Cobalt in PDB 3v1d: Crystal Structure of De Novo Designed MID1-Cobalt

The structure of Crystal Structure of De Novo Designed MID1-Cobalt, PDB code: 3v1d was solved by B.S.Der, M.Machius, M.J.Miley, B.Kuhlman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 1.24
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.720, 45.451, 62.112, 90.04, 90.00, 90.00
R / Rfree (%)	14.7 / 19.4

The binding sites of Cobalt atom in the Crystal Structure of De Novo Designed MID1-Cobalt (pdb code 3v1d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Crystal Structure of De Novo Designed MID1-Cobalt, PDB code: 3v1d:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ A:Co47 b:7.2 occ:1.00 HE2 F:HIS16 1.3 7.9 1.0 HE2 F:HIS12 1.4 10.5 1.0 NE2 A:HIS35 2.1 7.9 1.0 NE2 A:HIS39 2.1 8.1 0.5 OD1 A:ASP46 2.1 9.8 1.0 NE2 F:HIS16 2.1 6.6 1.0 NE2 A:HIS39 2.2 6.4 0.5 NE2 F:HIS12 2.2 8.8 1.0 OD2 A:ASP46 2.3 9.4 1.0 CG A:ASP46 2.5 9.5 1.0 CE1 A:HIS39 3.0 8.6 0.5 CD2 A:HIS35 3.0 6.9 1.0 CE1 A:HIS35 3.0 11.0 1.0 CE1 F:HIS16 3.1 9.3 1.0 CE1 A:HIS39 3.1 6.2 0.5 CD2 A:HIS39 3.1 6.8 0.5 CD2 F:HIS16 3.1 6.3 1.0 HE1 A:HIS39 3.2 10.4 0.5 CE1 F:HIS12 3.2 13.2 1.0 HD2 A:HIS35 3.2 8.3 1.0 HE1 A:HIS39 3.2 7.4 0.5 CD2 A:HIS39 3.2 7.0 0.5 HE1 F:HIS16 3.2 11.1 1.0 CD2 F:HIS12 3.2 8.0 1.0 HE1 A:HIS35 3.2 13.2 1.0 HE1 F:HIS12 3.3 15.9 1.0 HD2 F:HIS16 3.3 7.5 1.0 HD2 A:HIS39 3.4 8.2 0.5 HD2 A:HIS39 3.4 8.4 0.5 HD2 F:HIS12 3.4 9.6 1.0 CB A:ASP46 4.0 10.7 1.0 ND1 A:HIS35 4.1 11.2 1.0 ND1 A:HIS39 4.2 8.8 0.5 CG A:HIS35 4.2 8.6 1.0 ND1 F:HIS16 4.2 9.1 1.0 ND1 A:HIS39 4.2 7.6 0.5 CG A:HIS39 4.2 8.1 0.5 CG F:HIS16 4.3 5.6 1.0 ND1 F:HIS12 4.3 13.7 1.0 O A:HOH110 4.3 23.2 1.0 CG A:HIS39 4.3 7.3 0.5 CG F:HIS12 4.4 9.8 1.0 HB3 A:ASP46 4.4 12.8 1.0 HB2 A:ASP46 4.5 12.8 1.0 HA A:ASP46 4.6 11.9 1.0 CA A:ASP46 4.8 9.9 1.0 HD1 A:HIS35 4.9 13.4 1.0 N A:ASP46 4.9 12.0 1.0 HD1 A:HIS39 4.9 10.5 0.5 O A:HOH260 4.9 29.7 1.0 H A:ASP46 4.9 14.4 1.0 HD1 F:HIS16 4.9 10.9 1.0 HD1 A:HIS39 5.0 9.2 0.5 C12 A:1PE48 5.0 21.1 1.0

