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Calcium in PDB 5yvl: Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239

Protein crystallography data

The structure of Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239, PDB code: 5yvl 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) 24.99 / 2.06
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.390, 114.311, 132.439, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 (pdb code 5yvl). 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 HPIU5 From Fischerella Sp. Atcc 43239, PDB code: 5yvl:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5yvl

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Calcium binding site 1 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:32.0
occ:1.00
 OE1 A:GLU95 2.2 38.2 1.0
O A:ASN98 2.3 30.6 1.0
OE2 A:GLU39 2.4 35.8 1.0
O A:GLU95 2.4 29.7 1.0
OD1 A:ASP216 2.4 29.6 1.0
O A:GLY37 2.4 30.8 1.0
OD2 A:ASP216 2.8 34.9 1.0
CG A:ASP216 3.0 30.4 1.0
C A:GLU95 3.4 33.0 1.0
CD A:GLU95 3.4 34.5 1.0
C A:GLY37 3.4 34.7 1.0
C A:ASN98 3.5 33.6 1.0
CD A:GLU39 3.5 36.2 1.0
CA A:GLY37 3.7 31.6 1.0
CB A:GLU95 3.9 35.8 1.0
N A:ASN98 3.9 30.9 1.0
CG A:GLU39 4.1 33.9 1.0
CA A:GLU95 4.1 34.1 1.0
CA A:ASN98 4.2 30.4 1.0
CG A:GLU95 4.2 34.4 1.0
OE2 A:GLU95 4.2 33.4 1.0
N A:GLY96 4.3 36.4 1.0
CA A:GLY96 4.4 38.2 1.0
N A:GLU95 4.4 32.1 1.0
CB A:ASP216 4.5 30.1 1.0
N A:ARG97 4.5 34.8 1.0
C A:GLY96 4.5 32.7 1.0
N A:ILE99 4.5 32.4 1.0
OE1 A:GLU39 4.6 38.5 1.0
N A:PHE38 4.7 31.9 1.0
CB A:ALA93 4.7 30.9 1.0
CB A:ASN98 4.7 31.0 1.0
CA A:ILE99 4.8 29.4 1.0
N A:ASN217 4.9 30.1 1.0
C A:ARG97 4.9 37.1 1.0
N A:GLU39 4.9 33.4 1.0
C A:PHE38 5.0 33.6 1.0

Calcium binding site 2 out of 8 in 5yvl

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Calcium binding site 2 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:52.7
occ:1.00
 O A:GLY149 2.1 31.9 1.0
OD1 A:ASP175 2.2 34.9 1.0
O A:LEU147 2.3 33.9 1.0
N A:GLY149 2.4 36.1 1.0
O A:PHE138 2.7 40.2 1.0
C A:ALA148 2.8 30.0 1.0
OD1 A:ASN137 2.9 30.6 1.0
C A:GLY149 3.0 31.7 1.0
CA A:ALA148 3.0 30.0 1.0
O A:HOH437 3.1 40.5 1.0
CG A:ASP175 3.2 37.8 1.0
CA A:GLY149 3.3 34.2 1.0
C A:LEU147 3.3 39.6 1.0
N A:ALA148 3.6 30.0 1.0
O A:ALA148 3.7 30.0 1.0
CG A:ASN137 3.9 31.9 1.0
C A:PHE138 3.9 31.5 1.0
OD2 A:ASP175 4.0 47.8 1.0
ND2 A:ASN137 4.1 30.6 1.0
CB A:ASP175 4.2 35.1 1.0
N A:PHE150 4.2 30.3 1.0
CB A:ALA148 4.4 30.0 1.0
CB A:PHE210 4.5 34.4 1.0
CA A:ASP175 4.6 31.4 1.0
CA A:LEU147 4.6 32.4 1.0
N A:PHE138 4.7 30.7 1.0
CA A:PHE138 4.7 33.9 1.0
CB A:PHE138 4.8 37.2 1.0
N A:GLY139 4.8 29.8 1.0
CA A:PHE150 4.9 27.0 1.0
CA A:GLY139 4.9 36.7 1.0
N A:PHE210 5.0 30.9 1.0
C A:ASN137 5.0 30.0 1.0

