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Calcium in PDB 5z54: Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro

Protein crystallography data

The structure of Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro, PDB code: 5z54 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) 24.90 / 2.16
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 62.557, 113.374, 132.332, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 23

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro (pdb code 5z54). 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 in Complex with Cyclo-L-Arg-D-Pro, PDB code: 5z54:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 5z54

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Calcium binding site 1 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:36.9
occ:1.00
 OE1 A:GLU95 2.2 43.5 1.0
O A:ASN98 2.3 34.7 1.0
O A:GLY37 2.3 36.0 1.0
O A:GLU95 2.3 41.1 1.0
OD1 A:ASP216 2.4 37.5 1.0
OE2 A:GLU39 2.4 38.3 1.0
OD2 A:ASP216 2.5 33.1 1.0
CG A:ASP216 2.8 31.6 1.0
CD A:GLU95 2.9 48.3 1.0
CG A:GLU95 3.1 50.8 1.0
C A:GLY37 3.3 33.0 1.0
C A:GLU95 3.4 41.0 1.0
C A:ASN98 3.5 40.3 1.0
CD A:GLU39 3.6 45.7 1.0
CA A:GLY37 3.8 34.0 1.0
N A:ASN98 3.9 38.1 1.0
OE2 A:GLU95 3.9 59.0 1.0
CA A:GLU95 4.2 45.7 1.0
CA A:ASN98 4.2 34.4 1.0
CB A:GLU95 4.2 44.4 1.0
CG A:GLU39 4.3 39.2 1.0
CB A:ASP216 4.3 33.8 1.0
N A:GLU95 4.4 47.0 1.0
N A:GLY96 4.4 41.7 1.0
N A:ILE99 4.5 35.0 1.0
OE1 A:GLU39 4.5 46.7 1.0
N A:PHE38 4.6 30.3 1.0
CA A:GLY96 4.6 37.2 1.0
CB A:ASN98 4.6 30.9 1.0
N A:ARG97 4.7 39.9 1.0
C A:GLY96 4.8 37.4 1.0
CA A:ILE99 4.8 33.0 1.0
N A:ASN217 4.8 32.3 1.0
C A:ARG97 4.9 38.1 1.0
N A:GLU39 5.0 38.5 1.0
C A:PHE38 5.0 38.5 1.0

Calcium binding site 2 out of 8 in 5z54

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Calcium binding site 2 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:45.7
occ:1.00
 O A:GLY149 2.3 43.3 1.0
O A:PHE138 2.3 41.8 1.0
OD1 A:ASN137 2.3 39.1 1.0
O A:LEU147 2.3 44.9 1.0
OD1 A:ASP175 2.3 55.8 1.0
O A:HOH414 2.4 41.9 1.0
C A:PHE138 3.4 48.1 1.0
CG A:ASN137 3.4 42.9 1.0
C A:GLY149 3.5 43.5 1.0
C A:LEU147 3.5 45.7 1.0
CG A:ASP175 3.6 55.0 1.0
N A:GLY149 3.7 39.4 1.0
C A:ALA148 3.9 39.2 1.0
ND2 A:ASN137 4.1 41.4 1.0
N A:PHE138 4.1 43.3 1.0
CA A:ALA148 4.1 43.2 1.0
C A:ASN137 4.2 40.0 1.0
N A:GLY139 4.3 43.9 1.0
N A:ALA148 4.3 42.3 1.0
CA A:GLY149 4.3 36.3 1.0
CA A:GLY139 4.3 48.2 1.0
CA A:PHE138 4.4 48.3 1.0
CB A:ASP175 4.4 41.2 1.0
O A:ALA148 4.5 45.0 1.0
OD2 A:ASP175 4.5 52.1 1.0
N A:PHE150 4.5 39.1 1.0
O A:ASN137 4.5 41.6 1.0
CA A:LEU147 4.6 48.0 1.0
CB A:ASN137 4.6 34.1 1.0
CA A:ASP175 4.6 41.4 1.0
CA A:ASN137 4.7 39.2 1.0
CA A:PHE150 4.7 35.0 1.0
CB A:LEU147 4.7 44.0 1.0
O A:PHE210 4.9 54.8 1.0
CB A:PHE210 4.9 46.3 1.0
O A:GLY212 5.0 39.1 1.0

