Cobalt in PDB 1ovu: Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)

The structure of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I), PDB code: 1ovu was solved by L.Di Costanzo, S.Geremia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.10
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	89.780, 147.720, 37.600, 90.00, 90.00, 90.00
R / Rfree (%)	24.7 / 30.4

The binding sites of Cobalt atom in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) (pdb code 1ovu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I), PDB code: 1ovu:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


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 Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:49.0 occ:1.00 OE1 A:GLU36 1.9 55.3 1.0 ND1 A:HIS39 1.9 51.7 1.0 OE2 A:GLU10 2.0 51.7 1.0 OE1 A:GLU10 2.1 58.8 1.0 CD A:GLU10 2.3 63.2 1.0 CE1 A:HIS39 2.6 51.2 1.0 CD A:GLU36 2.8 53.4 1.0 CG A:HIS39 3.2 52.7 1.0 OE2 A:GLU36 3.3 51.4 1.0 NE2 A:HIS39 3.8 57.5 1.0 CB A:HIS39 3.8 50.4 1.0 CG A:GLU10 3.9 64.4 1.0 CG A:GLU36 4.0 42.8 1.0 CD2 A:HIS39 4.1 50.2 1.0 CB A:GLU36 4.1 42.1 1.0 CA A:GLU36 4.1 43.6 1.0 CB A:GLU10 4.8 59.0 1.0 N A:GLU36 4.9 43.6 1.0 O A:ASP35 4.9 42.6 1.0

Cobalt binding site 2 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


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 Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Co105 b:86.6 occ:1.00 OE1 A:GLU19 2.1 57.4 1.0 O A:HOH108 2.4 54.1 1.0 CD A:GLU19 3.1 62.8 1.0 OE2 A:GLU19 3.6 76.5 1.0 O A:HOH106 4.2 60.3 1.0 CG A:GLU19 4.3 52.6 1.0 O A:HOH107 4.5 22.8 1.0

Cobalt binding site 3 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


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 Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:45.6 occ:1.00 OE2 B:GLU10 1.9 52.1 1.0 ND1 B:HIS39 2.1 45.5 1.0 OE1 B:GLU36 2.1 49.5 1.0 OE1 B:GLU10 2.1 38.9 1.0 CD B:GLU10 2.3 37.4 1.0 CE1 B:HIS39 2.7 54.9 1.0 CD B:GLU36 3.2 52.5 1.0 CG B:HIS39 3.3 47.6 1.0 CG B:GLU10 3.7 33.9 1.0 OE2 B:GLU36 3.7 47.6 1.0 CB B:HIS39 3.8 47.4 1.0 NE2 B:HIS39 4.0 59.2 1.0 CD2 B:HIS39 4.2 46.8 1.0 CG B:GLU36 4.4 42.8 1.0 CB B:GLU36 4.4 45.2 1.0 CB B:GLU10 4.7 44.7 1.0 CA B:GLU36 4.7 48.0 1.0

Cobalt binding site 4 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


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 Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Co103 b:59.2 occ:1.00 OE2 D:GLU36 1.9 65.9 1.0 OE2 C:GLU10 2.0 63.0 1.0 OE1 C:GLU36 2.0 63.4 1.0 OE1 C:GLU10 2.0 66.4 1.0 ND1 C:HIS39 2.1 49.6 1.0 CD C:GLU10 2.3 62.8 1.0 CE1 C:HIS39 2.9 51.2 1.0 CD C:GLU36 3.1 68.8 1.0 CD D:GLU36 3.2 71.5 1.0 CG C:HIS39 3.2 48.0 1.0 CB C:HIS39 3.7 48.9 1.0 OE2 C:GLU36 3.7 63.4 1.0 CG C:GLU10 3.8 60.8 1.0 OE1 D:GLU36 4.0 68.0 1.0 CG D:GLU36 4.1 67.0 1.0 CO D:CO104 4.1 52.1 1.0 NE2 C:HIS39 4.1 41.4 1.0 CD2 C:HIS39 4.3 49.6 1.0 CG C:GLU36 4.3 67.7 1.0 CB C:GLU36 4.4 60.5 1.0 CG2 D:ILE32 4.4 60.0 1.0 CA C:GLU36 4.5 60.7 1.0 CB C:GLU10 4.7 60.5 1.0 OH D:TYR17 4.7 44.9 1.0 OE1 D:GLU10 4.7 59.5 1.0 CE1 D:TYR17 4.9 54.3 1.0 CE1 D:HIS39 5.0 37.9 1.0

