Cobalt in PDB 3koy: Crystal Structure of Ornithine 4,5 Aminomutase in Complex with Ornithine (Aerobic)

The structure of Crystal Structure of Ornithine 4,5 Aminomutase in Complex with Ornithine (Aerobic), PDB code: 3koy 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)	60.37 / 2.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.520, 233.220, 124.140, 90.00, 103.43, 90.00
R / Rfree (%)	18.3 / 26.3

The binding sites of Cobalt atom in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with Ornithine (Aerobic) (pdb code 3koy). 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 Ornithine (Aerobic), PDB code: 3koy:
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 Ornithine (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 Ornithine (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1801 b:87.3 occ:1.00 CO A:B121801 0.0 87.3 1.0 N24 A:B121801 1.9 96.2 1.0 N21 A:B121801 1.9 98.0 1.0 N22 A:B121801 1.9 99.2 1.0 N23 A:B121801 1.9 94.7 1.0 C5' C:5AD1500 2.1 86.2 1.0 NE2 A:HIS618 2.7 91.8 1.0 C19 A:B121801 2.7 94.2 1.0 C4 A:B121801 2.8 97.9 1.0 C14 A:B121801 2.8 95.9 1.0 C1 A:B121801 2.9 96.3 1.0 C9 A:B121801 2.9 98.8 1.0 C6 A:B121801 2.9 95.1 1.0 C11 A:B121801 2.9 96.5 1.0 C16 A:B121801 3.0 94.1 1.0 C5 A:B121801 3.2 93.7 1.0 C10 A:B121801 3.3 96.3 1.0 C15 A:B121801 3.3 95.0 1.0 CE1 A:HIS618 3.5 98.8 1.0 C4' C:5AD1500 3.5 91.4 1.0 CD2 A:HIS618 3.6 92.9 1.0 C2 A:B121801 3.9 98.8 1.0 C20 A:B121801 3.9 96.0 1.0 C13 A:B121801 4.0 94.7 1.0 C3 A:B121801 4.1 98.0 1.0 C18 A:B121801 4.1 88.1 1.0 C7 A:B121801 4.2 97.3 1.0 C8 A:B121801 4.2 95.6 1.0 C17 A:B121801 4.2 85.1 1.0 O4' C:5AD1500 4.2 88.0 1.0 C26 A:B121801 4.2 98.8 1.0 C12 A:B121801 4.3 93.3 1.0 ND1 A:HIS618 4.5 97.1 1.0 C48 A:B121801 4.6 90.3 1.0 CG A:HIS618 4.6 92.9 1.0 C35 A:B121801 4.7 95.1 1.0 C3' C:5AD1500 4.8 85.1 1.0 C42 A:B121801 4.8 91.2 1.0 C53 A:B121801 4.8 89.6 1.0 C37 A:B121801 4.8 95.9 1.0 C54 A:B121801 4.9 78.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with Ornithine (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 Ornithine (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1801 b:60.2 occ:1.00 CO B:B121801 0.0 60.2 1.0 N24 B:B121801 1.9 66.6 1.0 N21 B:B121801 1.9 63.1 1.0 N22 B:B121801 1.9 66.0 1.0 N23 B:B121801 1.9 61.7 1.0 C5' D:5AD1500 2.1 56.6 1.0 NE2 B:HIS618 2.3 51.0 1.0 C19 B:B121801 2.8 62.7 1.0 C4 B:B121801 2.8 67.8 1.0 C6 B:B121801 2.9 63.2 1.0 C1 B:B121801 2.9 63.2 1.0 C14 B:B121801 2.9 61.6 1.0 C9 B:B121801 2.9 59.1 1.0 C11 B:B121801 3.0 58.5 1.0 C16 B:B121801 3.0 65.7 1.0 CE1 B:HIS618 3.0 55.9 1.0 C5 B:B121801 3.2 67.3 1.0 C4' D:5AD1500 3.2 57.7 1.0 C10 B:B121801 3.3 58.2 1.0 C15 B:B121801 3.4 62.7 1.0 CD2 B:HIS618 3.4 55.7 1.0 O4' D:5AD1500 3.6 62.9 1.0 C2 B:B121801 3.9 66.6 1.0 C20 B:B121801 3.9 60.6 1.0 C3 B:B121801 4.0 70.3 1.0 C13 B:B121801 4.1 60.8 1.0 C18 B:B121801 4.1 61.4 1.0 C7 B:B121801 4.1 58.5 1.0 C8 B:B121801 4.2 58.0 1.0 C17 B:B121801 4.2 59.3 1.0 ND1 B:HIS618 4.2 56.8 1.0 C26 B:B121801 4.2 67.2 1.0 C12 B:B121801 4.3 59.3 1.0 CG B:HIS618 4.4 56.4 1.0 C3' D:5AD1500 4.6 59.4 1.0 C35 B:B121801 4.6 62.0 1.0 C48 B:B121801 4.7 54.9 1.0 C53 B:B121801 4.8 63.5 1.0 C37 B:B121801 4.8 60.4 1.0 C42 B:B121801 4.9 53.6 1.0 C54 B:B121801 4.9 55.0 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase in Complex with Ornithine (Aerobic)


