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

The structure of Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic), PDB code: 3kox 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)	64.23 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.960, 231.690, 123.890, 90.00, 103.16, 90.00
R / Rfree (%)	19 / 25.7

The binding sites of Cobalt atom in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic) (pdb code 3kox). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic), PDB code: 3kox:
Jump to Cobalt binding site number: 1; 2; 3; 4;

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


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1801 b:46.6 occ:1.00 CO A:B121801 0.0 46.6 1.0 N24 A:B121801 1.9 46.9 1.0 N21 A:B121801 1.9 47.7 1.0 N22 A:B121801 1.9 47.7 1.0 N23 A:B121801 1.9 44.9 1.0 NE2 A:HIS618 2.2 43.7 1.0 C19 A:B121801 2.7 45.3 1.0 C5' C:5AD1500 2.8 55.1 1.0 C1 A:B121801 2.8 45.7 1.0 C4 A:B121801 2.9 49.0 1.0 C14 A:B121801 2.9 43.8 1.0 C9 A:B121801 3.0 48.4 1.0 C6 A:B121801 3.0 48.5 1.0 C11 A:B121801 3.0 44.2 1.0 C16 A:B121801 3.0 44.8 1.0 CE1 A:HIS618 3.1 44.0 1.0 CD2 A:HIS618 3.2 43.3 1.0 C5 A:B121801 3.3 49.4 1.0 C4' C:5AD1500 3.3 54.3 1.0 C10 A:B121801 3.4 47.0 1.0 C15 A:B121801 3.4 44.6 1.0 C20 A:B121801 3.7 43.4 1.0 O4' C:5AD1500 3.8 54.6 1.0 C2 A:B121801 4.0 47.5 1.0 C18 A:B121801 4.1 44.8 1.0 C3 A:B121801 4.1 48.7 1.0 C13 A:B121801 4.1 41.2 1.0 ND1 A:HIS618 4.2 42.8 1.0 C17 A:B121801 4.2 43.9 1.0 C8 A:B121801 4.3 48.9 1.0 C7 A:B121801 4.3 49.8 1.0 CG A:HIS618 4.3 41.7 1.0 C12 A:B121801 4.4 42.7 1.0 C26 A:B121801 4.5 48.0 1.0 C48 A:B121801 4.7 38.6 1.0 C3' C:5AD1500 4.8 55.0 1.0 C35 A:B121801 4.8 49.4 1.0 C37 A:B121801 4.9 49.9 1.0 C53 A:B121801 4.9 44.8 1.0 C41 A:B121801 4.9 50.2 1.0 C54 A:B121801 5.0 44.9 1.0 C42 A:B121801 5.0 50.5 1.0

