Cobalt in PDB 3kow: Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex

The structure of Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex, PDB code: 3kow 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)	120.86 / 2.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	65.180, 229.010, 123.920, 90.00, 102.76, 90.00
R / Rfree (%)	19.1 / 27.9

The binding sites of Cobalt atom in the Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex (pdb code 3kow). 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 Backsoaked Complex, PDB code: 3kow:
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 Backsoaked Complex


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 Backsoaked Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1801 b:64.0 occ:1.00 CO A:B121801 0.0 64.0 1.0 N24 A:B121801 1.9 72.3 1.0 N22 A:B121801 1.9 75.6 1.0 N21 A:B121801 1.9 76.3 1.0 N23 A:B121801 1.9 71.2 1.0 C5' C:5AD1500 2.1 68.2 1.0 NE2 A:HIS618 2.3 66.9 1.0 C19 A:B121801 2.7 71.3 1.0 C4 A:B121801 2.8 73.4 1.0 C9 A:B121801 2.9 76.0 1.0 C1 A:B121801 2.9 70.8 1.0 C14 A:B121801 2.9 72.2 1.0 C6 A:B121801 2.9 74.8 1.0 C11 A:B121801 2.9 71.8 1.0 C16 A:B121801 3.0 74.3 1.0 CE1 A:HIS618 3.2 68.3 1.0 C4' C:5AD1500 3.2 77.9 1.0 C10 A:B121801 3.3 74.5 1.0 C5 A:B121801 3.3 75.0 1.0 CD2 A:HIS618 3.3 67.0 1.0 C15 A:B121801 3.4 71.8 1.0 O4' C:5AD1500 3.8 78.6 1.0 C20 A:B121801 3.9 65.4 1.0 C2 A:B121801 3.9 65.4 1.0 C18 A:B121801 4.1 67.4 1.0 C13 A:B121801 4.1 67.9 1.0 C3 A:B121801 4.1 69.2 1.0 C8 A:B121801 4.2 71.8 1.0 C7 A:B121801 4.2 71.3 1.0 C17 A:B121801 4.2 67.2 1.0 C12 A:B121801 4.2 67.8 1.0 C26 A:B121801 4.2 67.4 1.0 ND1 A:HIS618 4.3 70.0 1.0 CG A:HIS618 4.4 66.4 1.0 C3' C:5AD1500 4.5 83.2 1.0 C35 A:B121801 4.7 75.6 1.0 C53 A:B121801 4.8 57.9 1.0 C47 A:B121801 4.9 66.2 1.0 C48 A:B121801 4.9 60.1 1.0 C37 A:B121801 4.9 72.8 1.0 C54 A:B121801 4.9 64.4 1.0 C42 A:B121801 4.9 68.5 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex


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 Backsoaked Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Co1801 b:52.1 occ:1.00 CO D:B121801 0.0 52.1 1.0 N24 D:B121801 1.9 51.2 1.0 N21 D:B121801 1.9 59.4 1.0 N22 D:B121801 1.9 58.5 1.0 N23 D:B121801 1.9 56.9 1.0 NE2 D:HIS618 2.6 60.4 1.0 C19 D:B121801 2.7 52.3 1.0 C4 D:B121801 2.8 56.1 1.0 C14 D:B121801 2.8 52.8 1.0 C1 D:B121801 2.9 60.9 1.0 C9 D:B121801 2.9 51.8 1.0 C6 D:B121801 2.9 58.2 1.0 C11 D:B121801 2.9 62.7 1.0 C16 D:B121801 2.9 55.2 1.0 C5 D:B121801 3.2 56.7 1.0 C10 D:B121801 3.3 60.5 1.0 CD2 D:HIS618 3.3 62.1 1.0 C15 D:B121801 3.3 61.4 1.0 CE1 D:HIS618 3.7 64.8 1.0 C20 D:B121801 3.9 61.4 1.0 C2 D:B121801 3.9 62.4 1.0 C13 D:B121801 4.0 53.6 1.0 C3 D:B121801 4.1 61.6 1.0 C18 D:B121801 4.1 48.8 1.0 C7 D:B121801 4.1 62.3 1.0 C17 D:B121801 4.2 49.6 1.0 C8 D:B121801 4.2 60.0 1.0 C26 D:B121801 4.2 61.2 1.0 C12 D:B121801 4.3 59.1 1.0 C48 D:B121801 4.5 45.3 1.0 CG D:HIS618 4.6 67.7 1.0 C35 D:B121801 4.7 65.0 1.0 ND1 D:HIS618 4.7 71.1 1.0 C37 D:B121801 4.8 63.1 1.0 C53 D:B121801 4.8 59.3 1.0 C54 D:B121801 5.0 49.8 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex


