Cobalt in PDB 4q0s: Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol

The structure of Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol, PDB code: 4q0s was solved by H.Yoshida, A.Yoshihara, M.Teraoka, K.Izumori, S.Kamitori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.31 / 1.93
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	96.320, 106.360, 118.680, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 23.3

The binding sites of Cobalt atom in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol (pdb code 4q0s). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol, PDB code: 4q0s:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:34.3 occ:1.00 OE2 A:GLU113 1.9 27.0 1.0 O4 A:RB0502 2.1 44.6 1.0 NE2 A:HIS108 2.2 30.3 1.0 O5 A:RB0502 2.2 37.8 1.0 NE2 A:HIS106 2.3 28.0 1.0 NE2 A:HIS188 2.3 25.4 1.0 C4 A:RB0502 2.8 46.5 1.0 C5 A:RB0502 2.9 45.4 1.0 CD A:GLU113 2.9 25.7 1.0 CD2 A:HIS108 3.0 29.3 1.0 CE1 A:HIS188 3.1 25.6 1.0 OE1 A:GLU113 3.2 27.2 1.0 CE1 A:HIS108 3.2 27.5 1.0 CE1 A:HIS106 3.2 29.4 1.0 CD2 A:HIS106 3.3 28.1 1.0 CD2 A:HIS188 3.4 24.4 1.0 C3 A:RB0502 4.2 49.2 1.0 CG A:HIS108 4.2 30.2 1.0 CG A:GLU113 4.3 25.8 1.0 ND1 A:HIS108 4.3 29.6 1.0 ND1 A:HIS188 4.3 23.9 1.0 ND1 A:HIS106 4.3 29.8 1.0 CG A:HIS106 4.4 27.1 1.0 CE A:LYS111 4.4 33.1 1.0 O2 A:RB0502 4.5 52.0 1.0 CG A:HIS188 4.5 25.4 1.0 NZ A:LYS111 4.6 35.2 1.0 C2 A:RB0502 4.7 51.8 1.0 C1 A:RB0502 4.8 52.0 1.0 OH A:TYR115 5.0 25.9 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with Ribitol within 5.0Å range: probe atom residue distance (Å) B Occ A:Co504 b:45.1 occ:1.00 CO A:NCO504 0.0 45.1 1.0 N2 A:NCO504 1.8 47.4 1.0 N1 A:NCO504 1.8 47.1 1.0 N5 A:NCO504 1.8 45.2 1.0 N6 A:NCO504 1.8 46.7 1.0 N4 A:NCO504 1.8 46.6 1.0 N3 A:NCO504 1.8 47.0 1.0 O A:PHE234 3.8 43.3 1.0 OD1 A:ASP233 3.8 47.2 1.0 OD2 A:ASP237 4.0 58.5 1.0 CG A:ASP237 4.6 58.2 1.0 OD1 A:ASP237 4.6 58.5 1.0 O A:VAL235 4.6 46.3 1.0 CG A:ASP233 4.9 48.3 1.0 C A:PHE234 5.0 42.6 1.0

H.Yoshida, A.Yoshihara, M.Teraoka, Y.Terami, G.Takata, K.Izumori, S.Kamitori. X-Ray Structure of A Novel L-Ribose Isomerase Acting on A Non-Natural Sugar L-Ribose As Its Ideal Substrate Febs J. 2014.
ISSN: ISSN 1742-464X
PubMed: 24846739
DOI: 10.1111/FEBS.12850