Calcium in PDB 8dq6: Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)

The structure of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1), PDB code: 8dq6 was solved by R.Manjula, J.Basquin, E.Lolis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.53 / 1.56
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	66.737, 66.737, 132.32, 90, 90, 120
R / Rfree (%)	18.2 / 20.7

The binding sites of Calcium atom in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) (pdb code 8dq6). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1), PDB code: 8dq6:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:39.2 occ:1.00 N A:PRO1 3.1 26.0 1.0 N A:ILE65 3.3 28.1 1.0 CD A:PRO1 3.5 30.6 1.0 CA A:PRO1 3.6 26.5 1.0 CG A:PRO1 3.8 38.8 1.0 CB A:ILE65 3.9 30.4 1.0 OG A:SER64 4.0 30.6 1.0 OH B:TYR96 4.0 35.2 1.0 CG1 A:ILE65 4.0 35.1 1.0 CA A:SER64 4.0 24.6 1.0 NZ A:LYS33 4.0 47.3 1.0 CD1 A:ILE65 4.1 40.2 1.0 CE A:LYS33 4.1 44.1 1.0 CA A:ILE65 4.2 29.7 1.0 C A:SER64 4.2 26.7 1.0 CB A:PRO1 4.2 31.0 1.0 O A:ILE65 4.5 35.7 1.0 CB A:SER64 4.6 29.3 1.0 C A:ILE65 4.8 31.4 1.0 O A:ILE63 4.9 25.7 1.0 C A:PRO1 4.9 25.9 1.0

Calcium binding site 2 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:59.9 occ:1.00 N A:GLY71 3.0 27.6 1.0 N A:PRO70 3.4 26.4 1.0 CD A:PRO70 3.4 28.8 1.0 C A:GLY69 3.6 31.5 1.0 CA A:GLY71 3.6 29.4 1.0 CA A:GLY69 3.7 30.2 1.0 CG A:PRO70 3.8 31.2 1.0 C A:PRO70 4.0 26.1 1.0 CA A:PRO70 4.2 26.7 1.0 O A:GLY69 4.2 28.1 1.0 N A:VAL72 4.3 28.6 1.0 C A:GLY71 4.4 35.9 1.0 N A:GLY69 4.5 28.1 1.0 O A:LEU68 4.6 37.3 1.0 CB A:PRO70 4.6 30.3 1.0 C A:LEU68 4.8 31.3 1.0 CG2 A:VAL72 5.0 33.2 1.0

Calcium binding site 3 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:53.5 occ:1.00 N B:ILE65 3.1 27.0 1.0 CA B:CA202 3.4 53.7 1.0 N B:PRO1 3.6 30.7 1.0 CA B:SER64 3.7 32.3 1.0 CA B:PRO1 3.8 26.6 1.0 CD B:PRO1 3.8 36.3 1.0 CB B:PRO1 3.9 32.7 1.0 C B:SER64 3.9 33.4 1.0 CB B:SER64 3.9 33.7 1.0 CG1 B:ILE65 4.0 40.4 1.0 CB B:ILE65 4.0 35.6 1.0 CA B:ILE65 4.1 32.6 1.0 O B:ILE65 4.3 37.0 1.0 CG B:PRO1 4.4 37.1 1.0 C B:ILE65 4.7 31.9 1.0 O B:ILE63 4.7 25.4 1.0 CE2 B:PHE106 4.8 32.2 1.0 CD1 B:ILE65 4.9 40.2 1.0 N B:SER64 4.9 26.7 1.0

Calcium binding site 4 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:53.7 occ:1.00 N B:PRO1 3.1 30.7 1.0 CA B:CA201 3.4 53.5 1.0 CB B:TYR37 3.7 36.4 1.0 O B:TYR37 3.7 31.3 1.0 NH2 C:ARG94 3.8 30.4 1.0 CE2 B:PHE106 3.8 32.2 1.0 CD1 B:TYR37 3.8 51.2 1.0 CD B:PRO1 3.9 36.3 1.0 CD2 B:PHE106 4.0 30.1 1.0 CA B:PRO1 4.1 26.6 1.0 CG B:TYR37 4.2 51.0 1.0 CZ C:ARG94 4.4 29.5 1.0 CA B:TYR37 4.5 35.5 1.0 CG1 B:ILE65 4.5 40.4 1.0 C B:TYR37 4.5 30.7 1.0 NH1 C:ARG94 4.7 28.1 1.0 O B:HOH319 4.8 44.2 1.0 CE1 B:TYR37 4.9 57.7 1.0

Calcium binding site 5 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca201 b:63.0 occ:1.00 O C:HOH342 2.6 40.2 1.0 OG1 C:THR2 3.2 27.0 1.0 C C:PRO1 3.2 26.9 1.0 O C:PRO1 3.3 25.0 1.0 N C:PRO1 3.4 34.0 1.0 CA C:PRO1 3.5 26.2 1.0 N C:THR2 3.7 22.8 1.0 O C:TYR37 3.9 29.7 1.0 CD2 A:TYR96 4.1 25.5 1.0 CE2 A:TYR96 4.1 31.3 1.0 CB C:THR2 4.2 21.7 1.0 CA C:THR2 4.3 22.5 1.0 CG A:TYR96 4.6 26.8 1.0 CZ A:TYR96 4.7 39.9 1.0 CD C:PRO1 4.8 35.4 1.0 CB C:SER64 4.8 39.7 1.0 C C:TYR37 4.8 26.4 1.0 CB C:MET39 4.9 20.2 1.0 N C:MET39 4.9 21.0 1.0 CB C:PRO1 5.0 37.0 1.0

Calcium binding site 6 out of 6 in the Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (MDL1) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca202 b:72.1 occ:1.00 CA C:PRO70 3.6 65.8 1.0 CB C:PRO70 3.7 64.6 1.0 N C:PRO70 4.3 77.5 1.0 O C:GLY69 4.8 79.0 1.0 C C:GLY69 4.8 73.5 1.0 C C:PRO70 4.9 74.7 1.0 CD C:PRO70 4.9 68.4 1.0 CG C:PRO70 4.9 71.1 1.0 N C:GLY71 5.0 73.8 1.0

R.Manjula, J.Basquin, E.Lolis. Structure of A. Thaliana Mif/D-Dt-Like Protein-1 (ATMDL1) To Be Published.