Cobalt in PDB 4gjz: JMJD5 in Complex with 2-Oxoglutarate

All present enzymatic activity of JMJD5 in Complex with 2-Oxoglutarate:
1.14.11.27;

The structure of JMJD5 in Complex with 2-Oxoglutarate, PDB code: 4gjz was solved by P.A.Del Rizzo, R.C.Trievel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.41 / 1.05
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.695, 64.056, 76.801, 90.00, 90.00, 90.00
R / Rfree (%)	14.7 / 16.3

The binding sites of Cobalt atom in the JMJD5 in Complex with 2-Oxoglutarate (pdb code 4gjz). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the JMJD5 in Complex with 2-Oxoglutarate, PDB code: 4gjz:

Cobalt binding site 1 out of 1 in the JMJD5 in Complex with 2-Oxoglutarate


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of JMJD5 in Complex with 2-Oxoglutarate within 5.0Å range: probe atom residue distance (Å) B Occ A:Co501 b:11.0 occ:1.00 OD2 A:ASP323 2.1 8.4 1.0 O2 A:AKG502 2.1 8.3 1.0 O A:HOH601 2.1 9.4 1.0 O5 A:AKG502 2.2 7.9 1.0 NE2 A:HIS400 2.2 7.8 1.0 NE2 A:HIS321 2.2 8.0 1.0 C1 A:AKG502 2.9 7.6 1.0 C2 A:AKG502 2.9 7.7 1.0 CE1 A:HIS400 3.1 7.2 1.0 CE1 A:HIS321 3.1 8.1 1.0 CG A:ASP323 3.1 8.6 1.0 HE1 A:HIS400 3.2 8.7 1.0 CD2 A:HIS321 3.2 7.5 1.0 HE1 A:HIS321 3.2 9.8 1.0 CD2 A:HIS400 3.2 7.0 1.0 HD2 A:HIS321 3.4 9.0 1.0 OD1 A:ASP323 3.4 10.5 1.0 HD2 A:HIS400 3.4 8.4 1.0 HZ2 A:TRP414 3.7 14.4 1.0 O A:HOH625 3.8 13.5 1.0 O1 A:AKG502 4.1 9.3 1.0 HE1 A:TRP414 4.2 12.6 1.0 ND1 A:HIS400 4.2 6.8 1.0 ND1 A:HIS321 4.2 7.7 1.0 O A:HOH627 4.3 13.5 1.0 HD21 A:ASN327 4.3 9.5 1.0 C3 A:AKG502 4.3 7.8 1.0 CG A:HIS400 4.3 6.6 1.0 CG A:HIS321 4.3 7.1 1.0 CB A:ASP323 4.4 8.6 1.0 HB2 A:ASP323 4.5 10.3 1.0 CZ2 A:TRP414 4.5 12.0 1.0 HH2 A:TRP310 4.5 11.1 1.0 H42 A:AKG502 4.8 9.0 1.0 HD22 A:ASN327 4.8 9.5 1.0 H31 A:AKG502 4.8 9.4 1.0 H32 A:AKG502 4.8 9.4 1.0 NE1 A:TRP414 4.8 10.5 1.0 HZ2 A:TRP310 4.8 10.6 1.0 H41 A:AKG502 4.8 9.0 1.0 ND2 A:ASN327 4.9 7.9 1.0 C4 A:AKG502 4.9 7.5 1.0 HD1 A:HIS400 5.0 8.1 1.0 HB3 A:ASP323 5.0 10.3 1.0 CE2 A:TRP414 5.0 10.0 1.0 HD1 A:HIS321 5.0 9.2 1.0 CH2 A:TRP310 5.0 9.2 1.0

P.A.Del Rizzo, S.Krishnan, R.C.Trievel. Crystal Structure and Functional Analysis of JMJD5 Indicate An Alternate Specificity and Function. Mol.Cell.Biol. V. 32 4044 2012.
ISSN: ISSN 0270-7306
PubMed: 22851697
DOI: 10.1128/MCB.00513-12