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 Backsoaked Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1801 b:25.5 occ:1.00 CO C:B121801 0.0 25.5 1.0 N24 C:B121801 1.9 40.9 1.0 N23 C:B121801 1.9 35.3 1.0 N22 C:B121801 1.9 40.9 1.0 N21 C:B121801 1.9 36.1 1.0 C5' A:5AD1500 2.1 37.0 1.0 NE2 C:HIS618 2.4 33.9 1.0 C19 C:B121801 2.7 39.4 1.0 C14 C:B121801 2.9 34.4 1.0 C4 C:B121801 2.9 34.8 1.0 C1 C:B121801 2.9 37.7 1.0 C9 C:B121801 2.9 39.5 1.0 C11 C:B121801 2.9 39.1 1.0 C6 C:B121801 2.9 35.9 1.0 C16 C:B121801 2.9 41.8 1.0 C4' A:5AD1500 3.2 43.3 1.0 C10 C:B121801 3.3 38.6 1.0 C5 C:B121801 3.3 36.1 1.0 CD2 C:HIS618 3.3 37.7 1.0 C15 C:B121801 3.3 39.7 1.0 CE1 C:HIS618 3.4 35.8 1.0 O4' A:5AD1500 3.6 48.6 1.0 C20 C:B121801 3.9 38.0 1.0 C2 C:B121801 4.0 35.8 1.0 C18 C:B121801 4.1 35.0 1.0 C3 C:B121801 4.1 33.9 1.0 C13 C:B121801 4.1 35.0 1.0 C17 C:B121801 4.2 36.8 1.0 C7 C:B121801 4.2 40.9 1.0 C8 C:B121801 4.2 40.8 1.0 C12 C:B121801 4.3 41.3 1.0 C26 C:B121801 4.3 39.5 1.0 ND1 C:HIS618 4.5 40.3 1.0 CG C:HIS618 4.5 40.5 1.0 C3' A:5AD1500 4.6 49.3 1.0 C35 C:B121801 4.7 41.5 1.0 C53 C:B121801 4.8 43.9 1.0 C48 C:B121801 4.9 36.5 1.0 C37 C:B121801 4.9 44.5 1.0 C54 C:B121801 5.0 40.6 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Ornithine 4,5 Aminomutase Backsoaked Complex


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 Backsoaked Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1801 b:20.1 occ:1.00 CO B:B121801 0.0 20.1 1.0 N24 B:B121801 1.9 30.2 1.0 N22 B:B121801 1.9 27.5 1.0 N21 B:B121801 1.9 25.9 1.0 N23 B:B121801 1.9 21.5 1.0 C5' D:5AD1500 2.1 27.5 1.0 NE2 B:HIS618 2.6 25.2 1.0 C19 B:B121801 2.8 28.4 1.0 C4 B:B121801 2.8 26.4 1.0 C6 B:B121801 2.9 30.9 1.0 C9 B:B121801 2.9 26.0 1.0 C1 B:B121801 2.9 30.2 1.0 C14 B:B121801 2.9 22.4 1.0 C11 B:B121801 2.9 25.4 1.0 C16 B:B121801 3.0 26.3 1.0 C5 B:B121801 3.2 32.1 1.0 C10 B:B121801 3.2 28.8 1.0 C4' D:5AD1500 3.3 33.7 1.0 C15 B:B121801 3.4 23.6 1.0 CD2 B:HIS618 3.5 24.8 1.0 CE1 B:HIS618 3.6 27.3 1.0 O4' D:5AD1500 3.8 40.4 1.0 C20 B:B121801 3.9 30.3 1.0 C2 B:B121801 4.0 33.9 1.0 C7 B:B121801 4.1 27.4 1.0 C18 B:B121801 4.1 26.1 1.0 C3 B:B121801 4.1 31.9 1.0 C13 B:B121801 4.1 23.7 1.0 C8 B:B121801 4.2 24.6 1.0 C17 B:B121801 4.2 24.6 1.0 C12 B:B121801 4.3 25.9 1.0 C26 B:B121801 4.4 35.2 1.0 C3' D:5AD1500 4.5 44.8 1.0 ND1 B:HIS618 4.6 30.8 1.0 CG B:HIS618 4.6 29.4 1.0 C37 B:B121801 4.6 32.3 1.0 C35 B:B121801 4.7 31.2 1.0 C53 B:B121801 4.8 22.4 1.0 C54 B:B121801 4.8 25.3 1.0 C48 B:B121801 5.0 23.3 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