Calcium in PDB 2ff2: Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh

All present enzymatic activity of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh:
3.2.2.1;

The structure of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh, PDB code: 2ff2 was solved by W.Versees, J.Barlow, J.Steyaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.190, 74.390, 73.960, 90.00, 98.38, 90.00
R / Rfree (%)	16.7 / 22.6

The structure of Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh also contains other interesting chemical elements:

Nickel

(Ni)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh (pdb code 2ff2). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh, PDB code: 2ff2:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh


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 Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca601 b:13.2 occ:1.00 O2' A:IMH501 2.3 9.8 1.0 O3' A:IMH501 2.4 13.1 1.0 O A:HOH602 2.4 13.2 1.0 O A:THR137 2.4 19.1 1.0 OD2 A:ASP15 2.4 15.4 1.0 OD2 A:ASP261 2.4 11.1 1.0 OD2 A:ASP10 2.5 13.8 1.0 OD1 A:ASP15 2.6 12.6 1.0 CG A:ASP15 2.8 15.6 1.0 C2' A:IMH501 3.3 11.3 1.0 C3' A:IMH501 3.4 10.2 1.0 CG A:ASP261 3.4 14.8 1.0 CG A:ASP10 3.5 16.7 1.0 C A:THR137 3.5 15.5 1.0 OD1 A:ASP261 3.6 11.7 1.0 OD1 A:ASP10 3.9 16.1 1.0 OD1 A:ASP14 4.0 22.0 1.0 C1' A:IMH501 4.1 13.4 1.0 CB A:ASP15 4.3 15.0 1.0 OD2 A:ASP14 4.3 18.2 1.0 CA A:GLY138 4.3 9.9 1.0 N A:GLY138 4.3 14.1 1.0 CB A:THR137 4.4 19.0 1.0 OD1 A:ASN186 4.4 16.8 1.0 CG A:ASP14 4.5 19.3 1.0 C4' A:IMH501 4.5 12.8 1.0 CA A:THR137 4.6 17.2 1.0 N4' A:IMH501 4.6 15.6 1.0 OG1 A:THR137 4.6 25.0 1.0 OD2 A:ASP40 4.6 21.9 1.0 CB A:ASN12 4.6 11.1 1.0 ND2 A:ASN186 4.6 14.4 1.0 N A:ASP10 4.6 13.5 1.0 CB A:ASP261 4.7 12.7 1.0 N A:ASP15 4.8 13.4 1.0 CA A:ASP15 4.8 14.8 1.0 CB A:ASP10 4.8 13.1 1.0 CB A:ASP40 4.9 12.7 1.0 N A:ASN12 5.0 11.1 1.0 CG A:ASN186 5.0 18.7 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Trypanosoma Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh


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 Vivax Nucleoside Hydrolase Co-Crystallized with Immucillinh within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:11.1 occ:1.00 O3' B:IMH502 2.3 6.1 1.0 OD2 B:ASP261 2.4 14.2 1.0 O B:THR137 2.4 18.1 1.0 O B:HOH603 2.4 6.7 1.0 O2' B:IMH502 2.4 17.5 1.0 OD2 B:ASP15 2.5 14.3 1.0 OD2 B:ASP10 2.6 12.8 1.0 OD1 B:ASP15 2.6 8.3 1.0 CG B:ASP15 2.8 14.2 1.0 C2' B:IMH502 3.3 15.3 1.0 CG B:ASP261 3.4 14.0 1.0 C3' B:IMH502 3.4 16.9 1.0 C B:THR137 3.6 17.9 1.0 OD1 B:ASP261 3.6 13.7 1.0 CG B:ASP10 3.6 12.9 1.0 OD1 B:ASP14 3.9 15.3 1.0 OD1 B:ASP10 4.0 15.3 1.0 C1' B:IMH502 4.2 18.6 1.0 CA B:GLY138 4.2 15.7 1.0 CB B:ASP15 4.3 12.9 1.0 N B:GLY138 4.3 17.3 1.0 OD1 B:ASN186 4.5 15.9 1.0 CB B:THR137 4.5 17.1 1.0 C4' B:IMH502 4.5 17.0 1.0 ND2 B:ASN186 4.6 9.3 1.0 N4' B:IMH502 4.6 18.5 1.0 OD2 B:ASP14 4.6 13.6 1.0 CA B:THR137 4.6 18.4 1.0 CG B:ASP14 4.6 15.6 1.0 OD2 B:ASP40 4.6 15.0 1.0 CB B:ASN12 4.7 10.6 1.0 OG1 B:THR137 4.7 20.6 1.0 CB B:ASP261 4.7 13.1 1.0 N B:ASP10 4.8 12.7 1.0 CA B:ASP15 4.8 12.6 1.0 N B:ASP15 4.9 11.9 1.0 CB B:ASP40 4.9 13.3 1.0 CB B:ASP10 4.9 17.3 1.0 CG B:ASN186 5.0 11.0 1.0

W.Versees, J.Barlow, J.Steyaert. Transition-State Complex of the Purine-Specific Nucleoside Hydrolase of T.Vivax: Enzyme Conformational Changes and Implications For Catalysis. J.Mol.Biol. V. 359 331 2006.
ISSN: ISSN 0022-2836
PubMed: 16630632
DOI: 10.1016/J.JMB.2006.03.026