0 1.0 CB B:LEU138 4.5 55.4 1.0 N B:PHE150 4.5 35.7 1.0 CA B:ALA139 4.6 47.0 1.0 CG B:GLU175 4.6 53.3 1.0 CA B:PHE147 4.6 41.0 1.0 CB B:ASN137 4.7 35.9 1.0 CB B:PHE147 4.8 43.2 1.0 CB B:PHE210 4.8 40.4 1.0 CD2 B:PHE210 4.8 40.5 1.0 CA B:PHE150 4.9 32.3 1.0 CA B:ASN137 4.9 36.2 1.0 O B:ASN137 4.9 34.5 1.0 CB B:GLU175 5.0 49.6 1.0

Calcium binding site 5 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:35.5 occ:1.00 O C:ASN98 2.3 34.9 1.0 O C:GLY37 2.4 33.5 1.0 OE2 C:GLU95 2.4 50.8 1.0 OD1 C:ASP216 2.4 31.9 1.0 OE2 C:GLU39 2.5 35.1 1.0 O C:GLU95 2.5 34.7 1.0 OD2 C:ASP216 2.8 35.0 1.0 CG C:ASP216 2.9 33.0 1.0 CD C:GLU95 3.2 51.5 1.0 CG C:GLU95 3.4 52.6 1.0 C C:GLY37 3.4 33.1 1.0 C C:ASN98 3.4 35.2 1.0 C C:GLU95 3.5 41.0 1.0 CD C:GLU39 3.6 36.6 1.0 CA C:GLY37 3.8 33.5 1.0 N C:ASN98 3.9 35.0 1.0 CG C:GLU39 4.1 33.1 1.0 CA C:ASN98 4.2 35.2 1.0 CA C:GLU95 4.3 44.0 1.0 OE1 C:GLU95 4.4 51.9 1.0 CB C:ASP216 4.4 29.7 1.0 N C:GLY96 4.4 42.1 1.0 CB C:GLU95 4.4 48.8 1.0 N C:GLU95 4.5 44.5 1.0 N C:ILE99 4.5 34.0 1.0 CA C:GLY96 4.5 36.5 1.0 N C:PHE38 4.6 30.0 1.0 CB C:ASN98 4.6 33.8 1.0 OE1 C:GLU39 4.6 35.1 1.0 C C:GLY96 4.7 39.4 1.0 CB C:ALA93 4.7 36.3 1.0 CA C:ILE99 4.7 34.3 1.0 N C:ARG97 4.7 38.1 1.0 N C:GLU39 4.8 36.0 1.0 N C:ASN217 4.9 37.4 1.0 C C:ARG97 4.9 39.2 1.0 C C:PHE38 4.9 31.6 1.0

Calcium binding site 6 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:58.7 occ:1.00 O C:LEU138 2.3 40.7 1.0 O C:GLY149 2.3 29.5 1.0 OE1 C:GLU175 2.3 44.8 1.0 O C:PHE147 2.4 41.1 1.0 OD1 C:ASN137 2.4 39.2 1.0 CD C:GLU175 3.1 44.2 1.0 OE2 C:GLU175 3.2 44.9 1.0 N C:GLY149 3.2 29.6 1.0 C C:GLY149 3.3 32.4 1.0 O C:HOH407 3.4 40.0 1.0 CG C:ASN137 3.4 35.1 1.0 C C:PHE147 3.5 37.4 1.0 C C:LEU138 3.5 39.5 1.0 C C:ALA148 3.6 27.3 1.0 CA C:ALA148 3.8 31.4 1.0 ND2 C:ASN137 3.8 37.5 1.0 CA C:GLY149 3.9 31.8 1.0 N C:ALA148 4.1 33.5 1.0 N C:LEU138 4.1 34.5 1.0 CA C:LEU138 4.4 35.1 1.0 O C:ALA148 4.4 29.0 1.0 C C:ASN137 4.4 33.6 1.0 N C:ALA139 4.5 35.8 1.0 N C:PHE150 4.5 30.8 1.0 CG C:GLU175 4.5 45.2 1.0 CA C:ALA139 4.6 36.1 1.0 CB C:ASN137 4.7 29.1 1.0 CA C:PHE147 4.7 38.0 1.0 CD2 C:PHE210 4.7 41.6 1.0 CB C:PHE147 4.8 38.5 1.0 CB C:PHE210 4.9 35.1 1.0 O C:ASN137 4.9 35.0 1.0 CA C:PHE150 4.9 28.1 1.0 CA C:ASN137 4.9 30.1 1.0 CB C:LEU138 4.9 35.0 1.0 CB C:GLU175 4.9 41.9 1.0

