Calcium in PDB 8dzt: Crystal Structure of Human SAR1AH79G Mutant

The structure of Crystal Structure of Human SAR1AH79G Mutant, PDB code: 8dzt was solved by Q.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.48 / 1.80
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	55.718, 55.718, 222.972, 90, 90, 120
R / Rfree (%)	15.2 / 18.9

The structure of Crystal Structure of Human SAR1AH79G Mutant also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Human SAR1AH79G Mutant (pdb code 8dzt). 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 Human SAR1AH79G Mutant, PDB code: 8dzt:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human SAR1AH79G 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 SAR1AH79G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:10.7 occ:1.00 O2D A:G4P204 2.3 7.1 1.0 O2C A:G4P204 2.3 8.2 1.0 O A:HOH393 2.4 12.9 1.0 O A:HOH360 2.4 8.0 1.0 PD A:G4P204 3.4 9.4 1.0 PC A:G4P204 3.4 9.7 1.0 O3C A:G4P204 3.5 7.5 1.0 O A:HOH342 4.1 18.4 1.0 O1D A:G4P204 4.4 12.3 1.0 O A:HOH382 4.4 23.1 1.0 O3D A:G4P204 4.5 11.1 1.0 O3' A:G4P204 4.5 10.9 1.0 O1C A:G4P204 4.5 11.4 1.0 C3' A:G4P204 4.6 9.4 1.0 O A:HOH379 4.6 23.8 1.0 C5' A:G4P204 4.7 9.6 1.0 OD1 A:ASN35 4.7 12.3 1.0 C4' A:G4P204 4.7 8.3 1.0 O2A A:G4P204 4.8 9.9 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human SAR1AH79G 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 SAR1AH79G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:10.7 occ:1.00 O1C A:G4P204 2.3 11.4 1.0 O1D A:G4P204 2.3 12.3 1.0 PC A:G4P204 3.4 9.7 1.0 O3C A:G4P204 3.4 7.5 1.0 PD A:G4P204 3.4 9.4 1.0 O A:HOH419 3.9 26.6 1.0 O3D A:G4P204 4.3 11.1 1.0 O3' A:G4P204 4.4 10.9 1.0 O2C A:G4P204 4.5 8.2 1.0 O2D A:G4P204 4.5 7.1 1.0 O A:HOH392 4.5 24.1 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human SAR1AH79G 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 SAR1AH79G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:11.0 occ:1.00 O2C B:G4P204 2.3 12.1 1.0 O1D B:G4P204 2.3 11.6 1.0 PC B:G4P204 3.4 9.3 1.0 O3C B:G4P204 3.4 8.2 1.0 PD B:G4P204 3.5 10.2 1.0 O B:HOH426 4.0 28.9 1.0 O2D B:G4P204 4.3 10.5 1.0 O3' B:G4P204 4.4 10.9 1.0 O1C B:G4P204 4.5 8.0 1.0 O B:HOH394 4.5 24.2 1.0 O3D B:G4P204 4.6 8.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human SAR1AH79G 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 SAR1AH79G Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:10.6 occ:1.00 O3D B:G4P204 2.3 8.4 1.0 O1C B:G4P204 2.3 8.0 1.0 O B:HOH357 2.4 8.9 1.0 O B:HOH391 2.4 12.8 1.0 PD B:G4P204 3.4 10.2 1.0 PC B:G4P204 3.4 9.3 1.0 O3C B:G4P204 3.4 8.2 1.0 O B:HOH348 4.1 20.1 1.0 O1D B:G4P204 4.4 11.6 1.0 O B:HOH320 4.4 20.8 1.0 O2D B:G4P204 4.5 10.5 1.0 O3' B:G4P204 4.5 10.9 1.0 O2C B:G4P204 4.5 12.1 1.0 O B:HOH378 4.6 23.7 1.0 C3' B:G4P204 4.6 11.3 1.0 C5' B:G4P204 4.7 8.8 1.0 OD1 B:ASN35 4.7 11.1 1.0 C4' B:G4P204 4.7 9.3 1.0 O1A B:G4P204 4.8 8.9 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