Cobalt binding site 2 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ B:Co47 b:7.1 occ:1.00 NE2 B:HIS35 2.1 8.1 1.0 NE2 C:HIS16 2.1 6.8 1.0 NE2 B:HIS39 2.1 9.7 1.0 NE2 C:HIS12 2.2 7.4 1.0 CD2 B:HIS35 3.0 6.8 1.0 CE1 C:HIS16 3.0 7.8 1.0 CE1 B:HIS35 3.1 9.0 1.0 CE1 C:HIS12 3.1 10.2 1.0 CE1 B:HIS39 3.1 11.6 1.0 CD2 C:HIS16 3.1 6.4 1.0 CD2 B:HIS39 3.2 8.9 1.0 CD2 C:HIS12 3.2 6.9 1.0 HE1 C:HIS16 3.2 9.4 1.0 HD2 B:HIS35 3.2 8.2 1.0 HE1 B:HIS39 3.2 13.9 1.0 HE1 C:HIS12 3.2 12.2 1.0 HE1 B:HIS35 3.3 10.8 1.0 HD2 C:HIS16 3.3 7.7 1.0 HD2 B:HIS39 3.4 10.7 1.0 HD2 C:HIS12 3.4 8.3 1.0 ND1 B:HIS35 4.2 9.6 1.0 CG B:HIS35 4.2 7.3 1.0 ND1 C:HIS16 4.2 8.2 1.0 ND1 C:HIS12 4.2 11.1 1.0 ND1 B:HIS39 4.2 12.8 1.0 CG C:HIS16 4.3 6.7 1.0 O C:HOH163 4.3 12.3 1.0 CG C:HIS12 4.3 8.3 1.0 CG B:HIS39 4.3 10.2 1.0 HD1 B:HIS35 4.9 11.6 1.0 HD1 C:HIS16 4.9 9.9 1.0 HD1 C:HIS12 5.0 13.3 1.0 HD1 B:HIS39 5.0 15.4 1.0

Cobalt binding site 3 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ C:Co47 b:7.0 occ:1.00 NE2 C:HIS35 2.1 6.8 1.0 NE2 B:HIS16 2.1 6.5 1.0 NE2 C:HIS39 2.1 10.0 1.0 OD2 C:ASP46 2.2 9.9 1.0 NE2 B:HIS12 2.2 9.1 1.0 OD1 C:ASP46 2.2 10.8 1.0 CG C:ASP46 2.5 10.2 1.0 CE1 C:HIS35 3.0 9.3 1.0 CE1 B:HIS16 3.0 9.3 1.0 CE1 C:HIS39 3.0 13.2 1.0 CD2 C:HIS35 3.1 6.7 1.0 CE1 B:HIS12 3.1 13.4 1.0 CD2 B:HIS16 3.1 5.8 1.0 HE1 C:HIS39 3.2 15.8 1.0 HE1 C:HIS35 3.2 11.2 1.0 HE1 B:HIS16 3.2 11.1 1.0 CD2 C:HIS39 3.2 9.2 1.0 CD2 B:HIS12 3.2 7.6 1.0 HE1 B:HIS12 3.2 16.1 1.0 HD2 C:HIS35 3.3 8.0 1.0 HD2 B:HIS16 3.3 6.9 1.0 HD2 B:HIS12 3.4 9.1 1.0 HD2 C:HIS39 3.4 11.1 1.0 CB C:ASP46 4.0 11.8 1.0 ND1 C:HIS35 4.1 11.4 1.0 ND1 B:HIS16 4.2 8.9 1.0 CG C:HIS35 4.2 8.2 1.0 ND1 C:HIS39 4.2 14.3 1.0 ND1 B:HIS12 4.2 14.3 1.0 CG B:HIS16 4.2 6.5 1.0 CG C:HIS39 4.3 9.6 1.0 O B:HOH114 4.3 24.1 1.0 CG B:HIS12 4.3 10.3 1.0 HB3 C:ASP46 4.4 14.2 1.0 HB2 C:ASP46 4.5 14.2 1.0 HA C:ASP46 4.6 12.9 1.0 CA C:ASP46 4.8 10.7 1.0 H C:ASP46 4.9 14.9 1.0 O C:HOH445 4.9 30.6 1.0 N C:ASP46 4.9 12.4 1.0 HD1 C:HIS35 4.9 13.7 1.0 HD1 B:HIS16 4.9 10.7 1.0 HD1 C:HIS39 4.9 17.2 1.0 HD1 B:HIS12 5.0 17.1 1.0