Calcium binding site 3 out of 8 in 5z54

Go back to Calcium Binding Sites List in 5z54
Calcium binding site 3 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:36.6
occ:1.00
 OE1 B:GLU95 2.3 43.6 1.0
O B:GLU95 2.3 37.5 1.0
OD1 B:ASP216 2.3 38.9 1.0
O B:ASN98 2.3 33.9 1.0
OE2 B:GLU39 2.3 39.7 1.0
O B:GLY37 2.4 36.3 1.0
OD2 B:ASP216 2.5 36.7 1.0
CG B:ASP216 2.7 38.3 1.0
C B:GLU95 3.4 39.3 1.0
C B:GLY37 3.4 34.8 1.0
CD B:GLU95 3.4 45.3 1.0
C B:ASN98 3.5 35.2 1.0
CD B:GLU39 3.5 43.8 1.0
CA B:GLY37 3.7 32.1 1.0
N B:ASN98 4.0 36.0 1.0
CB B:GLU95 4.0 38.5 1.0
CA B:GLU95 4.1 38.0 1.0
CG B:GLU39 4.1 37.6 1.0
CB B:ASP216 4.2 37.4 1.0
CA B:ASN98 4.2 35.9 1.0
CG B:GLU95 4.3 43.9 1.0
OE2 B:GLU95 4.3 51.5 1.0
N B:GLU95 4.3 39.6 1.0
N B:GLY96 4.3 38.2 1.0
CA B:GLY96 4.5 33.1 1.0
OE1 B:GLU39 4.5 47.3 1.0
N B:ILE99 4.5 30.2 1.0
N B:PHE38 4.6 34.2 1.0
CB B:ASN98 4.6 32.1 1.0
C B:GLY96 4.7 36.3 1.0
CA B:ILE99 4.8 27.7 1.0
N B:ARG97 4.8 38.0 1.0
CB B:ALA93 4.8 31.7 1.0
N B:ASN217 4.9 41.2 1.0
CA B:ASP216 5.0 42.7 1.0

Calcium binding site 4 out of 8 in 5z54

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Calcium binding site 4 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:45.4
occ:1.00
 O B:GLY149 2.3 40.6 1.0
O B:LEU147 2.3 43.3 1.0
OD1 B:ASN137 2.3 40.5 1.0
O B:PHE138 2.3 42.7 1.0
OD1 B:ASP175 2.3 45.7 1.0
O B:HOH413 2.3 43.6 1.0
CG B:ASN137 3.4 39.9 1.0
C B:PHE138 3.4 46.3 1.0
C B:GLY149 3.5 40.5 1.0
C B:LEU147 3.5 47.6 1.0
CG B:ASP175 3.6 50.3 1.0
N B:GLY149 3.8 43.3 1.0
C B:ALA148 3.9 40.5 1.0
ND2 B:ASN137 3.9 34.9 1.0
CA B:ALA148 4.1 43.7 1.0
N B:PHE138 4.1 44.6 1.0
C B:ASN137 4.2 41.6 1.0
OD2 B:ASP175 4.2 51.8 1.0
N B:GLY139 4.2 47.0 1.0
N B:ALA148 4.2 41.7 1.0
CA B:GLY149 4.2 38.7 1.0
CA B:GLY139 4.3 51.3 1.0
O B:ALA148 4.4 39.1 1.0
CA B:PHE138 4.4 49.5 1.0
O B:ASN137 4.5 44.4 1.0
N B:PHE150 4.5 42.8 1.0
CB B:ASN137 4.6 36.0 1.0
CA B:LEU147 4.6 44.2 1.0
CA B:ASN137 4.7 37.4 1.0
CB B:ASP175 4.7 41.6 1.0
CB B:LEU147 4.7 40.5 1.0
O B:HOH426 4.7 49.0 1.0
CA B:PHE150 4.8 37.2 1.0
CB B:PHE210 4.8 45.6 1.0
CA B:ASP175 4.9 42.9 1.0
O B:PHE210 5.0 49.5 1.0
O B:GLY212 5.0 37.6 1.0