Calcium binding site 7 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:38.3 occ:1.00 O D:GLU95 2.3 41.4 1.0 OE1 D:GLU95 2.4 38.6 1.0 O D:ASN98 2.4 34.7 1.0 O D:GLY37 2.4 35.3 1.0 OD1 D:ASP216 2.4 32.1 1.0 OE2 D:GLU39 2.5 34.6 1.0 OD2 D:ASP216 2.7 36.6 1.0 CG D:ASP216 2.9 33.2 1.0 C D:GLU95 3.3 39.9 1.0 C D:GLY37 3.4 36.1 1.0 C D:ASN98 3.5 36.7 1.0 CD D:GLU95 3.5 40.8 1.0 CD D:GLU39 3.7 38.4 1.0 CA D:GLY37 3.8 35.4 1.0 N D:ASN98 4.0 35.4 1.0 CB D:GLU95 4.0 41.1 1.0 CA D:GLU95 4.1 35.9 1.0 CG D:GLU39 4.2 39.3 1.0 N D:GLY96 4.2 41.5 1.0 CA D:ASN98 4.3 36.4 1.0 N D:GLU95 4.3 33.2 1.0 OE2 D:GLU95 4.4 40.5 1.0 CG D:GLU95 4.4 41.9 1.0 CB D:ASP216 4.4 28.5 1.0 CA D:GLY96 4.4 40.5 1.0 N D:ILE99 4.6 36.1 1.0 C D:GLY96 4.6 39.1 1.0 N D:PHE38 4.6 33.6 1.0 N D:ARG97 4.7 37.2 1.0 OE1 D:GLU39 4.7 39.4 1.0 CB D:ASN98 4.7 36.9 1.0 CA D:ILE99 4.8 33.2 1.0 N D:ASN217 4.8 34.8 1.0 CB D:ALA93 4.8 38.1 1.0 C D:ARG97 4.9 39.6 1.0 N D:GLU39 4.9 39.4 1.0 C D:PHE38 5.0 36.6 1.0

Calcium binding site 8 out of 8 in the Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of An Apo Form Cyclase FILC1 From Fischerella Sp. Tau within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:64.8 occ:1.00 O D:GLY149 2.3 33.0 1.0 O D:PHE147 2.3 58.7 1.0 OE1 D:GLU175 2.3 55.4 1.0 OD1 D:ASN137 2.4 33.7 1.0 O D:LEU138 2.4 37.0 1.0 CD D:GLU175 3.1 52.7 1.0 OE2 D:GLU175 3.1 57.2 1.0 N D:GLY149 3.2 38.5 1.0 CG D:ASN137 3.3 33.6 1.0 C D:GLY149 3.3 33.9 1.0 C D:PHE147 3.5 49.9 1.0 O D:HOH414 3.5 38.9 1.0 C D:ALA148 3.6 40.8 1.0 C D:LEU138 3.6 38.4 1.0 ND2 D:ASN137 3.6 32.7 1.0 CA D:ALA148 3.7 42.8 1.0 CA D:GLY149 3.8 34.1 1.0 N D:ALA148 4.0 45.1 1.0 N D:LEU138 4.2 31.2 1.0 O D:ALA148 4.4 40.6 1.0 C D:ASN137 4.5 31.8 1.0 CA D:LEU138 4.5 34.9 1.0 CG D:GLU175 4.5 46.2 1.0 N D:PHE150 4.5 33.1 1.0 N D:ALA139 4.5 40.5 1.0 CA D:ALA139 4.6 39.6 1.0 CB D:ASN137 4.6 32.9 1.0 CA D:PHE147 4.7 47.7 1.0 CB D:PHE147 4.8 45.2 1.0 O D:ASN137 4.9 34.9 1.0 O D:HOH444 4.9 30.0 1.0 CA D:PHE150 4.9 29.6 1.0 CB D:GLU175 4.9 41.3 1.0 CA D:ASN137 4.9 31.5 1.0 CA D:GLU175 5.0 37.4 1.0 CD2 D:PHE210 5.0 36.1 1.0

C.C.Chen, X.Hu, X.Tang, Y.Yang, T.P.Ko, J.Gao, Y.Zheng, J.W.Huang, Z.Yu, L.Li, S.Han, N.Cai, Y.Zhang, W.Liu, R.T.Guo. The Crystal Structure of A Class of Cyclases That Catalyze the Cope Rearrangement Angew. Chem. Int. Ed. Engl. V. 57 15060 2018.
ISSN: ESSN 1521-3773
PubMed: 30222239
DOI: 10.1002/ANIE.201808231