Cobalt binding site 4 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ E:Co47 b:6.9 occ:1.00 NE2 E:HIS35 2.1 7.6 1.0 NE2 H:HIS16 2.1 5.6 1.0 NE2 H:HIS12 2.1 7.2 1.0 NE2 E:HIS39 2.1 10.5 1.0 CD2 E:HIS35 3.0 6.5 1.0 CE1 E:HIS35 3.0 8.2 1.0 CE1 H:HIS16 3.1 7.8 1.0 CE1 E:HIS39 3.1 13.5 1.0 CE1 H:HIS12 3.1 9.6 1.0 CD2 H:HIS12 3.2 5.9 1.0 CD2 H:HIS16 3.2 5.8 1.0 CD2 E:HIS39 3.2 8.8 1.0 HE1 E:HIS39 3.2 16.2 1.0 HD2 E:HIS35 3.2 7.9 1.0 HE1 H:HIS16 3.2 9.3 1.0 HE1 H:HIS12 3.2 11.5 1.0 HE1 E:HIS35 3.2 9.8 1.0 HD2 H:HIS16 3.3 6.9 1.0 HD2 H:HIS12 3.4 7.1 1.0 HD2 E:HIS39 3.4 10.6 1.0 ND1 E:HIS35 4.1 9.1 1.0 CG E:HIS35 4.2 6.6 1.0 ND1 H:HIS12 4.2 11.4 1.0 ND1 H:HIS16 4.2 8.2 1.0 ND1 E:HIS39 4.2 13.3 1.0 CG H:HIS12 4.3 8.7 1.0 CG H:HIS16 4.3 7.2 1.0 O H:HOH51 4.3 11.6 1.0 CG E:HIS39 4.3 10.2 1.0 HD1 E:HIS35 4.9 10.9 1.0 HD1 H:HIS12 5.0 13.7 1.0 HD1 H:HIS16 5.0 9.9 1.0 HD1 E:HIS39 5.0 16.0 1.0

Cobalt binding site 5 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ F:Co47 b:6.9 occ:1.00 HE2 A:HIS16 1.3 7.1 1.0 HE2 A:HIS12 1.4 8.4 1.0 NE2 F:HIS35 2.1 7.8 1.0 NE2 A:HIS16 2.1 5.9 1.0 NE2 F:HIS39 2.1 9.3 1.0 NE2 A:HIS12 2.2 7.0 1.0 CE1 F:HIS35 3.0 8.4 1.0 CD2 F:HIS35 3.1 6.5 1.0 CE1 A:HIS16 3.1 8.2 1.0 CE1 F:HIS39 3.1 12.5 1.0 CE1 A:HIS12 3.1 9.4 1.0 CD2 A:HIS16 3.2 5.8 1.0 CD2 F:HIS39 3.2 7.5 1.0 CD2 A:HIS12 3.2 6.7 1.0 HE1 A:HIS16 3.2 9.9 1.0 HE1 F:HIS35 3.2 10.0 1.0 HE1 F:HIS39 3.2 14.9 1.0 HD2 F:HIS35 3.2 7.8 1.0 HE1 A:HIS12 3.3 11.3 1.0 HD2 A:HIS16 3.4 7.0 1.0 HD2 A:HIS12 3.4 8.0 1.0 HD2 F:HIS39 3.4 9.0 1.0 ND1 F:HIS35 4.1 9.2 1.0 CG F:HIS35 4.2 6.4 1.0 ND1 A:HIS16 4.2 8.7 1.0 ND1 F:HIS39 4.2 13.3 1.0 ND1 A:HIS12 4.2 10.9 1.0 CG A:HIS16 4.3 6.7 1.0 CG F:HIS39 4.3 10.0 1.0 O A:HOH57 4.3 11.2 1.0 CG A:HIS12 4.3 8.1 1.0 HD1 F:HIS35 4.9 11.1 1.0 HD1 A:HIS16 5.0 10.5 1.0 HD1 F:HIS39 5.0 15.9 1.0