Cobalt binding site 5 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co104 b:52.1 occ:1.00 OE1 D:GLU36 1.8 68.0 1.0 OE2 C:GLU36 1.8 63.4 1.0 OE2 D:GLU10 1.9 73.5 1.0 ND1 D:HIS39 2.0 34.7 1.0 OE1 D:GLU10 2.0 59.5 1.0 CD D:GLU10 2.2 68.6 1.0 CD D:GLU36 2.5 71.5 1.0 CE1 D:HIS39 2.8 37.9 1.0 OE2 D:GLU36 2.9 65.9 1.0 CD C:GLU36 2.9 68.8 1.0 CG D:HIS39 3.2 43.3 1.0 OE1 C:GLU36 3.4 63.4 1.0 CB D:HIS39 3.7 49.8 1.0 CG D:GLU36 3.8 67.0 1.0 CG D:GLU10 3.8 59.0 1.0 NE2 D:HIS39 3.9 51.2 1.0 CG2 C:ILE32 4.1 52.1 1.0 CO C:CO103 4.1 59.2 1.0 CB D:GLU36 4.1 61.0 1.0 CD2 D:HIS39 4.2 42.4 1.0 CG C:GLU36 4.2 67.7 1.0 CA D:GLU36 4.3 62.4 1.0 CE1 C:TYR17 4.4 44.5 1.0 OH C:TYR17 4.5 45.4 1.0 CB D:GLU10 4.7 56.2 1.0 CZ C:TYR17 4.8 49.1 1.0 CE1 C:HIS39 4.9 51.2 1.0 O D:ASP35 5.0 62.4 1.0

Cobalt binding site 6 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co106 b:76.7 occ:1.00 OE1 D:GLU19 2.3 51.7 1.0 OE1 D:GLN16 2.8 85.2 1.0 CD D:GLU19 3.2 57.1 1.0 OE2 D:GLU19 3.5 65.3 1.0 CD D:GLN16 3.5 86.2 1.0 NE2 D:GLN16 3.5 90.3 1.0 CG D:GLU19 4.6 59.4 1.0 OE1 C:GLU5 4.7 77.2 1.0 OE2 C:GLU5 4.7 76.0 1.0 CB D:GLU19 4.8 63.1 1.0 CG D:GLN16 5.0 70.4 1.0

Cobalt binding site 7 out of 7 in the Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Four-Helix Bundle Model Di-Co(II)-DF1-L13A (Form I) within 5.0Å range: probe atom residue distance (Å) B Occ D:Co107 b:89.1 occ:1.00 O D:HOH110 2.9 36.9 1.0 O D:HOH109 2.9 51.2 1.0 O D:HOH108 3.1 49.9 1.0 OE1 D:GLU44 3.2 63.8 1.0 OE2 D:GLU44 3.5 65.7 1.0 CD D:GLU44 3.6 64.4 1.0 CG D:GLU44 4.8 59.1 1.0

S.Geremia, L.Di Costanzo, L.Randaccio, D.E.Engel, A.Lombardi, F.Nastri, W.F.Degrado. Response of A Designed Metalloprotein to Changes in Metal Ion Coordination, Exogenous Ligands, and Active Site Volume Determined By X-Ray Crystallography. J.Am.Chem.Soc. V. 127 17266 2005.
ISSN: ISSN 0002-7863
PubMed: 16332076
DOI: 10.1021/JA054199X