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Calcium in PDB 5zfj: Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One

Protein crystallography data

The structure of Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One, PDB code: 5zfj 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) 24.66 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.203, 255.055, 36.183, 90.00, 90.00, 90.00
R / Rfree (%) 16.9 / 20.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One (pdb code 5zfj). 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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One, PDB code: 5zfj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5zfj

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Calcium binding site 1 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:18.7
occ:1.00
 O A:ASN98 2.3 18.9 1.0
O A:GLU95 2.3 19.3 1.0
OE2 A:GLU95 2.4 25.9 1.0
OE2 A:GLU39 2.4 20.1 1.0
OD1 A:ASP216 2.4 17.3 1.0
O A:GLY37 2.4 18.2 1.0
OD2 A:ASP216 2.5 19.3 1.0
CG A:ASP216 2.8 20.8 1.0
C A:GLU95 3.3 23.8 1.0
C A:GLY37 3.4 18.3 1.0
CD A:GLU39 3.5 22.5 1.0
C A:ASN98 3.5 17.3 1.0
CD A:GLU95 3.5 26.7 1.0
CA A:GLY37 3.8 20.7 1.0
N A:ASN98 3.9 18.4 1.0
CG A:GLU39 4.0 20.2 1.0
CB A:GLU95 4.0 23.2 1.0
CA A:GLU95 4.1 21.4 1.0
CA A:ASN98 4.2 19.0 1.0
CB A:ASP216 4.3 19.1 1.0
N A:GLU95 4.3 22.5 1.0
N A:GLY96 4.3 19.6 1.0
CG A:GLU95 4.3 23.8 1.0
OE1 A:GLU95 4.5 27.7 1.0
OE1 A:GLU39 4.5 23.7 1.0
CA A:GLY96 4.5 21.3 1.0
N A:ILE99 4.6 17.6 1.0
N A:ARG97 4.6 20.7 1.0
CB A:ASN98 4.6 18.6 1.0
C A:GLY96 4.6 21.2 1.0
N A:PHE38 4.6 19.9 1.0
CB A:ALA93 4.7 21.6 1.0
CA A:ILE99 4.8 18.9 1.0
C A:ARG97 4.9 19.6 1.0
N A:ASN217 4.9 19.9 1.0
C A:PHE38 5.0 18.2 1.0

Calcium binding site 2 out of 8 in 5zfj

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Calcium binding site 2 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:30.6
occ:1.00
 O A:LEU138 2.3 26.6 1.0
OD1 A:ASN137 2.3 25.4 1.0
O A:PHE147 2.3 26.8 1.0
O A:GLY149 2.4 24.6 1.0
OE1 A:GLU175 2.4 37.2 1.0
O A:HOH461 2.4 40.8 1.0
OE2 A:GLU175 2.4 38.7 1.0
CD A:GLU175 2.8 35.3 1.0
C A:GLY149 3.5 25.0 1.0
CG A:ASN137 3.5 21.8 1.0
N A:GLY149 3.5 24.6 1.0
C A:LEU138 3.5 25.3 1.0
C A:PHE147 3.5 26.2 1.0
C A:ALA148 3.7 25.0 1.0
N A:LEU138 4.0 22.7 1.0
CA A:ALA148 4.0 25.1 1.0
ND2 A:ASN137 4.1 24.2 1.0
CA A:GLY149 4.1 24.2 1.0
N A:ALA148 4.2 26.3 1.0
C A:ASN137 4.2 24.0 1.0
CG A:GLU175 4.2 33.0 1.0
CA A:LEU138 4.3 25.4 1.0
O A:ALA148 4.4 23.7 1.0
N A:ALA139 4.5 23.3 1.0
N A:PHE150 4.5 22.3 1.0
CA A:PHE147 4.6 27.8 1.0
CB A:ASN137 4.7 20.5 1.0
CA A:ALA139 4.7 26.7 1.0
O A:ASN137 4.7 23.1 1.0
CA A:ASN137 4.7 20.1 1.0
CB A:PHE147 4.8 30.5 1.0
CA A:PHE150 4.8 21.1 1.0
CB A:PHE210 4.8 25.2 1.0
O A:HOH451 4.8 40.8 1.0
CB A:LEU138 4.9 30.8 1.0
CB A:PHE150 4.9 20.7 1.0
CD2 A:PHE210 4.9 25.6 1.0
CB A:GLU175 4.9 26.7 1.0
O A:HOH504 4.9 34.9 1.0

