Magnesium in PDB 6xyd: Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi

The structure of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi, PDB code: 6xyd was solved by Y.Roske, U.Heinemann, E.D.Andrea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.07 / 1.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.213, 44.771, 68.654, 90.00, 93.40, 90.00
R / Rfree (%)	18.3 / 21.6

The structure of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi (pdb code 6xyd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi, PDB code: 6xyd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:16.5 occ:1.00 O C:SER95 2.2 14.2 1.0 O D:SER95 2.2 14.5 1.0 O B:SER95 2.2 12.7 1.0 O A:SER95 2.2 11.4 1.0 CL A:CL203 2.6 17.2 1.0 C C:SER95 3.3 13.6 1.0 C D:SER95 3.4 12.8 1.0 C A:SER95 3.4 13.2 1.0 C B:SER95 3.4 15.4 1.0 N C:SER95 3.9 10.3 1.0 N A:SER95 3.9 12.7 1.0 N D:SER95 3.9 13.3 1.0 N B:SER95 4.0 11.9 1.0 OG B:SER95 4.1 21.5 0.5 CA C:SER95 4.1 9.6 1.0 CA D:SER95 4.2 11.3 1.0 CA A:SER95 4.2 10.5 1.0 CA B:SER95 4.2 11.4 0.5 CA B:SER95 4.2 12.3 0.5 N C:ASN96 4.2 12.8 1.0 N B:ASN96 4.3 12.1 1.0 N D:ASN96 4.3 11.9 1.0 N A:ASN96 4.3 9.7 1.0 CA C:ASN96 4.3 12.1 1.0 CA D:ASN96 4.4 10.9 1.0 CA B:ASN96 4.4 12.0 1.0 CA A:ASN96 4.4 10.8 1.0 CB C:SER95 4.6 11.7 1.0 CB A:SER95 4.6 12.8 1.0 CB D:SER95 4.6 13.6 1.0 CL A:CL202 4.6 13.4 1.0 CB B:SER95 4.7 10.9 0.5 CB C:ASN96 4.7 11.9 1.0 CB D:ASN96 4.7 12.8 1.0 CB B:ASN96 4.8 10.8 1.0 CB B:SER95 4.8 15.1 0.5 CB A:ASN96 4.8 13.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg201 b:18.1 occ:1.00 O B:SER97 2.2 14.1 1.0 O C:SER97 2.3 14.8 1.0 O A:SER97 2.3 13.7 1.0 O D:SER97 2.4 15.3 1.0 CL A:CL202 2.9 13.4 1.0 C B:SER97 3.4 16.3 1.0 C C:SER97 3.5 16.7 1.0 C A:SER97 3.5 15.7 1.0 C D:SER97 3.5 16.6 1.0 OG A:SER97 4.0 17.5 0.5 OG B:SER97 4.0 21.9 0.5 CL A:CL201 4.1 49.2 1.0 OG D:SER97 4.1 27.6 0.5 N B:SER97 4.1 11.4 1.0 N C:SER97 4.1 11.2 1.0 N D:SER97 4.2 12.1 1.0 N A:SER97 4.2 11.9 1.0 CA B:SER97 4.3 11.8 0.5 CA B:SER97 4.3 11.4 0.5 CA C:SER97 4.3 11.9 0.5 CA C:SER97 4.3 11.7 0.5 CA A:SER97 4.3 11.8 0.5 CA A:SER97 4.3 11.6 0.5 CA D:SER97 4.3 11.9 0.5 CA D:SER97 4.4 11.9 0.5 N B:ILE98 4.4 13.2 1.0 N C:ILE98 4.4 14.0 1.0 N A:ILE98 4.5 13.9 1.0 N D:ILE98 4.5 15.4 1.0 CA B:ILE98 4.6 15.1 1.0 CA C:ILE98 4.6 16.1 1.0 CG2 B:ILE98 4.6 20.8 1.0 CA D:ILE98 4.7 16.9 1.0 CA A:ILE98 4.7 15.0 1.0 CB C:SER97 4.7 16.4 0.5 CB A:SER97 4.7 15.1 0.5 CB C:SER97 4.7 15.5 0.5 CB B:SER97 4.7 14.3 0.5 CG2 C:ILE98 4.7 21.0 1.0 CB B:SER97 4.7 15.7 0.5 CG2 D:ILE98 4.8 21.3 1.0 CB A:SER97 4.8 14.0 0.5 CB D:SER97 4.8 15.4 0.5 CG2 A:ILE98 4.8 20.0 1.0 CB D:SER97 4.8 15.3 0.5

E.Dias D'andrea, Y.Roske, G.A.P.De Oliveira, N.Cremer, A.Diehl, P.Schmieder, U.Heinemann, H.Oschkinat, J.Ricardo Pires. Crystal Structure of Q4D6Q6, A Conserved Kinetoplastid-Specific Protein From Trypanosoma Cruzi. J.Struct.Biol. 07536 2020.
ISSN: ESSN 1095-8657
PubMed: 32473201
DOI: 10.1016/J.JSB.2020.107536