Cobalt binding site 6 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ G:Co47 b:7.0 occ:1.00 HE2 D:HIS35 1.3 9.3 1.0 HE2 D:HIS39 1.3 7.8 0.5 HE2 D:HIS39 1.4 11.5 0.5 NE2 D:HIS35 2.1 7.8 1.0 NE2 G:HIS16 2.1 7.2 1.0 OD1 D:ASP46 2.2 10.4 1.0 NE2 G:HIS12 2.2 9.6 1.0 NE2 D:HIS39 2.2 6.5 0.5 NE2 D:HIS39 2.2 9.6 0.5 OD2 D:ASP46 2.2 10.3 1.0 CG D:ASP46 2.5 10.6 1.0 CD2 D:HIS35 3.0 6.8 1.0 CE1 G:HIS16 3.1 9.0 1.0 CE1 D:HIS35 3.1 10.7 1.0 CE1 G:HIS12 3.1 13.0 1.0 CE1 D:HIS39 3.1 6.7 0.5 CD2 G:HIS16 3.1 6.0 1.0 CE1 D:HIS39 3.1 9.9 0.5 HE1 D:HIS39 3.2 8.1 0.5 CD2 D:HIS39 3.2 8.0 0.5 HE1 G:HIS16 3.2 10.8 1.0 HD2 D:HIS35 3.2 8.2 1.0 HE1 G:HIS12 3.2 15.6 1.0 CD2 G:HIS12 3.2 7.4 1.0 CD2 D:HIS39 3.2 6.0 0.5 HE1 D:HIS35 3.3 12.8 1.0 HE1 D:HIS39 3.3 11.9 0.5 HD2 G:HIS16 3.3 7.2 1.0 HD2 D:HIS39 3.4 9.6 0.5 HD2 G:HIS12 3.4 8.9 1.0 HD2 D:HIS39 3.5 7.2 0.5 CB D:ASP46 4.0 11.7 1.0 ND1 D:HIS35 4.1 11.1 1.0 ND1 G:HIS16 4.2 8.8 1.0 CG D:HIS35 4.2 8.1 1.0 ND1 G:HIS12 4.2 12.9 1.0 ND1 D:HIS39 4.2 8.0 0.5 CG G:HIS16 4.2 5.9 1.0 ND1 D:HIS39 4.3 10.2 0.5 O D:HOH167 4.3 21.7 1.0 CG D:HIS39 4.3 8.8 0.5 CG G:HIS12 4.3 9.3 1.0 CG D:HIS39 4.3 6.6 0.5 HB3 D:ASP46 4.4 14.0 1.0 HB2 D:ASP46 4.4 14.0 1.0 HA D:ASP46 4.6 13.2 1.0 CA D:ASP46 4.8 11.0 1.0 H D:ASP46 4.9 14.7 1.0 N D:ASP46 4.9 12.3 1.0 HD1 D:HIS35 4.9 13.3 1.0 HD1 G:HIS16 4.9 10.6 1.0 HD1 G:HIS12 5.0 15.5 1.0

Cobalt binding site 7 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


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 De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ G:Co48 b:7.0 occ:1.00 HE2 D:HIS16 1.4 7.7 1.0 HE2 D:HIS12 1.4 9.1 1.0 NE2 G:HIS35 2.1 8.5 1.0 NE2 G:HIS39 2.1 10.2 1.0 NE2 D:HIS16 2.2 6.4 1.0 NE2 D:HIS12 2.2 7.6 1.0 CE1 G:HIS35 3.0 8.0 1.0 CE1 G:HIS39 3.0 12.8 1.0 CD2 G:HIS35 3.1 6.5 1.0 CE1 D:HIS16 3.1 8.3 1.0 CE1 D:HIS12 3.1 10.1 1.0 CD2 G:HIS39 3.2 9.0 1.0 CD2 D:HIS16 3.2 5.6 1.0 HE1 G:HIS39 3.2 15.4 1.0 HE1 G:HIS35 3.2 9.6 1.0 CD2 D:HIS12 3.2 7.3 1.0 HE1 D:HIS16 3.2 9.9 1.0 HE1 D:HIS12 3.2 12.1 1.0 HD2 G:HIS35 3.3 7.9 1.0 HD2 G:HIS39 3.4 10.8 1.0 HD2 D:HIS16 3.4 6.7 1.0 HD2 D:HIS12 3.4 8.8 1.0 ND1 G:HIS35 4.1 9.4 1.0 ND1 G:HIS39 4.2 13.7 1.0 CG G:HIS35 4.2 7.3 1.0 ND1 D:HIS12 4.2 11.4 1.0 ND1 D:HIS16 4.2 8.2 1.0 CG G:HIS39 4.3 10.6 1.0 O D:HOH47 4.3 11.6 1.0 CG D:HIS16 4.3 6.4 1.0 CG D:HIS12 4.3 8.9 1.0 HD1 G:HIS35 4.9 11.2 1.0 HD1 G:HIS39 4.9 16.4 1.0 HD1 D:HIS12 5.0 13.7 1.0 HD1 D:HIS16 5.0 9.9 1.0

