Calcium in PDB 5dqq: Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana

The structure of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana, PDB code: 5dqq was solved by A.F.Kintzer, R.M.Stroud, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.70 / 2.87
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.180, 154.810, 219.770, 90.00, 90.00, 90.00
R / Rfree (%)	29.7 / 33.9

The structure of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Calcium atom in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana (pdb code 5dqq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana, PDB code: 5dqq:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca801 b:0.7 occ:1.00 O A:HOH908 4.0 95.0 1.0 O A:HOH911 4.1 0.7 1.0 OD2 A:ASP39 4.4 0.5 1.0

Calcium binding site 2 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:0.4 occ:1.00 OE2 A:GLU374 2.9 0.5 1.0 CD A:GLU374 3.9 0.4 1.0 OE1 A:GLU374 4.3 0.1 1.0 O A:GLU374 4.5 0.7 1.0

Calcium binding site 3 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca803 b:57.9 occ:1.00 ND2 A:ASN612 2.7 61.5 1.0 ND2 A:ASN625 3.7 65.5 1.0 O A:LEU609 3.8 0.6 1.0 CG A:ASN612 3.9 84.6 1.0 OD1 A:ASN612 4.4 64.7 1.0 CZ2 A:TRP635 4.4 68.8 1.0 CA A:LEU609 4.5 94.4 1.0 CD2 A:PHE611 4.5 0.9 1.0 C A:LEU609 4.6 0.5 1.0 O A:TYR608 4.6 0.4 1.0 CG A:ASN625 4.8 50.4 1.0

Calcium binding site 4 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca804 b:0.5 occ:1.00 O A:HOH943 2.7 58.9 1.0 O A:ILE455 4.4 0.6 1.0

Calcium binding site 5 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca805 b:1.0 occ:1.00 OD2 A:ASP454 2.6 89.6 1.0 OE1 A:GLU528 3.0 0.5 1.0 O A:HOH932 3.0 76.2 1.0 CG A:ASP454 3.4 91.2 1.0 OD1 A:ASP454 3.5 86.8 1.0 CD A:GLU528 3.8 0.2 1.0 OE2 A:GLU528 3.8 99.6 1.0 CB A:ASP454 4.8 87.8 1.0

Calcium binding site 6 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:0.8 occ:1.00 O A:GLU341 2.3 0.2 1.0 OD2 A:ASP337 2.5 0.1 1.0 OD1 A:ASP337 2.5 0.3 1.0 OD1 A:ASP335 2.6 0.2 1.0 CG A:ASP337 2.8 0.5 1.0 OE1 A:GLN346 3.1 0.7 1.0 OD1 A:ASN339 3.2 0.0 1.0 OD1 A:ASP343 3.3 0.9 1.0 C A:GLU341 3.5 0.5 1.0 ND2 A:ASN339 3.6 0.5 1.0 CA A:ILE342 3.8 0.3 1.0 CG A:ASN339 3.8 0.2 1.0 CG A:ASP335 3.9 0.8 1.0 N A:ILE342 4.0 94.3 1.0 CD A:GLN346 4.1 0.9 1.0 CG A:ASP343 4.2 0.6 1.0 N A:ASP343 4.2 0.9 1.0 CB A:ASP337 4.4 0.5 1.0 C A:ILE342 4.4 0.2 1.0 NE2 A:GLN346 4.5 0.1 1.0 CA A:ASP335 4.5 0.8 1.0 OD2 A:ASP343 4.5 0.4 1.0 CB A:ASP335 4.5 0.6 1.0 CA A:GLU341 4.7 0.4 1.0 N A:GLU341 4.7 0.1 1.0 N A:ASP337 4.7 0.3 1.0 OD2 A:ASP335 4.8 0.8 1.0 CB A:ILE342 4.9 91.8 1.0

Calcium binding site 7 out of 7 in the Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca807 b:0.2 occ:1.00 OE2 A:GLU124 2.4 0.5 1.0 CZ2 A:TRP92 2.8 0.3 1.0 O A:HOH918 2.9 71.9 1.0 NE1 A:TRP92 3.0 0.7 1.0 CE2 A:TRP92 3.1 0.3 1.0 CD A:GLU124 3.4 0.9 1.0 OE1 A:GLU124 3.6 0.6 1.0 OD2 A:ASP170 3.6 0.7 1.0 O A:HOH905 3.6 58.8 1.0 CG A:ASP170 3.8 0.7 1.0 CH2 A:TRP92 4.0 0.6 1.0 OD1 A:ASP170 4.1 0.5 1.0 CD1 A:TRP92 4.3 0.8 1.0 OG A:SER120 4.4 0.7 1.0 CB A:ASP170 4.5 0.8 1.0 CD2 A:TRP92 4.5 0.1 1.0 CG A:GLU124 4.8 0.4 1.0 NH2 A:ARG191 4.9 94.0 1.0 OD2 A:ASP166 5.0 0.8 1.0

A.F.Kintzer, R.M.Stroud. Structure, Inhibition and Regulation of Two-Pore Channel TPC1 From Arabidopsis Thaliana Nature V. 531 258 2016.
ISSN: ESSN 1476-4687