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Calcium in PDB 5z53: Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with Cyclo-L-Arg-D-Pro

Protein crystallography data

The structure of Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with Cyclo-L-Arg-D-Pro, PDB code: 5z53 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) 25.00 / 1.86
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.815, 252.304, 36.337, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 21.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with Cyclo-L-Arg-D-Pro (pdb code 5z53). 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 Cyclo-L-Arg-D-Pro, PDB code: 5z53:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:20.4
occ:1.00
 O A:ASN98 2.3 19.1 1.0
O A:GLU95 2.3 22.8 1.0
OE2 A:GLU95 2.4 21.7 1.0
O A:GLY37 2.4 23.7 1.0
OE2 A:GLU39 2.4 22.7 1.0
OD1 A:ASP216 2.4 20.3 1.0
OD2 A:ASP216 2.8 18.9 1.0
CG A:ASP216 2.9 18.0 1.0
C A:GLU95 3.3 22.1 1.0
C A:GLY37 3.4 21.8 1.0
C A:ASN98 3.5 17.7 1.0
CD A:GLU39 3.5 20.6 1.0
CD A:GLU95 3.5 24.3 1.0
CA A:GLY37 3.8 20.1 1.0
N A:ASN98 3.9 20.3 1.0
CB A:GLU95 3.9 22.2 1.0
CA A:GLU95 4.1 22.4 1.0
CG A:GLU39 4.1 23.8 1.0
CA A:ASN98 4.2 18.8 1.0
CG A:GLU95 4.3 24.8 1.0
N A:GLY96 4.3 20.9 1.0
N A:GLU95 4.4 20.7 1.0
CB A:ASP216 4.4 19.6 1.0
OE1 A:GLU95 4.4 27.8 1.0
CA A:GLY96 4.5 23.8 1.0
N A:ILE99 4.5 19.1 1.0
OE1 A:GLU39 4.5 23.5 1.0
CB A:ASN98 4.6 19.3 1.0
N A:PHE38 4.6 18.6 1.0
N A:ARG97 4.6 21.9 1.0
C A:GLY96 4.7 23.1 1.0
CB A:ALA93 4.8 21.5 1.0
CA A:ILE99 4.8 17.8 1.0
N A:ASN217 4.9 21.8 1.0
C A:PHE38 4.9 20.5 1.0
C A:ARG97 5.0 20.9 1.0
N A:GLU39 5.0 23.8 1.0

Calcium binding site 2 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:33.3
occ:1.00
 O A:PHE147 2.3 25.8 1.0
O A:GLY149 2.3 25.1 1.0
OD1 A:ASN137 2.3 25.9 1.0
O A:LEU138 2.3 27.5 1.0
OE1 A:GLU175 2.4 31.3 1.0
OE2 A:GLU175 2.4 36.0 1.0
CD A:GLU175 2.7 29.4 1.0
C A:GLY149 3.4 24.3 1.0
N A:GLY149 3.4 26.7 1.0
CG A:ASN137 3.4 23.0 1.0
C A:PHE147 3.5 25.6 1.0
C A:LEU138 3.6 27.3 1.0
C A:ALA148 3.8 26.5 1.0
ND2 A:ASN137 3.9 27.1 1.0
CA A:GLY149 4.0 27.1 1.0
CA A:ALA148 4.1 26.9 1.0
CG A:GLU175 4.2 29.8 1.0
N A:ALA148 4.3 24.6 1.0
N A:LEU138 4.3 23.7 1.0
C A:ASN137 4.3 28.2 1.0
CA A:LEU138 4.5 27.0 1.0
N A:ALA139 4.5 26.5 1.0
O A:ASN137 4.5 27.8 1.0
O A:ALA148 4.5 25.3 1.0
N A:PHE150 4.5 25.4 1.0
CA A:ALA139 4.5 27.1 1.0
O A:HOH416 4.6 31.4 1.0
CA A:PHE147 4.6 26.3 1.0
CB A:PHE147 4.6 29.7 1.0
CB A:ASN137 4.7 25.8 1.0
CD2 A:PHE210 4.7 27.7 1.0
CB A:LEU138 4.8 31.6 1.0
CA A:ASN137 4.8 24.6 1.0
CB A:PHE210 4.8 27.8 1.0
CB A:GLU175 4.9 28.9 1.0
CA A:PHE150 4.9 25.5 1.0
CB A:PHE150 4.9 24.7 1.0
CA A:GLU175 5.0 30.3 1.0