Calcium binding site 3 out of 8 in 5yvl

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Calcium binding site 3 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:28.7
occ:1.00
 OE1 B:GLU95 2.3 32.2 1.0
OD1 B:ASP216 2.3 25.3 1.0
O B:ASN98 2.3 31.2 1.0
O B:GLU95 2.3 33.2 1.0
OE2 B:GLU39 2.4 32.8 1.0
O B:GLY37 2.5 28.5 1.0
OD2 B:ASP216 2.5 32.4 1.0
CG B:ASP216 2.8 31.1 1.0
C B:GLU95 3.3 35.5 1.0
C B:GLY37 3.5 29.0 1.0
CD B:GLU95 3.5 33.0 1.0
CD B:GLU39 3.5 35.0 1.0
C B:ASN98 3.5 37.2 1.0
CB B:GLU95 3.8 31.8 1.0
CA B:GLY37 3.8 24.4 1.0
N B:ASN98 4.0 31.5 1.0
CA B:GLU95 4.0 35.5 1.0
CG B:GLU39 4.0 29.1 1.0
CG B:GLU95 4.2 31.3 1.0
N B:GLU95 4.2 29.5 1.0
CA B:ASN98 4.3 31.4 1.0
N B:GLY96 4.3 37.5 1.0
CB B:ASP216 4.3 26.4 1.0
OE2 B:GLU95 4.4 35.9 1.0
CA B:GLY96 4.5 31.2 1.0
OE1 B:GLU39 4.6 34.2 1.0
N B:ILE99 4.6 30.4 1.0
C B:GLY96 4.6 30.6 1.0
N B:ARG97 4.6 33.5 1.0
N B:PHE38 4.7 26.6 1.0
CB B:ALA93 4.8 31.5 1.0
CB B:ASN98 4.8 30.9 1.0
N B:ASN217 4.8 31.4 1.0
CA B:ILE99 4.8 30.1 1.0
N B:GLU39 4.9 32.7 1.0
C B:ARG97 4.9 33.5 1.0
C B:PHE38 5.0 29.9 1.0

Calcium binding site 4 out of 8 in 5yvl

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Calcium binding site 4 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:59.4
occ:1.00
 O B:LEU147 2.1 38.9 1.0
O B:GLY149 2.2 33.5 1.0
OD1 B:ASP175 2.3 34.0 1.0
N B:GLY149 2.3 35.7 1.0
C B:ALA148 2.7 30.0 1.0
CA B:ALA148 2.8 30.0 1.0
OD1 B:ASN137 2.9 33.2 1.0
O B:PHE138 3.0 37.9 1.0
C B:GLY149 3.0 36.3 1.0
C B:LEU147 3.1 44.8 1.0
CG B:ASP175 3.2 41.4 1.0
CA B:GLY149 3.2 32.4 1.0
O B:HOH419 3.3 38.2 1.0
N B:ALA148 3.4 30.0 1.0
O B:ALA148 3.6 30.0 1.0
OD2 B:ASP175 3.9 39.4 1.0
CG B:ASN137 3.9 34.4 1.0
C B:PHE138 4.0 36.0 1.0
CB B:ASP175 4.2 36.8 1.0
ND2 B:ASN137 4.2 34.2 1.0
CB B:ALA148 4.2 30.0 1.0
N B:PHE150 4.3 32.9 1.0
CB B:PHE210 4.4 34.1 1.0
CA B:LEU147 4.5 41.6 1.0
N B:PHE138 4.5 38.1 1.0
CA B:ASP175 4.5 35.0 1.0
O B:HOH499 4.6 44.1 1.0
CA B:PHE138 4.7 33.6 1.0
CB B:PHE138 4.8 36.4 1.0
CB B:LEU147 4.8 40.4 1.0
N B:PHE210 4.9 31.2 1.0
CA B:PHE150 4.9 32.9 1.0
C B:ASN137 4.9 31.4 1.0

