Cobalt in PDB 4q0q: Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribulose

The structure of Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribulose, PDB code: 4q0q 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)	20.45 / 1.93
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.420, 107.420, 118.120, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.6

The binding sites of Cobalt atom in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribulose (pdb code 4q0q). 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 L-Ribulose, PDB code: 4q0q:
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 L-Ribulose


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 L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:31.4 occ:1.00 OE2 A:GLU113 2.1 25.0 1.0 NE2 A:HIS188 2.2 24.2 1.0 NE2 A:HIS108 2.2 27.7 1.0 O2 A:RUU502 2.3 37.0 1.0 O1 A:RUU502 2.3 34.0 1.0 NE2 A:HIS106 2.3 27.3 1.0 CE1 A:HIS188 2.9 23.8 1.0 CD A:GLU113 2.9 25.6 1.0 CD2 A:HIS108 3.1 25.9 1.0 C2 A:RUU502 3.1 37.2 1.0 C1 A:RUU502 3.1 36.5 1.0 OE1 A:GLU113 3.2 28.3 1.0 CE1 A:HIS108 3.2 25.7 1.0 CE1 A:HIS106 3.3 28.8 1.0 CD2 A:HIS106 3.3 27.6 1.0 O5 A:RUU502 3.4 41.9 1.0 CD2 A:HIS188 3.4 21.6 1.0 ND1 A:HIS188 4.1 21.8 1.0 CG A:HIS108 4.2 27.3 1.0 CG A:GLU113 4.3 28.0 1.0 ND1 A:HIS108 4.3 26.7 1.0 CE A:LYS111 4.3 37.0 1.0 CG A:HIS188 4.4 23.4 1.0 ND1 A:HIS106 4.4 29.4 1.0 CG A:HIS106 4.4 27.5 1.0 NZ A:LYS111 4.4 41.4 1.0 C3 A:RUU502 4.5 37.5 1.0 C5 A:RUU502 4.6 39.4 1.0 O3 A:RUU502 4.8 36.0 1.0 OE1 A:GLU204 4.8 40.8 1.0 O4 A:RUU502 5.0 38.8 1.0 OH A:TYR115 5.0 26.9 1.0

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


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 L-Ribulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Co510 b:47.1 occ:1.00 CO A:NCO510 0.0 47.1 1.0 N5 A:NCO510 1.8 48.0 1.0 N1 A:NCO510 1.8 46.6 1.0 N6 A:NCO510 1.8 48.0 1.0 N4 A:NCO510 1.8 49.3 1.0 N2 A:NCO510 1.8 49.2 1.0 N3 A:NCO510 1.8 48.6 1.0 O A:PHE234 3.9 39.6 1.0 OD1 A:ASP233 4.0 47.4 1.0 OD2 A:ASP237 4.1 51.9 1.0 O A:VAL235 4.4 41.7 1.0 CG A:ASP237 4.7 50.4 1.0 OD1 A:ASP237 4.8 53.5 1.0 C A:VAL235 4.9 40.5 1.0 C A:PHE234 5.0 39.3 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