Cobalt in PDB 3kp0: Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic)

The structure of Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic), PDB code: 3kp0 was solved by K.R.Wolthers, C.W.Levy, N.S.Scrutton, D.Leys, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.11 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.090, 231.950, 124.320, 90.00, 103.24, 90.00
R / Rfree (%)	19.1 / 27

The binding sites of Cobalt atom in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic) (pdb code 3kp0). 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 Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic), PDB code: 3kp0:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic)


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 Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1801 b:41.6 occ:1.00 CO B:B121801 0.0 41.6 1.0 N24 B:B121801 1.9 38.6 1.0 N22 B:B121801 1.9 45.5 1.0 N21 B:B121801 1.9 44.7 1.0 N23 B:B121801 1.9 40.2 1.0 C5' D:5AD1500 2.1 36.5 1.0 NE2 B:HIS618 2.1 37.8 1.0 C19 B:B121801 2.8 41.5 1.0 C4 B:B121801 2.8 44.0 1.0 C6 B:B121801 2.9 43.4 1.0 C14 B:B121801 2.9 42.7 1.0 C9 B:B121801 2.9 42.1 1.0 C1 B:B121801 2.9 42.5 1.0 C11 B:B121801 2.9 37.1 1.0 C16 B:B121801 3.0 44.5 1.0 CE1 B:HIS618 3.1 33.3 1.0 CD2 B:HIS618 3.1 39.9 1.0 C4' D:5AD1500 3.2 38.4 1.0 C5 B:B121801 3.2 47.6 1.0 C10 B:B121801 3.3 41.2 1.0 C15 B:B121801 3.4 46.1 1.0 O4' D:5AD1500 3.9 46.5 1.0 C20 B:B121801 3.9 36.4 1.0 C2 B:B121801 4.0 42.5 1.0 C3 B:B121801 4.1 42.8 1.0 C18 B:B121801 4.1 42.3 1.0 C13 B:B121801 4.1 34.2 1.0 C7 B:B121801 4.2 42.0 1.0 C17 B:B121801 4.2 40.6 1.0 C8 B:B121801 4.2 39.0 1.0 ND1 B:HIS618 4.2 34.9 1.0 CG B:HIS618 4.3 39.0 1.0 C12 B:B121801 4.3 38.0 1.0 C26 B:B121801 4.5 44.2 1.0 C3' D:5AD1500 4.6 33.1 1.0 C35 B:B121801 4.7 47.0 1.0 C48 B:B121801 4.7 31.6 1.0 C37 B:B121801 4.8 46.4 1.0 C53 B:B121801 4.8 38.6 1.0 C54 B:B121801 4.9 35.0 1.0 C41 B:B121801 4.9 39.3 1.0 O3' D:5AD1500 5.0 41.3 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic)


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 Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Dab) (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1801 b:42.3 occ:1.00 CO C:B121801 0.0 42.3 1.0 N24 C:B121801 1.9 38.9 1.0 N22 C:B121801 1.9 46.3 1.0 N21 C:B121801 1.9 45.2 1.0 N23 C:B121801 1.9 44.5 1.0 C5' A:5AD1500 2.1 37.2 1.0 NE2 C:HIS618 2.1 43.4 1.0 C19 C:B121801 2.8 38.0 1.0 C4 C:B121801 2.8 36.6 1.0 C14 C:B121801 2.9 43.2 1.0 C1 C:B121801 2.9 45.2 1.0 C6 C:B121801 2.9 42.2 1.0 C9 C:B121801 2.9 42.7 1.0 C11 C:B121801 2.9 41.5 1.0 C16 C:B121801 3.0 41.2 1.0 CE1 C:HIS618 3.0 40.8 1.0 C4' A:5AD1500 3.2 37.3 1.0 CD2 C:HIS618 3.2 42.1 1.0 C5 C:B121801 3.3 40.0 1.0 C10 C:B121801 3.3 39.0 1.0 C15 C:B121801 3.3 43.3 1.0 O4' A:5AD1500 3.7 36.9 1.0 C20 C:B121801 3.9 39.0 1.0 C2 C:B121801 4.0 45.7 1.0 C13 C:B121801 4.1 40.7 1.0 C3 C:B121801 4.1 39.1 1.0 C18 C:B121801 4.1 44.1 1.0 C7 C:B121801 4.1 40.1 1.0 ND1 C:HIS618 4.1 44.7 1.0 C8 C:B121801 4.2 42.1 1.0 C17 C:B121801 4.2 40.0 1.0 CG C:HIS618 4.3 38.7 1.0 C12 C:B121801 4.3 42.8 1.0 C26 C:B121801 4.5 46.4 1.0 C3' A:5AD1500 4.6 41.9 1.0 C48 C:B121801 4.7 44.7 1.0 C35 C:B121801 4.7 43.0 1.0 C37 C:B121801 4.7 42.9 1.0 C53 C:B121801 4.8 51.4 1.0

K.R.Wolthers, C.Levy, N.S.Scrutton, D.Leys. Large-Scale Domain Dynamics and Adenosylcobalamin Reorientation Orchestrate Radical Catalysis in Ornithine 4,5-Aminomutase. J.Biol.Chem. V. 285 13942 2010.
ISSN: ISSN 0021-9258
PubMed: 20106986
DOI: 10.1074/JBC.M109.068908