Calcium binding site 5 out of 8 in 5z54

Go back to Calcium Binding Sites List in 5z54
Calcium binding site 5 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:39.4
occ:1.00
 O C:GLU95 2.3 32.5 1.0
O C:GLY37 2.3 44.3 1.0
OE1 C:GLU95 2.3 47.0 1.0
O C:ASN98 2.3 35.1 1.0
OD1 C:ASP216 2.4 43.6 1.0
OE2 C:GLU39 2.4 47.0 1.0
OD2 C:ASP216 2.5 43.8 1.0
CG C:ASP216 2.8 41.6 1.0
C C:GLY37 3.3 39.7 1.0
C C:GLU95 3.4 45.3 1.0
C C:ASN98 3.5 38.0 1.0
CD C:GLU95 3.5 57.9 1.0
CD C:GLU39 3.6 47.2 1.0
CA C:GLY37 3.7 38.8 1.0
N C:ASN98 3.9 35.8 1.0
CA C:ASN98 4.2 36.4 1.0
CB C:GLU95 4.2 48.3 1.0
CG C:GLU39 4.2 46.6 1.0
CA C:GLU95 4.2 44.7 1.0
CB C:ASP216 4.3 40.5 1.0
OE2 C:GLU95 4.3 60.0 1.0
CG C:GLU95 4.3 50.9 1.0
N C:GLY96 4.4 42.7 1.0
N C:GLU95 4.4 42.0 1.0
N C:PHE38 4.5 34.5 1.0
N C:ILE99 4.5 36.3 1.0
CA C:GLY96 4.6 39.8 1.0
OE1 C:GLU39 4.6 50.2 1.0
CB C:ASN98 4.6 39.2 1.0
CB C:ALA93 4.7 40.7 1.0
C C:GLY96 4.7 35.6 1.0
N C:ARG97 4.7 40.4 1.0
CA C:ILE99 4.8 32.4 1.0
N C:GLU39 4.9 45.8 1.0
C C:PHE38 4.9 44.3 1.0
C C:ARG97 4.9 40.1 1.0
N C:ASN217 4.9 39.6 1.0
CB C:PHE38 4.9 36.9 1.0
CA C:PHE38 5.0 41.5 1.0

Calcium binding site 6 out of 8 in 5z54

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Calcium binding site 6 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:42.4
occ:1.00
 O C:PHE138 2.3 41.9 1.0
OD1 C:ASP175 2.3 44.4 1.0
O C:GLY149 2.3 34.8 1.0
OD1 C:ASN137 2.3 33.8 1.0
O C:HOH437 2.3 41.9 1.0
O C:LEU147 2.3 38.4 1.0
C C:PHE138 3.4 43.7 1.0
C C:GLY149 3.5 39.8 1.0
CG C:ASN137 3.5 36.9 1.0
CG C:ASP175 3.5 42.6 1.0
C C:LEU147 3.6 44.3 1.0
N C:GLY149 3.7 36.7 1.0
C C:ALA148 3.9 34.6 1.0
N C:PHE138 4.1 44.9 1.0
ND2 C:ASN137 4.1 29.0 1.0
C C:ASN137 4.2 38.9 1.0
CA C:ALA148 4.2 39.5 1.0
OD2 C:ASP175 4.2 42.0 1.0
CA C:GLY149 4.2 36.3 1.0
N C:ALA148 4.3 39.1 1.0
N C:GLY139 4.3 40.5 1.0
CA C:PHE138 4.4 44.7 1.0
CA C:GLY139 4.4 39.9 1.0
O C:ALA148 4.5 35.9 1.0
O C:ASN137 4.5 43.3 1.0
N C:PHE150 4.5 40.1 1.0
CB C:ASP175 4.6 34.8 1.0
CA C:LEU147 4.6 38.6 1.0
CB C:ASN137 4.7 30.0 1.0
CA C:ASN137 4.7 34.4 1.0
CB C:LEU147 4.7 37.2 1.0
CA C:PHE150 4.8 38.7 1.0
O C:HOH431 4.8 41.6 1.0
O C:PHE210 4.8 44.3 1.0
CA C:ASP175 4.8 39.5 1.0
CD1 C:PHE138 4.9 54.4 1.0
CB C:PHE210 4.9 38.1 1.0