Calcium binding site 3 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:25.2
occ:1.00
 O B:ASN98 2.3 23.0 1.0
O B:GLU95 2.3 25.2 1.0
O B:GLY37 2.3 24.9 1.0
OE2 B:GLU39 2.3 25.4 1.0
OE2 B:GLU95 2.3 29.2 1.0
OD1 B:ASP216 2.4 24.5 1.0
OD2 B:ASP216 2.7 25.6 1.0
CG B:ASP216 2.8 23.8 1.0
C B:GLY37 3.3 26.2 1.0
C B:GLU95 3.4 30.5 1.0
CD B:GLU39 3.5 28.2 1.0
C B:ASN98 3.5 23.5 1.0
CD B:GLU95 3.5 33.5 1.0
CA B:GLY37 3.7 25.9 1.0
N B:ASN98 3.9 23.3 1.0
CG B:GLU39 4.0 30.8 1.0
CB B:GLU95 4.0 30.6 1.0
CA B:GLU95 4.2 28.5 1.0
CA B:ASN98 4.2 25.0 1.0
CG B:GLU95 4.3 30.2 1.0
CB B:ASP216 4.3 23.5 1.0
N B:GLY96 4.3 28.2 1.0
OE1 B:GLU95 4.4 29.8 1.0
N B:GLU95 4.4 24.8 1.0
CA B:GLY96 4.5 26.7 1.0
OE1 B:GLU39 4.5 30.8 1.0
N B:ILE99 4.5 26.5 1.0
N B:ARG97 4.6 23.5 1.0
N B:PHE38 4.6 22.4 1.0
CB B:ASN98 4.6 23.2 1.0
C B:GLY96 4.6 26.9 1.0
CA B:ILE99 4.8 22.6 1.0
N B:ASN217 4.8 25.1 1.0
CB B:ALA93 4.9 23.6 1.0
C B:ARG97 4.9 23.3 1.0
N B:GLU39 5.0 30.1 1.0
C B:PHE38 5.0 26.0 1.0

Calcium binding site 4 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:36.7
occ:1.00
 OD1 B:ASN137 2.3 26.9 1.0
O B:LEU138 2.4 33.1 1.0
O B:GLY149 2.4 25.2 1.0
O B:PHE147 2.4 25.7 1.0
OE1 B:GLU175 2.4 32.7 1.0
OE2 B:GLU175 2.4 38.5 1.0
CD B:GLU175 2.8 28.6 1.0
CG B:ASN137 3.4 21.8 1.0
C B:GLY149 3.5 27.8 1.0
N B:GLY149 3.5 27.6 1.0
C B:LEU138 3.5 31.7 1.0
C B:PHE147 3.6 24.9 1.0
O B:HOH418 3.6 37.2 1.0
ND2 B:ASN137 3.8 23.3 1.0
C B:ALA148 3.9 30.4 1.0
CA B:ALA148 4.0 27.7 1.0
CA B:GLY149 4.1 29.4 1.0
N B:LEU138 4.2 29.3 1.0
N B:ALA148 4.2 25.7 1.0
CG B:GLU175 4.3 32.6 1.0
C B:ASN137 4.3 30.1 1.0
CA B:LEU138 4.4 34.5 1.0
N B:ALA139 4.5 29.8 1.0
CA B:ALA139 4.5 28.4 1.0
O B:ALA148 4.6 26.2 1.0
N B:PHE150 4.6 25.5 1.0
O B:ASN137 4.6 28.1 1.0
CD2 B:PHE210 4.6 29.1 1.0
O B:HOH419 4.6 32.8 1.0
CB B:ASN137 4.7 23.6 1.0
CA B:PHE147 4.7 29.6 1.0
CB B:PHE147 4.7 28.9 1.0
CB B:PHE210 4.7 28.3 1.0
CA B:ASN137 4.8 23.1 1.0
CA B:PHE150 4.9 25.2 1.0
CB B:GLU175 4.9 27.9 1.0
CB B:LEU138 4.9 39.3 1.0

