Calcium in PDB 3h9d: Crystal Structure of Trypanosoma Brucei ATG8

The structure of Crystal Structure of Trypanosoma Brucei ATG8, PDB code: 3h9d was solved by R.Koopmann, K.Muhammad, M.Perbandt, C.Betzel, M.Duszenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.100, 48.600, 127.920, 90.00, 90.00, 90.00
R / Rfree (%)	23.4 / 31

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Brucei ATG8 (pdb code 3h9d). 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 Trypanosoma Brucei ATG8, PDB code: 3h9d:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Trypanosoma Brucei ATG8


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 Trypanosoma Brucei ATG8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca119 b:29.9 occ:1.00 N A:ASP47 3.6 28.1 1.0 O A:HOH125 3.8 18.1 1.0 CD A:ARG48 3.9 36.2 1.0 CB A:ASP47 4.0 28.0 1.0 NH1 A:ARG48 4.1 38.7 1.0 N A:ARG48 4.1 31.8 1.0 CD2 A:LEU46 4.2 21.2 1.0 CA A:LEU46 4.3 27.2 1.0 O A:HOH152 4.3 29.9 1.0 CB A:LEU46 4.3 26.0 1.0 CA A:ASP47 4.4 28.8 1.0 C A:LEU46 4.4 27.5 1.0 CG A:ASP47 4.6 27.7 1.0 OD2 A:ASP47 4.6 27.7 1.0 CG A:ARG48 4.7 34.1 1.0 CB A:ARG48 4.8 32.7 1.0 C A:ASP47 4.8 30.6 1.0 CG A:LEU46 4.9 23.1 1.0 NE A:ARG48 4.9 36.0 1.0 O A:ARG48 4.9 32.3 1.0 CZ A:ARG48 5.0 37.6 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Trypanosoma Brucei ATG8


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 Trypanosoma Brucei ATG8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca119 b:52.5 occ:1.00 O B:HOH131 3.7 14.7 1.0 OE1 B:GLN92 3.9 15.4 1.0 O B:HOH133 4.0 28.1 1.0 CG B:GLN92 4.0 12.9 1.0 CG A:PHE13 4.1 24.7 1.0 CD B:GLN92 4.1 12.6 1.0 CB A:PHE13 4.2 24.6 1.0 CD2 A:PHE13 4.2 26.7 1.0 CB B:GLN92 4.4 16.0 1.0 O B:HOH139 4.4 16.7 1.0 O B:HOH148 4.4 34.5 1.0 CD1 A:PHE13 4.5 26.9 1.0 CB B:ALA94 4.5 19.2 1.0 O B:SER55 4.7 26.0 1.0 CA B:ASP56 4.7 24.9 1.0 CE2 A:PHE13 4.8 30.8 1.0 NE2 B:GLN92 5.0 7.2 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Trypanosoma Brucei ATG8


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 Trypanosoma Brucei ATG8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca120 b:27.2 occ:1.00 N B:ASP47 3.6 28.7 1.0 CB B:ARG48 3.7 25.5 1.0 NE B:ARG48 3.7 22.0 1.0 CD2 B:LEU46 3.9 28.3 1.0 NH2 B:ARG69 3.9 19.3 1.0 NE B:ARG69 4.0 24.7 1.0 NH2 B:ARG48 4.0 21.9 1.0 CB B:ASP47 4.1 28.5 1.0 O B:HOH175 4.1 27.6 1.0 CZ B:ARG48 4.4 21.7 1.0 CA B:LEU46 4.4 29.1 1.0 CA B:ASP47 4.4 28.0 1.0 CZ B:ARG69 4.4 18.5 1.0 C B:LEU46 4.5 28.4 1.0 CG B:ARG48 4.5 23.0 1.0 OD2 B:ASP47 4.6 34.6 1.0 CD B:ARG48 4.8 20.5 1.0 O B:HOH197 4.8 38.5 1.0 N B:LEU46 4.8 30.8 1.0 CG B:ASP47 4.8 29.9 1.0 CA B:ARG48 4.8 24.3 1.0 O B:ARG48 4.9 20.9 1.0 O B:ARG69 5.0 31.5 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Trypanosoma Brucei ATG8


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 Trypanosoma Brucei ATG8 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca121 b:27.5 occ:1.00 N B:ASP29 3.5 34.1 1.0 CB B:ASP29 3.7 34.7 1.0 CA B:HIS27 3.8 38.0 1.0 CB B:HIS27 3.8 37.7 1.0 C B:HIS27 3.8 37.9 1.0 CD B:PRO28 3.8 38.2 1.0 N B:PRO28 3.9 37.4 1.0 CA B:ASP29 4.0 33.1 1.0 CG B:ARG30 4.0 25.4 1.0 ND1 B:HIS27 4.1 38.4 1.0 C B:ASP29 4.2 32.2 1.0 N B:ARG30 4.3 30.1 1.0 NE B:ARG30 4.3 21.0 1.0 CD B:ARG30 4.3 23.9 1.0 CG B:HIS27 4.5 36.1 1.0 O B:HIS27 4.5 37.0 1.0 C B:PRO28 4.6 34.8 1.0 CB B:ARG30 4.6 27.0 1.0 CG B:ASP29 4.7 39.8 1.0 CA B:PRO28 4.8 36.0 1.0 O B:ASP29 4.8 32.9 1.0

R.Koopmann, K.Muhammad, M.Perbandt, C.Betzel, M.Duszenko. Trypanosoma Brucei ATG8: Structural Insights Into Autophagic-Like Mechanisms in Protozoa. Autophagy V. 5 1085 2009.
ISSN: ISSN 1554-8627
PubMed: 19736525