Calcium binding site 7 out of 8 in 5z54

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Calcium binding site 7 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:49.1
occ:1.00
 OE1 D:GLU95 2.3 54.9 1.0
O D:ASN98 2.3 43.0 1.0
O D:GLY37 2.3 42.4 1.0
OE2 D:GLU39 2.4 64.1 1.0
O D:GLU95 2.4 50.7 1.0
OD1 D:ASP216 2.4 45.1 1.0
OD2 D:ASP216 2.5 57.5 1.0
CG D:ASP216 2.8 47.7 1.0
C D:GLU95 3.3 50.7 1.0
C D:GLY37 3.3 36.7 1.0
CD D:GLU39 3.5 62.7 1.0
C D:ASN98 3.5 49.9 1.0
CD D:GLU95 3.6 59.8 1.0
CA D:GLY37 3.7 35.8 1.0
N D:ASN98 3.9 50.0 1.0
CB D:GLU95 4.0 47.0 1.0
CG D:GLU39 4.0 56.9 1.0
CA D:GLU95 4.1 52.1 1.0
CA D:ASN98 4.2 46.9 1.0
N D:GLY96 4.2 55.6 1.0
CB D:ASP216 4.3 47.4 1.0
N D:GLU95 4.3 51.5 1.0
CG D:GLU95 4.4 56.2 1.0
CA D:GLY96 4.5 45.0 1.0
OE2 D:GLU95 4.5 60.3 1.0
N D:PHE38 4.6 40.2 1.0
OE1 D:GLU39 4.6 57.2 1.0
N D:ARG97 4.6 47.7 1.0
N D:ILE99 4.6 44.6 1.0
CB D:ASN98 4.6 45.8 1.0
C D:GLY96 4.6 44.5 1.0
CB D:ALA93 4.8 48.2 1.0
CA D:ILE99 4.9 41.1 1.0
C D:ARG97 4.9 50.9 1.0
N D:GLU39 4.9 55.5 1.0
C D:PHE38 5.0 50.4 1.0

Calcium binding site 8 out of 8 in 5z54

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Calcium binding site 8 out of 8 in the Crystal Structure of A Cyclase HPIU5 From Fischerella Sp. Atcc 43239 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 HPIU5 From Fischerella Sp. Atcc 43239 in Complex with Cyclo-L-Arg-D-Pro within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:43.4
occ:1.00
 O D:GLY149 2.3 40.5 1.0
O D:PHE138 2.3 50.1 1.0
O D:HOH429 2.3 44.8 1.0
OD1 D:ASN137 2.3 42.5 1.0
OD1 D:ASP175 2.3 54.2 1.0
O D:LEU147 2.4 46.3 1.0
CG D:ASN137 3.4 38.2 1.0
C D:PHE138 3.5 46.8 1.0
C D:GLY149 3.5 46.5 1.0
CG D:ASP175 3.5 55.1 1.0
C D:LEU147 3.6 45.6 1.0
N D:GLY149 3.8 44.7 1.0
C D:ALA148 4.0 45.0 1.0
ND2 D:ASN137 4.0 39.3 1.0
N D:PHE138 4.2 46.1 1.0
OD2 D:ASP175 4.2 56.8 1.0
CA D:ALA148 4.2 48.4 1.0
C D:ASN137 4.2 43.9 1.0
CA D:GLY149 4.2 41.8 1.0
N D:ALA148 4.3 44.6 1.0
N D:GLY139 4.3 49.6 1.0
O D:ASN137 4.4 47.2 1.0
CA D:GLY139 4.4 41.8 1.0
CA D:PHE138 4.4 42.8 1.0
O D:HOH428 4.5 45.5 1.0
N D:PHE150 4.5 45.2 1.0
O D:ALA148 4.6 42.7 1.0
CB D:ASN137 4.6 33.1 1.0
CB D:ASP175 4.6 52.5 1.0
CA D:LEU147 4.7 42.7 1.0
CA D:ASN137 4.7 38.9 1.0
CA D:PHE150 4.7 46.0 1.0
CB D:LEU147 4.7 37.5 1.0
CA D:ASP175 4.8 47.9 1.0
O D:PHE210 4.8 43.8 1.0
CD1 D:PHE138 4.9 45.3 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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