Calcium in PDB 8dzo: Crystal Structure of Human SAR1T39N Mutant

The structure of Crystal Structure of Human SAR1T39N Mutant, PDB code: 8dzo was solved by Q.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.40 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	55.605, 55.605, 222.404, 90, 90, 120
R / Rfree (%)	16 / 19.3

The structure of Crystal Structure of Human SAR1T39N Mutant also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human SAR1T39N Mutant (pdb code 8dzo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Crystal Structure of Human SAR1T39N Mutant, PDB code: 8dzo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in the Crystal Structure of Human SAR1T39N Mutant


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 Human SAR1T39N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:14.8 occ:1.00 O2D A:G4P204 2.3 14.1 1.0 O A:HOH374 2.3 16.2 1.0 O2C A:G4P204 2.3 15.5 1.0 O A:HOH375 2.4 15.4 1.0 PD A:G4P204 3.5 15.6 1.0 PC A:G4P204 3.5 15.6 1.0 O3C A:G4P204 3.5 15.0 1.0 O A:HOH335 4.1 23.3 1.0 O1D A:G4P204 4.4 18.0 1.0 O3D A:G4P204 4.5 16.9 1.0 O A:HOH382 4.5 33.3 1.0 O A:HOH357 4.5 29.4 1.0 O3' A:G4P204 4.5 14.2 1.0 O1C A:G4P204 4.5 16.8 1.0 OD1 A:ASN35 4.6 16.1 1.0 C3' A:G4P204 4.6 15.0 1.0 C5' A:G4P204 4.6 16.5 1.0 C4' A:G4P204 4.7 13.8 1.0 O2A A:G4P204 4.8 17.8 1.0

Calcium binding site 2 out of 5 in the Crystal Structure of Human SAR1T39N Mutant


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 Human SAR1T39N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:15.6 occ:1.00 O1D A:G4P204 2.3 18.0 1.0 O1C A:G4P204 2.3 16.8 1.0 PC A:G4P204 3.4 15.6 1.0 PD A:G4P204 3.4 15.6 1.0 O3C A:G4P204 3.4 15.0 1.0 O A:HOH363 4.3 23.9 1.0 O3D A:G4P204 4.3 16.9 1.0 O A:HOH370 4.4 28.6 1.0 O3' A:G4P204 4.4 14.2 1.0 O2C A:G4P204 4.5 15.5 1.0 O2D A:G4P204 4.5 14.1 1.0

Calcium binding site 3 out of 5 in the Crystal Structure of Human SAR1T39N Mutant


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 Human SAR1T39N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:19.6 occ:1.00 OD2 B:ASP34 2.2 20.3 1.0 O1B B:G4P204 2.3 17.6 1.0 O B:HOH425 2.4 24.2 1.0 O B:HOH332 2.4 20.0 1.0 O B:HOH369 2.5 25.7 1.0 OD2 B:ASP75 2.5 20.4 1.0 OD1 B:ASP75 2.7 16.6 1.0 CG B:ASP75 2.9 18.4 1.0 CG B:ASP34 3.4 23.1 1.0 PB B:G4P204 3.6 14.6 1.0 O2B B:G4P204 3.7 16.2 1.0 O B:HOH368 3.8 30.8 1.0 CB B:ASP34 4.1 15.1 1.0 CA B:ASP34 4.1 17.1 1.0 O B:HOH433 4.2 44.1 1.0 CB B:ASP75 4.4 19.3 1.0 OD1 B:ASP34 4.4 25.6 1.0 N B:ASN35 4.4 11.9 1.0 O B:HOH449 4.5 43.7 1.0 OE1 B:GLN39 4.5 24.3 1.0 O3B B:G4P204 4.5 14.9 1.0 NZ B:LYS38 4.5 14.8 1.0 O B:HOH358 4.6 22.1 1.0 O B:HOH312 4.7 34.0 1.0 O3A B:G4P204 4.7 13.1 1.0 CB B:THR60 4.7 47.0 1.0 O2A B:G4P204 4.7 16.5 1.0 C B:ASP34 4.9 15.3 1.0 OG1 B:THR60 4.9 49.0 1.0

Calcium binding site 4 out of 5 in the Crystal Structure of Human SAR1T39N Mutant


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 Human SAR1T39N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:15.0 occ:1.00 O1D B:G4P204 2.3 15.4 1.0 O B:HOH363 2.3 16.2 1.0 O1C B:G4P204 2.3 14.9 1.0 O B:HOH370 2.4 16.7 1.0 PD B:G4P204 3.5 15.7 1.0 O3C B:G4P204 3.5 15.0 1.0 PC B:G4P204 3.5 15.7 1.0 O B:HOH348 4.2 22.9 1.0 O2D B:G4P204 4.4 17.3 1.0 O B:HOH371 4.5 28.9 1.0 O B:HOH368 4.5 30.8 1.0 O3D B:G4P204 4.5 16.9 1.0 O3' B:G4P204 4.5 14.2 1.0 O2C B:G4P204 4.5 17.3 1.0 OD1 B:ASN35 4.6 15.1 1.0 C3' B:G4P204 4.6 14.7 1.0 C5' B:G4P204 4.6 14.1 1.0 C4' B:G4P204 4.7 12.1 1.0 O2A B:G4P204 4.8 16.5 1.0

Calcium binding site 5 out of 5 in the Crystal Structure of Human SAR1T39N Mutant


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 Human SAR1T39N Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:15.2 occ:1.00 O2D B:G4P204 2.3 17.3 1.0 O2C B:G4P204 2.3 17.3 1.0 PC B:G4P204 3.4 15.7 1.0 O3C B:G4P204 3.4 15.0 1.0 PD B:G4P204 3.4 15.7 1.0 O B:HOH367 4.2 25.7 1.0 O3D B:G4P204 4.3 16.9 1.0 O3' B:G4P204 4.4 14.2 1.0 O B:HOH357 4.5 29.5 1.0 O1C B:G4P204 4.5 14.9 1.0 O1D B:G4P204 4.5 15.4 1.0

Q.Huang, D.M.E.Szebenyi. The Alarmone Ppgpp Selectively Inhibits the Isoform A of the Human Small Gtpase SAR1. Proteins 2022.
ISSN: ESSN 1097-0134
PubMed: 36369712
DOI: 10.1002/PROT.26445