Calcium in PDB 4n2p: Structure of Archease From Pyrococcus Horikoshii

The structure of Structure of Archease From Pyrococcus Horikoshii, PDB code: 4n2p was solved by K.K.Desai, C.A.Bingman, G.N.Phillips Jr, R.T.Raines, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.95 / 1.44
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.219, 55.386, 87.085, 90.00, 91.13, 90.00
R / Rfree (%)	14.3 / 17.9

The binding sites of Calcium atom in the Structure of Archease From Pyrococcus Horikoshii (pdb code 4n2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Structure of Archease From Pyrococcus Horikoshii, PDB code: 4n2p:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Structure of Archease From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Archease From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca201 b:13.8 occ:1.00 OD1 A:ASP142 2.2 15.8 1.0 O B:HOH308 2.3 14.8 1.0 O A:HOH374 2.3 25.0 1.0 O A:ILE143 2.4 12.9 1.0 OD1 A:ASP13 2.4 12.1 1.0 O B:HOH324 2.4 18.8 1.0 H A:ILE143 3.3 11.3 1.0 CG A:ASP13 3.4 13.0 1.0 CG A:ASP142 3.5 15.1 1.0 C A:ILE143 3.5 12.2 1.0 HZ3 A:LYS118 3.6 25.7 1.0 N A:ILE143 3.6 9.4 1.0 OD2 A:ASP13 3.6 15.5 1.0 HA A:ASP142 3.7 12.4 1.0 HD2 A:LYS118 3.9 18.8 1.0 CA A:ILE143 4.2 11.3 1.0 C A:ASP142 4.2 10.1 1.0 O A:HOH326 4.2 20.5 1.0 OD2 A:ASP142 4.2 17.6 1.0 CA A:ASP142 4.3 10.3 1.0 HG13 A:ILE143 4.3 17.1 1.0 OD1 B:ASP142 4.3 16.4 1.0 O A:HOH439 4.4 35.3 1.0 NZ A:LYS118 4.4 21.4 1.0 CB A:ASP142 4.4 11.6 1.0 O A:HOH308 4.5 17.6 1.0 OXT A:ILE143 4.5 15.2 1.0 OD2 B:ASP142 4.5 16.0 1.0 CG B:ASP142 4.6 15.1 1.0 O A:HOH523 4.6 59.9 1.0 HZ1 A:LYS118 4.6 25.7 1.0 HA A:ASP13 4.6 13.5 1.0 CB A:ASP13 4.7 10.9 1.0 O B:HOH394 4.8 21.4 1.0 CD A:LYS118 4.8 15.6 1.0 H A:ASP13 4.8 14.1 1.0 O B:HOH356 4.8 21.6 1.0 HA A:ILE143 4.9 13.6 1.0 HB2 A:ASP142 4.9 13.9 1.0 HZ2 A:LYS118 5.0 25.7 1.0 HG12 A:ILE143 5.0 17.1 1.0 CG1 A:ILE143 5.0 14.2 1.0

Calcium binding site 2 out of 2 in the Structure of Archease From Pyrococcus Horikoshii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Archease From Pyrococcus Horikoshii within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca200 b:14.9 occ:1.00 OD1 C:ASP142 2.2 14.6 1.0 O C:ILE143 2.3 13.2 1.0 O D:HOH318 2.3 18.7 1.0 O C:HOH368 2.4 26.6 1.0 OD1 C:ASP13 2.4 12.2 1.0 O D:HOH339 2.5 22.6 1.0 H C:ILE143 3.3 13.3 1.0 CG C:ASP13 3.4 12.3 1.0 CG C:ASP142 3.5 13.9 1.0 C C:ILE143 3.5 14.3 1.0 N C:ILE143 3.7 11.1 1.0 OD2 C:ASP13 3.7 14.3 1.0 HZ2 C:LYS118 3.7 28.0 1.0 HA C:ASP142 3.7 12.5 1.0 O D:HOH510 3.8 45.7 1.0 HD2 C:LYS118 3.9 22.6 1.0 O C:HOH330 4.1 25.6 1.0 CA C:ILE143 4.2 12.0 1.0 OD2 C:ASP142 4.2 16.5 1.0 C C:ASP142 4.2 10.3 1.0 CA C:ASP142 4.3 10.4 1.0 HG13 C:ILE143 4.3 20.0 1.0 OD1 D:ASP142 4.4 16.4 1.0 OXT C:ILE143 4.4 15.9 1.0 CB C:ASP142 4.4 10.7 1.0 O C:HOH311 4.5 17.9 1.0 OD2 D:ASP142 4.5 16.4 1.0 NZ C:LYS118 4.5 23.3 1.0 O C:HOH422 4.5 40.8 1.0 CG D:ASP142 4.5 14.6 1.0 O D:HOH406 4.6 17.5 1.0 HZ3 C:LYS118 4.6 28.0 1.0 HA C:ASP13 4.7 13.2 1.0 H C:ASP13 4.8 13.2 1.0 CB C:ASP13 4.8 11.5 1.0 CD C:LYS118 4.8 18.8 1.0 HA C:ILE143 4.8 14.4 1.0 HB2 C:ASP142 4.9 12.8 1.0 HB3 D:ASP142 5.0 15.7 1.0

K.K.Desai, C.L.Cheng, C.A.Bingman, G.N.Phillips, R.T.Raines. A Trna Splicing Operon: Archease Endows Rtcb with Dual Gtp/Atp Cofactor Specificity and Accelerates Rna Ligation. Nucleic Acids Res. V. 42 3931 2014.
ISSN: ISSN 0305-1048
PubMed: 24435797
DOI: 10.1093/NAR/GKT1375