Calcium binding site 5 out of 8 in 5z53

Go back to Calcium Binding Sites List in 5z53
Calcium binding site 5 out of 8 in the Crystal Structure of A Cyclase Filc From Fischerella Sp. in Complex with Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:28.5
occ:1.00
 O C:ASN98 2.3 29.8 1.0
O C:GLU95 2.3 30.9 1.0
OE2 C:GLU95 2.3 31.2 1.0
OE2 C:GLU39 2.4 32.0 1.0
O C:GLY37 2.4 27.7 1.0
OD1 C:ASP216 2.4 29.2 1.0
OD2 C:ASP216 2.7 33.4 1.0
CG C:ASP216 2.9 31.3 1.0
C C:GLU95 3.3 30.8 1.0
C C:GLY37 3.4 25.2 1.0
C C:ASN98 3.5 28.8 1.0
CD C:GLU39 3.5 36.0 1.0
CD C:GLU95 3.5 34.3 1.0
CA C:GLY37 3.8 28.2 1.0
N C:ASN98 3.8 30.7 1.0
CB C:GLU95 4.1 30.6 1.0
CA C:GLU95 4.1 32.5 1.0
CG C:GLU39 4.1 30.6 1.0
CA C:ASN98 4.2 28.4 1.0
N C:GLY96 4.3 32.4 1.0
CB C:ASP216 4.3 30.6 1.0
CG C:GLU95 4.4 33.1 1.0
N C:GLU95 4.4 31.5 1.0
OE1 C:GLU95 4.4 39.1 1.0
OE1 C:GLU39 4.5 35.6 1.0
CA C:GLY96 4.5 29.0 1.0
N C:ILE99 4.5 29.1 1.0
N C:ARG97 4.6 29.6 1.0
N C:PHE38 4.6 27.5 1.0
C C:GLY96 4.6 29.9 1.0
CB C:ASN98 4.6 29.6 1.0
CB C:ALA93 4.8 37.6 1.0
C C:ARG97 4.8 30.6 1.0
CA C:ILE99 4.8 31.1 1.0
N C:ASN217 4.9 30.7 1.0
N C:GLU39 5.0 25.0 1.0
C C:PHE38 5.0 27.7 1.0

Calcium binding site 6 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:45.9
occ:1.00
 OD1 C:ASN137 2.3 30.3 1.0
O C:LEU138 2.3 36.0 1.0
O C:PHE147 2.3 42.5 1.0
O C:GLY149 2.4 32.6 1.0
OE1 C:GLU175 2.4 50.4 1.0
OE2 C:GLU175 2.4 50.3 1.0
CD C:GLU175 2.7 42.9 1.0
O C:HOH457 3.2 41.6 1.0
C C:GLY149 3.4 39.4 1.0
N C:GLY149 3.4 36.0 1.0
CG C:ASN137 3.5 30.1 1.0
C C:LEU138 3.5 39.5 1.0
C C:PHE147 3.5 44.0 1.0
C C:ALA148 3.8 37.2 1.0
N C:LEU138 4.0 32.2 1.0
CA C:ALA148 4.0 40.1 1.0
CA C:GLY149 4.1 37.7 1.0
ND2 C:ASN137 4.1 27.4 1.0
CG C:GLU175 4.2 39.6 1.0
C C:ASN137 4.2 30.1 1.0
N C:ALA148 4.3 42.7 1.0
CA C:LEU138 4.3 37.7 1.0
CD2 C:PHE210 4.5 43.0 1.0
N C:ALA139 4.5 38.1 1.0
N C:PHE150 4.5 33.4 1.0
O C:ALA148 4.6 33.7 1.0
O C:ASN137 4.6 30.2 1.0
CB C:ASN137 4.6 28.1 1.0
CB C:PHE147 4.6 35.3 1.0
CA C:PHE147 4.6 39.8 1.0
CA C:ALA139 4.7 41.6 1.0
CA C:ASN137 4.7 26.6 1.0
CA C:PHE150 4.8 31.7 1.0
CB C:PHE150 4.8 29.4 1.0
CB C:GLU175 4.9 39.5 1.0
CB C:PHE210 4.9 42.6 1.0
CB C:LEU138 4.9 40.7 1.0