Calcium binding site 5 out of 8 in 5yvl

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Calcium binding site 5 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:32.1
occ:1.00
 O C:GLY37 2.1 30.0 1.0
OE1 C:GLU95 2.2 35.8 1.0
OD1 C:ASP216 2.4 25.2 1.0
O C:ASN98 2.4 29.3 1.0
O C:GLU95 2.5 39.8 1.0
OE2 C:GLU39 2.5 32.4 1.0
OD2 C:ASP216 2.9 30.1 1.0
CG C:ASP216 3.0 27.0 1.0
C C:GLY37 3.0 30.0 1.0
CA C:GLY37 3.4 30.0 1.0
CD C:GLU95 3.4 39.3 1.0
C C:GLU95 3.4 33.9 1.0
CD C:GLU39 3.6 35.8 1.0
C C:ASN98 3.6 32.7 1.0
CB C:GLU95 4.0 32.2 1.0
CG C:GLU39 4.0 31.5 1.0
N C:ASN98 4.1 29.2 1.0
CA C:GLU95 4.2 35.2 1.0
N C:PHE38 4.2 27.6 1.0
OE2 C:GLU95 4.3 36.9 1.0
CG C:GLU95 4.3 35.5 1.0
N C:GLY96 4.4 39.2 1.0
CA C:ASN98 4.4 27.2 1.0
N C:GLU95 4.5 31.3 1.0
CB C:ASP216 4.5 27.5 1.0
CA C:GLY96 4.6 32.3 1.0
N C:ILE99 4.6 30.3 1.0
N C:ASN217 4.7 28.9 1.0
OE1 C:GLU39 4.7 36.4 1.0
N C:GLU39 4.7 27.4 1.0
C C:PHE38 4.7 29.2 1.0
N C:GLY37 4.8 30.0 1.0
N C:ARG97 4.8 31.7 1.0
C C:GLY96 4.8 33.0 1.0
CB C:ASN98 4.8 27.9 1.0
CA C:PHE38 4.9 29.0 1.0
CA C:ILE99 4.9 31.4 1.0

Calcium binding site 6 out of 8 in 5yvl

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Calcium binding site 6 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:63.5
occ:1.00
 O C:LEU147 2.0 38.8 1.0
OD1 C:ASP175 2.3 40.3 1.0
O C:GLY149 2.3 32.9 1.0
N C:GLY149 2.4 40.5 1.0
C C:ALA148 2.6 30.0 1.0
CA C:ALA148 2.7 30.0 1.0
O C:PHE138 2.9 41.2 1.0
C C:LEU147 2.9 42.4 1.0
OD1 C:ASN137 3.0 39.6 1.0
C C:GLY149 3.1 36.9 1.0
CG C:ASP175 3.2 45.2 1.0
N C:ALA148 3.2 30.0 1.0
CA C:GLY149 3.3 36.6 1.0
O C:HOH427 3.3 39.4 1.0
O C:ALA148 3.5 30.0 1.0
OD2 C:ASP175 3.9 50.8 1.0
CG C:ASN137 3.9 35.0 1.0
C C:PHE138 4.0 37.5 1.0
CB C:ASP175 4.1 38.4 1.0
CB C:ALA148 4.1 30.0 1.0
ND2 C:ASN137 4.2 31.8 1.0
CA C:LEU147 4.3 43.0 1.0
N C:PHE150 4.4 35.0 1.0
CA C:ASP175 4.5 39.9 1.0
CB C:PHE210 4.5 38.3 1.0
N C:PHE138 4.7 35.6 1.0
CA C:PHE138 4.8 35.6 1.0
CB C:LEU147 4.8 38.7 1.0
N C:GLY139 4.9 39.0 1.0
CB C:PHE138 4.9 36.6 1.0
CA C:GLY139 5.0 35.1 1.0

