Cobalt in PDB 4q0p: Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribose

The structure of Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribose, PDB code: 4q0p 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)	20.49 / 1.93
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	95.380, 107.930, 119.410, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 24.2

The binding sites of Cobalt atom in the Crystal Structure of Acinetobacter Sp. DL28 L-Ribose Isomerase in Complex with L-Ribose (pdb code 4q0p). 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-Ribose, PDB code: 4q0p:
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-Ribose


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:31.5 occ:1.00 OE2 A:GLU113 2.1 23.6 1.0 NE2 A:HIS188 2.2 24.7 1.0 NE2 A:HIS108 2.2 26.3 1.0 O A:HOH601 2.2 23.5 1.0 NE2 A:HIS106 2.3 25.8 1.0 O5 A:0MK502 2.4 49.0 1.0 CD A:GLU113 2.9 25.9 1.0 CE1 A:HIS188 3.0 24.6 1.0 OE1 A:GLU113 3.1 26.5 1.0 CD2 A:HIS108 3.1 24.9 1.0 CD2 A:HIS106 3.2 26.6 1.0 CE1 A:HIS108 3.2 26.5 1.0 C1 A:0MK502 3.2 51.5 1.0 CD2 A:HIS188 3.2 24.4 1.0 CE1 A:HIS106 3.2 27.6 1.0 C5 A:0MK502 3.6 51.7 1.0 O1 A:0MK502 3.9 49.8 1.0 ND1 A:HIS188 4.2 24.6 1.0 CG A:GLU113 4.3 24.0 1.0 ND1 A:HIS108 4.3 27.0 1.0 CG A:HIS188 4.3 24.5 1.0 CG A:HIS108 4.3 26.6 1.0 ND1 A:HIS106 4.3 28.0 1.0 CG A:HIS106 4.3 25.9 1.0 C2 A:0MK502 4.5 51.6 1.0 O2 A:0MK502 4.6 50.3 1.0 CE A:LYS111 4.7 32.8 1.0 C4 A:0MK502 4.8 52.2 1.0 OH A:TYR115 4.9 25.3 1.0 O4 A:0MK502 5.0 53.7 1.0

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


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-Ribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Co506 b:56.1 occ:1.00 CO A:NCO506 0.0 56.1 1.0 N5 A:NCO506 1.8 57.4 1.0 N2 A:NCO506 1.8 57.0 1.0 N1 A:NCO506 1.8 56.2 1.0 N6 A:NCO506 1.8 55.8 1.0 N4 A:NCO506 1.8 57.0 1.0 N3 A:NCO506 1.8 56.2 1.0 O A:PHE234 3.9 44.0 1.0 OD1 A:ASP233 4.1 55.7 1.0 OD2 A:ASP237 4.2 60.5 1.0 O A:VAL235 4.5 45.7 1.0 CG A:ASP237 4.8 60.6 1.0 CG A:ASP233 5.0 53.4 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