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


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 (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1801 b:22.4 occ:1.00 CO B:B121801 0.0 22.4 1.0 N24 B:B121801 1.9 22.8 1.0 N21 B:B121801 1.9 25.3 1.0 N22 B:B121801 1.9 23.7 1.0 N23 B:B121801 1.9 21.6 1.0 NE2 B:HIS618 2.2 17.5 1.0 C5' D:5AD1500 2.4 38.8 1.0 C19 B:B121801 2.7 23.8 1.0 C1 B:B121801 2.8 24.8 1.0 C4 B:B121801 2.8 25.6 1.0 C14 B:B121801 2.9 20.4 1.0 C6 B:B121801 2.9 22.8 1.0 C16 B:B121801 3.0 22.1 1.0 C9 B:B121801 3.0 21.1 1.0 C11 B:B121801 3.0 20.7 1.0 C4' D:5AD1500 3.1 38.6 1.0 CE1 B:HIS618 3.1 18.7 1.0 CD2 B:HIS618 3.2 19.9 1.0 C5 B:B121801 3.3 25.8 1.0 C15 B:B121801 3.3 19.6 1.0 C10 B:B121801 3.4 21.2 1.0 O4' D:5AD1500 3.7 40.3 1.0 C20 B:B121801 3.8 24.4 1.0 C2 B:B121801 4.0 26.1 1.0 C3 B:B121801 4.1 27.0 1.0 C18 B:B121801 4.1 22.8 1.0 C13 B:B121801 4.2 20.3 1.0 C7 B:B121801 4.2 23.1 1.0 C17 B:B121801 4.2 22.2 1.0 C8 B:B121801 4.2 23.1 1.0 ND1 B:HIS618 4.2 21.3 1.0 CG B:HIS618 4.3 21.5 1.0 C12 B:B121801 4.4 21.6 1.0 C26 B:B121801 4.4 27.7 1.0 C3' D:5AD1500 4.5 38.9 1.0 C37 B:B121801 4.8 24.5 1.0 C35 B:B121801 4.8 26.0 1.0 C53 B:B121801 4.8 19.4 1.0 C41 B:B121801 4.9 24.3 1.0 C48 B:B121801 4.9 19.2 1.0 C30 B:B121801 4.9 28.8 1.0 O3' D:5AD1500 4.9 39.0 1.0 C54 B:B121801 4.9 23.4 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1801 b:25.4 occ:1.00 CO C:B121801 0.0 25.4 1.0 N24 C:B121801 1.9 25.1 1.0 N21 C:B121801 1.9 25.6 1.0 N23 C:B121801 1.9 22.9 1.0 N22 C:B121801 1.9 27.7 1.0 NE2 C:HIS618 2.0 24.7 1.0 C5' A:5AD1500 2.3 41.2 1.0 C19 C:B121801 2.7 25.7 1.0 C1 C:B121801 2.8 25.6 1.0 CE1 C:HIS618 2.8 28.8 1.0 C4 C:B121801 2.9 24.4 1.0 C14 C:B121801 2.9 21.3 1.0 C6 C:B121801 2.9 26.5 1.0 C11 C:B121801 3.0 23.6 1.0 C9 C:B121801 3.0 26.9 1.0 C16 C:B121801 3.0 23.8 1.0 C4' A:5AD1500 3.1 40.9 1.0 CD2 C:HIS618 3.1 26.2 1.0 C5 C:B121801 3.3 26.4 1.0 C15 C:B121801 3.3 23.7 1.0 C10 C:B121801 3.4 25.6 1.0 C20 C:B121801 3.6 25.2 1.0 O4' A:5AD1500 3.6 41.2 1.0 C2 C:B121801 4.0 25.4 1.0 ND1 C:HIS618 4.0 29.1 1.0 C3 C:B121801 4.1 25.7 1.0 C18 C:B121801 4.1 26.5 1.0 C13 C:B121801 4.1 19.6 1.0 CG C:HIS618 4.2 27.3 1.0 C7 C:B121801 4.2 29.4 1.0 C17 C:B121801 4.2 25.7 1.0 C8 C:B121801 4.2 27.3 1.0 C12 C:B121801 4.3 21.8 1.0 C26 C:B121801 4.4 27.4 1.0 C3' A:5AD1500 4.5 40.7 1.0 C37 C:B121801 4.8 32.1 1.0 C35 C:B121801 4.8 20.9 1.0 C48 C:B121801 4.8 20.6 1.0 C53 C:B121801 4.8 24.3 1.0 C46 C:B121801 4.9 21.8 1.0 C41 C:B121801 5.0 26.8 1.0 C54 C:B121801 5.0 23.1 1.0

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


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Ornithine 4,5 Aminomutase in Complex with 2,4- Diaminobutyrate (Anaerobic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1801 b:28.6 occ:1.00 CO D:B121801 0.0 28.6 1.0 N24 D:B121801 1.9 29.2 1.0 N21 D:B121801 1.9 31.2 1.0 N22 D:B121801 1.9 32.0 1.0 N23 D:B121801 1.9 28.3 1.0 C5' B:5AD1500 2.2 30.6 1.0 NE2 D:HIS618 2.4 38.4 1.0 C19 D:B121801 2.7 28.7 1.0 C1 D:B121801 2.8 31.8 1.0 C4 D:B121801 2.8 32.5 1.0 C14 D:B121801 2.9 27.1 1.0 C6 D:B121801 3.0 34.1 1.0 C11 D:B121801 3.0 29.6 1.0 C9 D:B121801 3.0 33.4 1.0 C4' B:5AD1500 3.0 30.6 1.0 C16 D:B121801 3.0 28.8 1.0 CD2 D:HIS618 3.3 37.8 1.0 C5 D:B121801 3.3 33.0 1.0 C15 D:B121801 3.4 27.9 1.0 O4' B:5AD1500 3.4 32.7 1.0 C10 D:B121801 3.4 32.4 1.0 CE1 D:HIS618 3.5 37.7 1.0 C20 D:B121801 3.8 32.1 1.0 C2 D:B121801 4.0 33.1 1.0 C3 D:B121801 4.1 34.3 1.0 C18 D:B121801 4.1 27.8 1.0 C13 D:B121801 4.1 26.4 1.0 C17 D:B121801 4.2 28.1 1.0 C7 D:B121801 4.3 36.8 1.0 C8 D:B121801 4.3 35.0 1.0 C12 D:B121801 4.4 28.9 1.0 C26 D:B121801 4.4 33.4 1.0 C3' B:5AD1500 4.5 28.5 1.0 CG D:HIS618 4.5 37.1 1.0 ND1 D:HIS618 4.5 36.8 1.0 C35 D:B121801 4.8 29.6 1.0 C37 D:B121801 4.8 38.6 1.0 C48 D:B121801 4.8 24.9 1.0 C1' B:5AD1500 4.8 34.0 1.0 C53 D:B121801 4.9 28.8 1.0 C41 D:B121801 5.0 37.7 1.0 C54 D:B121801 5.0 23.0 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