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Calcium in PDB 6sir: Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp

Protein crystallography data

The structure of Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp, PDB code: 6sir was solved by A.Butryn, A.M.Orville, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.95 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.650, 95.170, 138.660, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 20.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp (pdb code 6sir). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp, PDB code: 6sir:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 6sir

Go back to Calcium Binding Sites List in 6sir
Calcium binding site 1 out of 4 in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp


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 the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:22.7
occ:1.00
 OD2 A:ASP457 2.2 26.4 1.0
O2B A:GTP703 2.3 23.2 1.0
O A:ILE458 2.3 24.5 1.0
O1A A:GTP703 2.3 27.4 1.0
OD2 A:ASP501 2.3 25.2 1.0
O2G A:GTP703 2.4 28.1 1.0
CG A:ASP457 3.4 30.2 1.0
C A:ILE458 3.4 21.9 1.0
PB A:GTP703 3.4 26.5 1.0
PA A:GTP703 3.5 30.9 1.0
CG A:ASP501 3.5 21.8 1.0
O3A A:GTP703 3.7 27.1 1.0
PG A:GTP703 3.7 25.1 1.0
O A:HOH806 3.9 31.9 1.0
O3B A:GTP703 3.9 24.6 1.0
N A:ILE458 3.9 18.5 1.0
OD1 A:ASP501 4.0 25.6 1.0
CB A:ASP457 4.0 20.8 1.0
CB A:PHE461 4.1 19.0 1.0
NH1 A:ARG545 4.2 24.1 1.0
O A:HOH913 4.2 43.7 1.0
CA A:ILE458 4.2 18.9 1.0
O5' A:GTP703 4.3 30.9 1.0
OD1 A:ASP457 4.3 26.7 1.0
N A:THR459 4.4 21.3 1.0
C A:ASP457 4.4 18.2 1.0
O3G A:GTP703 4.5 27.0 1.0
CA A:THR459 4.5 26.2 1.0
N A:PHE461 4.5 22.3 1.0
CB A:ASP501 4.7 17.9 1.0
O2A A:GTP703 4.7 32.9 1.0
O1B A:GTP703 4.7 26.2 1.0
N A:ASN460 4.7 24.6 1.0
C5' A:GTP703 4.7 25.9 1.0
O1G A:GTP703 4.8 28.1 1.0
CB A:ILE458 4.8 21.3 1.0
C A:THR459 4.8 25.6 1.0
CA A:ASP457 4.9 16.9 1.0

Calcium binding site 2 out of 4 in 6sir

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Calcium binding site 2 out of 4 in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp


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 the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:21.9
occ:1.00
 OD2 B:ASP457 2.2 28.2 1.0
O B:ILE458 2.3 25.0 1.0
O1A B:GTP702 2.3 37.0 1.0
O2G B:GTP702 2.3 26.9 1.0
O2B B:GTP702 2.3 27.8 1.0
OD2 B:ASP501 2.4 33.9 1.0
CG B:ASP457 3.4 32.4 1.0
C B:ILE458 3.4 22.8 1.0
PB B:GTP702 3.5 27.9 1.0
PA B:GTP702 3.5 39.9 1.0
CG B:ASP501 3.6 25.5 1.0
PG B:GTP702 3.7 27.4 1.0
O3A B:GTP702 3.7 30.7 1.0
O B:HOH913 3.8 44.8 1.0
O3B B:GTP702 3.9 26.8 1.0
N B:ILE458 4.0 18.9 1.0
O B:HOH807 4.0 30.9 1.0
CB B:PHE461 4.1 22.7 1.0
OD1 B:ASP501 4.1 31.1 1.0
CB B:ASP457 4.1 25.6 1.0
NH1 B:ARG545 4.1 25.8 1.0
OD1 B:ASP457 4.3 34.0 1.0
CA B:ILE458 4.3 21.7 1.0
O5' B:GTP702 4.4 41.8 1.0
N B:THR459 4.4 22.6 1.0
CA B:THR459 4.4 23.7 1.0
O3G B:GTP702 4.5 28.8 1.0
C B:ASP457 4.5 22.3 1.0
N B:PHE461 4.5 20.9 1.0
O1G B:GTP702 4.7 26.6 1.0
O2A B:GTP702 4.7 40.1 1.0
CB B:ASP501 4.7 25.1 1.0
C B:THR459 4.8 27.5 1.0
N B:ASN460 4.8 25.6 1.0
O1B B:GTP702 4.8 30.1 1.0
C5' B:GTP702 4.8 41.6 1.0
CA B:ASP457 4.9 22.4 1.0
CB B:ILE458 4.9 24.8 1.0
CA B:PHE461 5.0 19.0 1.0

Calcium binding site 3 out of 4 in 6sir

Go back to Calcium Binding Sites List in 6sir
Calcium binding site 3 out of 4 in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp


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 the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:26.3
occ:1.00
 OD2 D:ASP457 2.1 37.7 1.0
O2B D:GTP702 2.2 31.6 1.0
OD2 D:ASP501 2.3 37.5 1.0
O2G D:GTP702 2.4 28.2 1.0
O1A D:GTP702 2.4 41.1 1.0
O D:ILE458 2.4 28.2 1.0
CG D:ASP457 3.3 33.8 1.0
PB D:GTP702 3.5 31.1 1.0
CG D:ASP501 3.5 28.3 1.0
C D:ILE458 3.6 26.7 1.0
PA D:GTP702 3.6 41.3 1.0
O3A D:GTP702 3.7 42.2 1.0
PG D:GTP702 3.7 29.1 1.0
O D:HOH801 3.9 40.4 1.0
O3B D:GTP702 3.9 34.9 1.0
CB D:ASP457 4.0 24.7 1.0
N D:ILE458 4.0 21.7 1.0
CB D:PHE461 4.0 21.2 1.0
OD1 D:ASP501 4.1 34.2 1.0
NH1 D:ARG545 4.1 33.3 1.0
OD1 D:ASP457 4.3 35.7 1.0
CA D:ILE458 4.4 23.5 1.0
O5' D:GTP702 4.4 49.1 1.0
N D:THR459 4.5 24.4 1.0
CA D:THR459 4.5 27.1 1.0
C D:ASP457 4.5 25.4 1.0
O3G D:GTP702 4.5 32.3 1.0
N D:PHE461 4.6 20.0 1.0
CB D:ASP501 4.7 25.2 1.0
O1B D:GTP702 4.7 31.4 1.0
C5' D:GTP702 4.7 44.5 1.0
O1G D:GTP702 4.8 29.7 1.0
O2A D:GTP702 4.8 53.3 1.0
N D:ASN460 4.8 24.3 1.0
CA D:ASP457 4.8 22.9 1.0
C D:THR459 4.9 23.3 1.0
CA D:PHE461 5.0 20.5 1.0
CB D:ILE458 5.0 24.2 1.0

Calcium binding site 4 out of 4 in 6sir

Go back to Calcium Binding Sites List in 6sir
Calcium binding site 4 out of 4 in the Crystal Structure of the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp


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 the Guanylate Cyclase Domain of Rhgc From Catenaria Anguillulae in Complex with Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:28.3
occ:1.00
 O2B C:GTP702 2.2 37.6 1.0
OD2 C:ASP457 2.3 32.3 1.0
O1A C:GTP702 2.3 51.9 1.0
OD2 C:ASP501 2.4 28.0 1.0
O C:ILE458 2.4 25.5 1.0
O2G C:GTP702 2.5 49.8 1.0
CG C:ASP457 3.4 32.1 1.0
PA C:GTP702 3.4 44.3 1.0
PB C:GTP702 3.5 34.1 1.0
CG C:ASP501 3.5 25.2 1.0
C C:ILE458 3.6 23.2 1.0
O3A C:GTP702 3.6 44.4 1.0
O C:HOH879 3.8 37.0 1.0
CB C:PHE461 3.8 24.3 1.0
PG C:GTP702 3.9 44.4 1.0
CB C:ASP457 4.0 17.1 1.0
N C:ILE458 4.0 18.3 1.0
O3B C:GTP702 4.0 32.1 1.0
OD1 C:ASP501 4.0 31.3 1.0
O5' C:GTP702 4.1 48.0 1.0
NH1 C:ARG545 4.2 38.5 1.0
CA C:ILE458 4.4 19.0 1.0
O C:HOH913 4.4 48.6 1.0
OD1 C:ASP457 4.4 31.0 1.0
N C:PHE461 4.4 21.2 1.0
C C:ASP457 4.5 18.6 1.0
N C:THR459 4.6 22.3 1.0
C5' C:GTP702 4.7 39.8 1.0
O1B C:GTP702 4.7 40.4 1.0
CA C:THR459 4.7 25.1 1.0
O2A C:GTP702 4.7 48.4 1.0
CB C:ASP501 4.8 23.5 1.0
O3G C:GTP702 4.8 38.9 1.0
CA C:PHE461 4.8 23.3 1.0
O1G C:GTP702 4.8 31.5 1.0
CA C:ASP457 4.8 19.2 1.0
CG C:PHE461 4.9 21.9 1.0
N C:ASN460 4.9 27.6 1.0
CB C:ILE458 4.9 21.1 1.0
C C:THR459 5.0 29.1 1.0

Reference:

A.Butryn, H.Raza, H.Rada, I.Moraes, R.J.Owens, A.M.Orville. Molecular Basis For Gtp Recognition By Light-Activated Guanylate Cyclase Rhgc. Febs J. 2019.
ISSN: ISSN 1742-464X
PubMed: 31808997
DOI: 10.1111/FEBS.15167
Page generated: Tue Jul 16 14:48:00 2024

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