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 Ornithine (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 42.1 1.0 N21 C:B121801 1.9 40.4 1.0 N22 C:B121801 1.9 45.4 1.0 N23 C:B121801 1.9 40.4 1.0 C5' A:5AD1500 2.1 37.8 1.0 NE2 C:HIS618 2.3 37.1 1.0 C19 C:B121801 2.7 34.2 1.0 C4 C:B121801 2.8 44.0 1.0 C1 C:B121801 2.9 39.3 1.0 C14 C:B121801 2.9 34.4 1.0 C6 C:B121801 2.9 46.5 1.0 C9 C:B121801 2.9 39.9 1.0 C11 C:B121801 2.9 40.9 1.0 C16 C:B121801 3.0 39.5 1.0 CE1 C:HIS618 3.1 39.7 1.0 C4' A:5AD1500 3.2 40.7 1.0 C5 C:B121801 3.2 43.2 1.0 C10 C:B121801 3.3 38.7 1.0 CD2 C:HIS618 3.3 35.2 1.0 C15 C:B121801 3.4 41.3 1.0 O4' A:5AD1500 3.7 43.1 1.0 C20 C:B121801 3.9 38.7 1.0 C2 C:B121801 4.0 39.7 1.0 C3 C:B121801 4.1 41.1 1.0 C18 C:B121801 4.1 34.4 1.0 C13 C:B121801 4.1 36.8 1.0 C7 C:B121801 4.2 44.4 1.0 C8 C:B121801 4.2 42.2 1.0 C17 C:B121801 4.2 34.9 1.0 ND1 C:HIS618 4.3 40.5 1.0 C12 C:B121801 4.3 42.2 1.0 C26 C:B121801 4.4 46.2 1.0 CG C:HIS618 4.4 37.8 1.0 C3' A:5AD1500 4.6 38.5 1.0 C35 C:B121801 4.7 40.7 1.0 C37 C:B121801 4.8 49.2 1.0 C48 C:B121801 4.8 31.1 1.0 C53 C:B121801 4.8 49.0 1.0 C30 C:B121801 5.0 38.1 1.0

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


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 Ornithine (Aerobic) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1801 b:74.8 occ:1.00 CO D:B121801 0.0 74.8 1.0 N24 D:B121801 1.9 84.1 1.0 N21 D:B121801 1.9 78.1 1.0 N22 D:B121801 1.9 85.2 1.0 N23 D:B121801 1.9 78.8 1.0 C5' B:5AD1500 2.1 74.0 1.0 NE2 D:HIS618 2.4 76.3 1.0 C19 D:B121801 2.8 78.3 1.0 C4 D:B121801 2.8 82.5 1.0 C1 D:B121801 2.9 77.2 1.0 C14 D:B121801 2.9 78.2 1.0 C9 D:B121801 2.9 82.2 1.0 C6 D:B121801 2.9 85.4 1.0 C11 D:B121801 2.9 79.4 1.0 C16 D:B121801 3.0 77.7 1.0 CE1 D:HIS618 3.2 79.6 1.0 C5 D:B121801 3.3 82.6 1.0 C10 D:B121801 3.3 80.3 1.0 C4' B:5AD1500 3.3 76.7 1.0 C15 D:B121801 3.4 77.0 1.0 CD2 D:HIS618 3.4 73.7 1.0 O4' B:5AD1500 3.8 84.7 1.0 C2 D:B121801 3.9 82.3 1.0 C20 D:B121801 3.9 77.2 1.0 C3 D:B121801 4.0 81.3 1.0 C13 D:B121801 4.1 77.7 1.0 C18 D:B121801 4.1 70.4 1.0 C26 D:B121801 4.2 83.5 1.0 C17 D:B121801 4.2 74.0 1.0 C7 D:B121801 4.2 86.5 1.0 C8 D:B121801 4.2 85.2 1.0 C12 D:B121801 4.3 78.3 1.0 ND1 D:HIS618 4.3 80.7 1.0 CG D:HIS618 4.4 81.0 1.0 C35 D:B121801 4.7 79.8 1.0 C3' B:5AD1500 4.7 70.8 1.0 C48 D:B121801 4.7 75.1 1.0 C53 D:B121801 4.8 77.8 1.0 C37 D:B121801 4.9 82.3 1.0 C54 D:B121801 5.0 70.1 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