Calcium binding site 3 out of 8 in 5zfj

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Calcium binding site 3 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:24.1
occ:1.00
 O B:GLU95 2.3 25.8 1.0
O B:ASN98 2.3 24.5 1.0
OD1 B:ASP216 2.4 22.0 1.0
O B:GLY37 2.4 25.6 1.0
OE2 B:GLU95 2.4 27.6 1.0
OE2 B:GLU39 2.4 27.8 1.0
OD2 B:ASP216 2.5 23.9 1.0
CG B:ASP216 2.7 22.7 1.0
C B:GLU95 3.3 26.9 1.0
C B:GLY37 3.4 23.1 1.0
C B:ASN98 3.5 29.1 1.0
CD B:GLU39 3.5 31.7 1.0
CD B:GLU95 3.5 33.5 1.0
CA B:GLY37 3.8 21.8 1.0
N B:ASN98 3.9 25.1 1.0
CB B:GLU95 4.0 28.9 1.0
CA B:GLU95 4.1 26.9 1.0
CG B:GLU39 4.2 31.5 1.0
CA B:ASN98 4.3 25.9 1.0
CB B:ASP216 4.3 22.6 1.0
N B:GLU95 4.3 27.0 1.0
N B:GLY96 4.3 26.0 1.0
CG B:GLU95 4.3 28.9 1.0
OE1 B:GLU95 4.5 30.7 1.0
CA B:GLY96 4.5 23.6 1.0
OE1 B:GLU39 4.6 29.9 1.0
N B:ARG97 4.6 25.3 1.0
N B:ILE99 4.6 26.6 1.0
C B:GLY96 4.6 23.4 1.0
N B:PHE38 4.6 22.2 1.0
CB B:ASN98 4.7 23.9 1.0
CB B:ALA93 4.8 24.0 1.0
C B:ARG97 4.8 26.5 1.0
N B:ASN217 4.8 23.3 1.0
CA B:ILE99 4.9 23.5 1.0

Calcium binding site 4 out of 8 in 5zfj

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Calcium binding site 4 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:30.9
occ:1.00
 O B:LEU138 2.3 30.3 1.0
OD1 B:ASN137 2.3 26.9 1.0
O B:PHE147 2.3 26.0 1.0
O B:GLY149 2.4 24.5 1.0
OE1 B:GLU175 2.4 38.2 1.0
O B:HOH487 2.4 38.2 1.0
OE2 B:GLU175 2.4 39.1 1.0
CD B:GLU175 2.8 36.3 1.0
CG B:ASN137 3.5 23.6 1.0
C B:GLY149 3.5 25.4 1.0
C B:LEU138 3.5 32.0 1.0
C B:PHE147 3.5 29.1 1.0
N B:GLY149 3.6 25.2 1.0
C B:ALA148 3.8 28.4 1.0
ND2 B:ASN137 4.0 23.6 1.0
N B:LEU138 4.1 27.0 1.0
CA B:ALA148 4.1 29.7 1.0
CA B:GLY149 4.2 26.8 1.0
C B:ASN137 4.3 27.5 1.0
CG B:GLU175 4.3 31.7 1.0
N B:ALA148 4.3 25.4 1.0
CA B:LEU138 4.4 29.6 1.0
N B:ALA139 4.5 30.4 1.0
O B:ALA148 4.5 25.7 1.0
N B:PHE150 4.6 22.4 1.0
CA B:ALA139 4.6 31.4 1.0
CA B:PHE147 4.6 29.4 1.0
O B:ASN137 4.6 27.8 1.0
CB B:PHE147 4.7 30.5 1.0
CB B:ASN137 4.7 21.9 1.0
CA B:ASN137 4.7 22.5 1.0
CA B:PHE150 4.8 21.6 1.0
CB B:PHE210 4.9 26.3 1.0
O B:HOH508 4.9 32.7 1.0
CB B:LEU138 4.9 38.1 1.0
CB B:PHE150 4.9 22.2 1.0
CD2 B:PHE210 5.0 29.6 1.0