Calcium binding site 7 out of 8 in 5yvl

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Calcium binding site 7 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:42.9
occ:1.00
 OE1 D:GLU95 2.2 41.5 1.0
O D:ASN98 2.3 37.2 1.0
OE2 D:GLU39 2.3 47.6 1.0
O D:GLY37 2.4 43.2 1.0
OD1 D:ASP216 2.4 36.4 1.0
O D:GLU95 2.5 43.8 1.0
OD2 D:ASP216 2.7 43.8 1.0
CG D:ASP216 2.9 41.6 1.0
C D:GLY37 3.4 42.5 1.0
C D:GLU95 3.4 50.7 1.0
CD D:GLU95 3.4 45.6 1.0
C D:ASN98 3.4 39.8 1.0
CD D:GLU39 3.5 47.5 1.0
CA D:GLY37 3.7 41.6 1.0
N D:ASN98 3.9 42.5 1.0
CB D:GLU95 3.9 43.2 1.0
CG D:GLU39 4.0 42.0 1.0
CA D:GLU95 4.1 46.0 1.0
CA D:ASN98 4.2 43.4 1.0
N D:GLY96 4.3 50.9 1.0
CG D:GLU95 4.3 38.1 1.0
OE2 D:GLU95 4.3 45.2 1.0
CB D:ASP216 4.4 40.6 1.0
CA D:GLY96 4.4 41.8 1.0
N D:GLU95 4.5 43.9 1.0
OE1 D:GLU39 4.5 49.8 1.0
N D:ILE99 4.5 37.7 1.0
C D:GLY96 4.6 40.4 1.0
N D:PHE38 4.6 41.3 1.0
N D:ARG97 4.6 39.8 1.0
CB D:ASN98 4.7 36.5 1.0
N D:ASN217 4.8 39.4 1.0
CA D:ILE99 4.8 42.2 1.0
C D:ARG97 4.9 49.1 1.0
CB D:ALA93 4.9 45.6 1.0
N D:GLU39 4.9 41.8 1.0
C D:PHE38 5.0 43.8 1.0

Calcium binding site 8 out of 8 in 5yvl

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Calcium binding site 8 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239


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 HPIU5 From Fischerella Sp. Atcc 43239 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca303

b:66.7
occ:1.00
 O D:GLY149 2.0 35.1 1.0
O D:LEU147 2.1 42.7 1.0
O D:PHE138 2.6 48.1 1.0
OD1 D:ASN137 2.6 37.0 1.0
OD1 D:ASP175 2.7 41.4 1.0
N D:GLY149 2.9 40.7 1.0
C D:GLY149 3.0 38.5 1.0
C D:ALA148 3.2 30.0 1.0
C D:LEU147 3.3 42.9 1.0
CA D:ALA148 3.5 30.0 1.0
CA D:GLY149 3.6 38.5 1.0
CG D:ASN137 3.7 37.8 1.0
C D:PHE138 3.7 43.7 1.0
N D:ALA148 3.8 30.0 1.0
CG D:ASP175 3.9 43.7 1.0
O D:ALA148 3.9 30.0 1.0
ND2 D:ASN137 4.2 33.1 1.0
N D:PHE138 4.2 46.0 1.0
N D:PHE150 4.2 34.8 1.0
CB D:PHE210 4.3 36.6 1.0
CA D:PHE138 4.4 47.0 1.0
CB D:PHE138 4.5 46.8 1.0
CA D:LEU147 4.5 37.6 1.0
C D:ASN137 4.6 43.7 1.0
OD2 D:ASP175 4.6 44.6 1.0
CD2 D:PHE210 4.7 39.5 1.0
CA D:PHE150 4.7 34.5 1.0
O D:PHE210 4.7 30.6 1.0
N D:GLY139 4.7 48.2 1.0
CB D:ASP175 4.8 39.9 1.0
CB D:LEU147 4.8 41.8 1.0
CB D:ALA148 4.9 30.0 1.0
N D:PHE210 4.9 34.0 1.0
CA D:GLY139 4.9 45.0 1.0
CA D:ASP175 5.0 43.6 1.0
CB D:ASN137 5.0 32.0 1.0
CG D:PHE210 5.0 38.7 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 15:36:39 2024

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