Cobalt binding site 8 out of 8 in the Crystal Structure of De Novo Designed MID1-Cobalt


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of De Novo Designed MID1-Cobalt within 5.0Å range: probe atom residue distance (Å) B Occ H:Co47 b:7.1 occ:1.00 NE2 H:HIS35 2.1 7.8 1.0 NE2 E:HIS16 2.1 6.5 1.0 OD2 H:ASP46 2.1 9.5 1.0 NE2 H:HIS39 2.1 8.8 0.5 NE2 H:HIS39 2.2 6.7 0.5 NE2 E:HIS12 2.2 8.5 1.0 OD1 H:ASP46 2.2 10.8 1.0 CG H:ASP46 2.5 10.1 1.0 CE1 H:HIS35 3.0 10.1 1.0 CE1 E:HIS16 3.0 8.8 1.0 CE1 H:HIS39 3.0 9.5 0.5 CD2 H:HIS35 3.1 6.7 1.0 CE1 H:HIS39 3.1 7.6 0.5 CE1 E:HIS12 3.1 12.6 1.0 CD2 E:HIS16 3.1 5.3 1.0 HE1 H:HIS39 3.2 11.4 0.5 CD2 H:HIS39 3.2 7.5 0.5 HE1 E:HIS16 3.2 10.6 1.0 CD2 H:HIS39 3.2 6.5 0.5 HE1 H:HIS35 3.2 12.1 1.0 HE1 E:HIS12 3.2 15.2 1.0 HE1 H:HIS39 3.2 9.1 0.5 CD2 E:HIS12 3.3 8.2 1.0 HD2 H:HIS35 3.3 8.0 1.0 HD2 E:HIS16 3.4 6.3 1.0 HD2 H:HIS39 3.4 7.8 0.5 HD2 H:HIS39 3.4 9.0 0.5 HD2 E:HIS12 3.5 9.8 1.0 CB H:ASP46 4.0 11.2 1.0 ND1 H:HIS35 4.1 11.4 1.0 ND1 E:HIS16 4.2 8.9 1.0 ND1 H:HIS39 4.2 9.9 0.5 CG H:HIS35 4.2 8.5 1.0 ND1 H:HIS39 4.2 7.4 0.5 CG E:HIS16 4.2 6.2 1.0 ND1 E:HIS12 4.3 13.6 1.0 O H:HOH135 4.3 21.2 1.0 CG H:HIS39 4.3 8.4 0.5 CG H:HIS39 4.3 6.8 0.5 CG E:HIS12 4.4 9.4 1.0 HB3 H:ASP46 4.4 13.5 1.0 HB2 H:ASP46 4.4 13.5 1.0 HA H:ASP46 4.6 13.1 1.0 CA H:ASP46 4.8 10.9 1.0 H H:ASP46 4.9 15.0 1.0 N H:ASP46 4.9 12.5 1.0 O H:HOH409 4.9 32.0 1.0 HD1 H:HIS35 4.9 13.7 1.0 HD1 E:HIS16 4.9 10.8 1.0 HD1 H:HIS39 4.9 11.9 0.5 HD1 H:HIS39 5.0 8.9 0.5

B.S.Der, M.Machius, M.J.Miley, J.L.Mills, T.Szyperski, B.Kuhlman. Metal-Mediated Affinity and Orientation Specificity in A Computationally Designed Protein Homodimer. J.Am.Chem.Soc. V. 134 375 2012.
ISSN: ISSN 0002-7863
PubMed: 22092237
DOI: 10.1021/JA208015J