Calcium binding site 5 out of 8 in 5zfj

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Calcium binding site 5 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:24.5
occ:1.00
 O C:ASN98 2.3 24.9 1.0
O C:GLU95 2.3 25.7 1.0
OE2 C:GLU95 2.3 30.5 1.0
OD1 C:ASP216 2.4 22.8 1.0
O C:GLY37 2.4 24.1 1.0
OE2 C:GLU39 2.4 25.8 1.0
OD2 C:ASP216 2.6 29.5 1.0
CG C:ASP216 2.8 25.1 1.0
C C:GLU95 3.3 30.4 1.0
C C:GLY37 3.4 21.1 1.0
C C:ASN98 3.5 23.1 1.0
CD C:GLU95 3.5 30.2 1.0
CD C:GLU39 3.5 25.6 1.0
CA C:GLY37 3.8 22.3 1.0
N C:ASN98 3.9 24.3 1.0
CB C:GLU95 4.0 28.7 1.0
CG C:GLU39 4.1 26.1 1.0
CA C:GLU95 4.1 26.4 1.0
CA C:ASN98 4.2 24.2 1.0
N C:GLY96 4.3 24.7 1.0
CG C:GLU95 4.3 31.7 1.0
CB C:ASP216 4.3 25.3 1.0
N C:GLU95 4.4 27.8 1.0
OE1 C:GLU95 4.4 33.9 1.0
N C:ILE99 4.5 23.8 1.0
CA C:GLY96 4.6 24.9 1.0
OE1 C:GLU39 4.6 26.8 1.0
N C:PHE38 4.6 23.4 1.0
N C:ARG97 4.6 25.1 1.0
C C:GLY96 4.6 22.8 1.0
CB C:ASN98 4.7 24.1 1.0
CA C:ILE99 4.8 24.3 1.0
CB C:ALA93 4.8 32.0 1.0
N C:ASN217 4.9 25.8 1.0
C C:ARG97 4.9 25.6 1.0
N C:GLU39 4.9 22.9 1.0
C C:PHE38 5.0 23.1 1.0

Calcium binding site 6 out of 8 in 5zfj

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Calcium binding site 6 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:36.8
occ:1.00
 O C:LEU138 2.3 35.7 1.0
OD1 C:ASN137 2.3 29.3 1.0
O C:PHE147 2.3 32.0 1.0
O C:GLY149 2.3 27.4 1.0
OE1 C:GLU175 2.4 43.2 1.0
O C:HOH426 2.4 43.1 1.0
OE2 C:GLU175 2.5 47.6 1.0
CD C:GLU175 2.8 38.3 1.0
C C:GLY149 3.5 35.2 1.0
CG C:ASN137 3.5 26.2 1.0
C C:PHE147 3.5 33.7 1.0
C C:LEU138 3.5 38.7 1.0
N C:GLY149 3.6 32.3 1.0
C C:ALA148 3.9 33.2 1.0
CA C:ALA148 4.0 38.3 1.0
N C:LEU138 4.1 27.8 1.0
ND2 C:ASN137 4.1 24.3 1.0
CA C:GLY149 4.1 29.7 1.0
N C:ALA148 4.2 38.7 1.0
C C:ASN137 4.3 27.4 1.0
CG C:GLU175 4.3 37.8 1.0
CA C:LEU138 4.3 37.0 1.0
N C:PHE150 4.5 27.7 1.0
N C:ALA139 4.5 32.9 1.0
O C:ALA148 4.5 28.6 1.0
CA C:PHE147 4.6 35.8 1.0
CB C:ASN137 4.7 23.4 1.0
CB C:LEU138 4.7 42.8 1.0
O C:ASN137 4.7 31.6 1.0
CA C:PHE150 4.7 26.2 1.0
CB C:PHE147 4.7 34.6 1.0
CA C:ALA139 4.7 36.3 1.0
CA C:ASN137 4.7 22.8 1.0
CB C:PHE150 4.8 25.4 1.0
CB C:PHE210 4.8 30.8 1.0
CD2 C:PHE210 4.8 36.6 1.0
CB C:GLU175 5.0 31.1 1.0