Calcium binding site 7 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:34.6
occ:1.00
 O D:GLU95 2.3 33.1 1.0
O D:ASN98 2.3 36.0 1.0
O D:GLY37 2.3 41.1 1.0
OE1 D:GLU95 2.3 41.1 1.0
OE2 D:GLU39 2.4 38.6 1.0
OD1 D:ASP216 2.4 31.5 1.0
OD2 D:ASP216 2.7 36.7 1.0
CG D:ASP216 2.9 32.0 1.0
C D:GLU95 3.3 33.8 1.0
C D:GLY37 3.4 33.4 1.0
C D:ASN98 3.4 41.8 1.0
CD D:GLU95 3.5 33.4 1.0
CD D:GLU39 3.5 39.8 1.0
CA D:GLY37 3.7 32.0 1.0
N D:ASN98 3.8 38.1 1.0
CB D:GLU95 3.9 38.6 1.0
CA D:GLU95 4.1 37.4 1.0
CG D:GLU39 4.1 34.0 1.0
CA D:ASN98 4.1 41.1 1.0
CG D:GLU95 4.3 34.1 1.0
N D:GLY96 4.3 40.5 1.0
CB D:ASP216 4.4 29.8 1.0
N D:GLU95 4.4 36.0 1.0
OE2 D:GLU95 4.4 48.9 1.0
CA D:GLY96 4.4 37.4 1.0
N D:ILE99 4.5 36.2 1.0
N D:ARG97 4.5 40.5 1.0
OE1 D:GLU39 4.5 46.5 1.0
C D:GLY96 4.6 36.8 1.0
CB D:ASN98 4.6 44.1 1.0
N D:PHE38 4.6 34.9 1.0
CB D:ALA93 4.8 42.0 1.0
C D:ARG97 4.8 43.7 1.0
CA D:ILE99 4.8 33.8 1.0
N D:ASN217 4.9 31.5 1.0

Calcium binding site 8 out of 8 in 5z53

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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 Cyclo-L-Arg-D-Pro


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 Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:49.4
occ:1.00
 OD1 D:ASN137 2.3 32.1 1.0
O D:GLY149 2.3 42.2 1.0
O D:LEU138 2.3 38.2 1.0
OE1 D:GLU175 2.4 50.0 1.0
O D:PHE147 2.4 46.9 1.0
OE2 D:GLU175 2.4 51.1 1.0
CD D:GLU175 2.7 44.1 1.0
O D:HOH432 3.2 46.9 1.0
CG D:ASN137 3.4 36.3 1.0
C D:GLY149 3.4 42.2 1.0
N D:GLY149 3.4 42.4 1.0
C D:LEU138 3.5 44.7 1.0
C D:PHE147 3.6 52.3 1.0
C D:ALA148 3.9 39.2 1.0
ND2 D:ASN137 3.9 32.6 1.0
CA D:GLY149 4.0 42.5 1.0
N D:LEU138 4.0 42.4 1.0
CA D:ALA148 4.2 47.1 1.0
CG D:GLU175 4.2 39.6 1.0
C D:ASN137 4.3 36.2 1.0
N D:ALA148 4.3 46.7 1.0
CA D:LEU138 4.4 43.7 1.0
N D:PHE150 4.5 37.5 1.0
N D:ALA139 4.5 46.9 1.0
O D:ALA148 4.6 44.7 1.0
CB D:PHE150 4.6 33.1 1.0
CB D:ASN137 4.6 33.7 1.0
O D:ASN137 4.6 27.7 1.0
CA D:PHE150 4.7 33.5 1.0
CA D:PHE147 4.7 47.6 1.0
CA D:ASN137 4.8 32.6 1.0
CA D:ALA139 4.8 45.9 1.0
CD2 D:PHE210 4.8 48.7 1.0
CB D:PHE147 4.9 41.3 1.0
CB D:LEU138 4.9 43.4 1.0
CB D:GLU175 4.9 42.7 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 15:42:57 2024

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