Calcium binding site 7 out of 8 in 5zfj

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Calcium binding site 7 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:23.8
occ:1.00
 O D:ASN98 2.3 24.7 1.0
O D:GLU95 2.3 26.5 1.0
OE1 D:GLU95 2.4 27.6 1.0
OD1 D:ASP216 2.4 22.1 1.0
OE2 D:GLU39 2.4 28.4 1.0
O D:GLY37 2.4 24.1 1.0
OD2 D:ASP216 2.6 23.3 1.0
CG D:ASP216 2.8 22.9 1.0
C D:GLU95 3.3 29.3 1.0
C D:GLY37 3.4 24.6 1.0
C D:ASN98 3.5 25.1 1.0
CD D:GLU39 3.5 27.0 1.0
CD D:GLU95 3.5 30.1 1.0
CA D:GLY37 3.8 23.8 1.0
N D:ASN98 3.9 26.9 1.0
CB D:GLU95 4.0 31.6 1.0
CA D:GLU95 4.1 27.6 1.0
CG D:GLU39 4.1 24.6 1.0
N D:GLY96 4.2 28.3 1.0
CA D:ASN98 4.2 24.5 1.0
N D:GLU95 4.3 25.9 1.0
CB D:ASP216 4.3 21.5 1.0
CG D:GLU95 4.4 32.1 1.0
OE2 D:GLU95 4.4 30.1 1.0
CA D:GLY96 4.4 29.0 1.0
OE1 D:GLU39 4.6 31.0 1.0
N D:ILE99 4.6 22.4 1.0
C D:GLY96 4.6 25.6 1.0
N D:PHE38 4.6 25.0 1.0
N D:ARG97 4.7 25.8 1.0
CB D:ALA93 4.7 29.6 1.0
CB D:ASN98 4.7 24.7 1.0
CA D:ILE99 4.9 24.5 1.0
C D:ARG97 4.9 28.0 1.0
N D:ASN217 4.9 23.3 1.0
C D:PHE38 5.0 26.0 1.0
N D:GLU39 5.0 25.6 1.0

Calcium binding site 8 out of 8 in 5zfj

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Calcium binding site 8 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One


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 A Cyclase Filc From Fischerella Sp. in Complex with 4-(1H-Indol-3-Yl)Butan-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:36.0
occ:1.00
 O D:LEU138 2.3 34.5 1.0
O D:PHE147 2.3 28.6 1.0
OD1 D:ASN137 2.3 26.1 1.0
O D:GLY149 2.4 25.6 1.0
OE1 D:GLU175 2.4 40.4 1.0
O D:HOH423 2.4 38.1 1.0
CD D:GLU175 3.2 39.7 1.0
OE2 D:GLU175 3.3 45.0 1.0
C D:GLY149 3.5 28.2 1.0
CG D:ASN137 3.5 26.2 1.0
C D:LEU138 3.5 33.8 1.0
C D:PHE147 3.5 30.1 1.0
N D:GLY149 3.6 28.2 1.0
C D:ALA148 3.8 30.7 1.0
N D:LEU138 3.9 25.1 1.0
CA D:ALA148 4.1 31.0 1.0
ND2 D:ASN137 4.1 22.9 1.0
CA D:GLY149 4.2 26.8 1.0
C D:ASN137 4.2 26.0 1.0
CA D:LEU138 4.2 31.9 1.0
N D:ALA148 4.3 28.1 1.0
O D:ALA148 4.5 27.1 1.0
N D:PHE150 4.5 25.6 1.0
N D:ALA139 4.5 29.7 1.0
CB D:LEU138 4.6 36.4 1.0
O D:ASN137 4.6 24.7 1.0
CA D:PHE147 4.6 31.5 1.0
CG D:GLU175 4.6 37.3 1.0
CB D:PHE147 4.6 34.7 1.0
CA D:ALA139 4.7 33.8 1.0
CB D:ASN137 4.7 21.5 1.0
CA D:PHE150 4.7 25.0 1.0
CA D:ASN137 4.7 21.5 1.0
CD2 D:PHE210 4.9 32.0 1.0
CB D:PHE150 4.9 23.5 1.0
CB D:PHE210 4.9 28.2 1.0
O D:HOH535 4.9 45.6 1.0

Reference:

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
Page generated: Mon Jul 15 15:50:17 2024

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