Cobalt in PDB 9d2a: Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3

The structure of Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3, PDB code: 9d2a was solved by M.N.Gaynes, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.41 / 2.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	274.483, 90.769, 193.942, 90, 134.79, 90
R / Rfree (%)	19.8 / 22.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3 (pdb code 9d2a). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 13 binding sites of Cobalt where determined in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3, PDB code: 9d2a:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co702 b:85.6 occ:1.00 OD2 C:ASP360 2.0 87.9 1.0 OD1 C:ASP356 2.2 66.9 1.0 O C:HOH849 2.8 63.1 1.0 CG C:ASP360 3.2 82.7 1.0 CG C:ASP356 3.3 58.5 1.0 OD2 C:ASP356 3.7 70.8 1.0 OD1 C:ASP360 3.9 86.8 1.0 OD1 C:ASP357 4.3 67.7 1.0 CB C:ASP360 4.3 66.8 1.0 O C:ASP356 4.4 66.1 1.0 CB C:ASP356 4.6 49.5 1.0 C C:ASP356 4.7 68.5 1.0

Cobalt binding site 2 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co703 b:84.6 occ:1.00 SG C:CYS83 2.3 51.5 1.0 O C:HOH866 3.0 50.7 1.0 ND1 C:HIS82 3.2 60.2 1.0 N C:CYS83 3.6 48.4 1.0 CB C:CYS83 3.6 39.4 1.0 CB C:HIS82 3.8 58.5 1.0 CG C:HIS82 3.9 69.4 1.0 CA C:CYS83 3.9 43.9 1.0 C C:HIS82 4.2 60.7 1.0 CE1 C:HIS82 4.2 76.2 1.0 CA C:HIS82 4.5 60.1 1.0 N C:HIS82 4.9 51.3 1.0 O C:HIS82 5.0 48.0 1.0

Cobalt binding site 3 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co704 b:127.5 occ:1.00 NE2 C:HIS174 2.1 86.6 1.0 CE1 C:HIS174 3.1 79.0 1.0 CD2 C:HIS174 3.2 75.0 1.0 ND1 C:HIS174 4.2 63.0 1.0 CG C:HIS174 4.3 58.7 1.0 CA C:VAL171 4.9 45.8 1.0

Cobalt binding site 4 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co702 b:104.8 occ:1.00 OD1 D:ASP356 2.2 59.8 1.0 O D:HOH864 2.8 56.2 1.0 OD2 D:ASP360 3.0 95.9 1.0 CG D:ASP356 3.1 48.7 1.0 OD2 D:ASP356 3.3 64.5 1.0 CG D:ASP360 4.0 83.2 1.0 CB D:ASP360 4.2 64.4 1.0 CB D:ASP356 4.5 42.2 1.0 OD1 D:ASP357 4.7 75.1 1.0 O D:ASP356 4.9 62.4 1.0 C D:ASP356 4.9 59.8 1.0

Cobalt binding site 5 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co703 b:101.0 occ:1.00 SG D:CYS83 2.1 65.4 1.0 O D:HOH882 2.9 55.4 1.0 CB D:CYS83 3.3 45.9 1.0 N D:CYS83 3.3 49.3 1.0 ND1 D:HIS82 3.3 61.1 1.0 CA D:CYS83 3.6 48.1 1.0 C D:HIS82 4.0 57.6 1.0 CB D:HIS82 4.0 60.4 1.0 CG D:HIS82 4.1 68.9 1.0 CE1 D:HIS82 4.3 70.3 1.0 CA D:HIS82 4.5 59.2 1.0 O D:HIS82 4.8 52.3 1.0 N D:HIS82 4.9 52.0 1.0

Cobalt binding site 6 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co704 b:90.6 occ:1.00 NE2 D:HIS174 2.2 76.8 1.0 O D:HOH852 2.6 68.7 1.0 CE1 D:HIS174 2.7 62.6 1.0 O D:HOH885 3.4 59.6 1.0 CD2 D:HIS174 3.4 64.7 1.0 ND1 D:HIS174 3.9 54.4 1.0 CG D:HIS174 4.3 60.9 1.0 O D:ASP170 4.6 48.4 1.0 OH B:TYR442 4.7 61.6 1.0 CB D:ASP170 5.0 55.3 1.0 C D:ASP170 5.0 42.6 1.0

Cobalt binding site 7 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co702 b:82.2 occ:1.00 SG A:CYS83 2.2 49.4 1.0 O A:HOH894 2.8 40.9 1.0 ND1 A:HIS82 3.2 53.4 1.0 CB A:CYS83 3.4 33.8 1.0 N A:CYS83 3.5 45.1 1.0 CA A:CYS83 3.8 37.1 1.0 CB A:HIS82 4.0 49.8 1.0 CG A:HIS82 4.1 64.2 1.0 CE1 A:HIS82 4.2 68.5 1.0 C A:HIS82 4.2 45.7 1.0 CA A:HIS82 4.7 49.1 1.0

Cobalt binding site 8 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


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 (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co703 b:96.0 occ:1.00 NE2 A:HIS174 2.1 76.3 1.0 O A:HOH882 2.7 53.8 1.0 CE1 A:HIS174 3.0 75.9 1.0 CD2 A:HIS174 3.2 54.3 1.0 ND1 A:HIS174 4.1 61.8 1.0 CG A:HIS174 4.3 66.2 1.0 CA A:VAL171 4.9 37.4 1.0

Cobalt binding site 9 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co704 b:89.3 occ:1.00 OD2 A:ASP356 2.3 63.6 1.0 OD2 A:ASP360 2.5 83.4 1.0 CG A:ASP356 3.3 51.3 1.0 CG A:ASP360 3.4 90.5 1.0 OD1 A:ASP360 3.5 92.6 1.0 OD1 A:ASP356 3.6 63.0 1.0 O A:HOH905 4.1 64.2 1.0 OD1 A:ASP357 4.3 65.9 1.0 CB A:ASP356 4.6 40.5 1.0 O A:ASP356 4.7 52.9 1.0 CB A:ASP360 4.9 71.1 1.0 C A:ASP356 4.9 51.2 1.0

Cobalt binding site 10 out of 13 in the Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of (+)-Sabinene Synthase From Thuja Plicata: Condition 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co703 b:73.7 occ:1.00 O B:HOH802 2.1 55.7 1.0 OD2 B:ASP356 2.3 47.7 1.0 OD2 B:ASP360 2.3 70.3 1.0 O B:HOH933 2.5 55.1 1.0 CO B:CO705 2.7 112.8 1.0 CG B:ASP360 3.3 65.9 1.0 CG B:ASP356 3.4 44.2 1.0 O B:HOH931 3.6 60.3 1.0 OD1 B:ASP360 3.7 76.2 1.0 OD1 B:ASP356 3.8 51.5 1.0 OD1 B:ASP357 4.3 59.0 1.0 CB B:ASP360 4.5 66.0 1.0 CB B:ASP356 4.6 43.4 1.0 O B:HOH934 4.8 53.0 1.0 O B:ASP356 4.9 48.2 1.0 C B:ASP356 5.0 48.8 1.0

M.N.Gaynes, K.R.Osika, D.W.Christianson. Structure and Function of Sabinene Synthase, A Monoterpene Cyclase That Generates A Highly Strained [3.1.0] Bicyclic Product. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39527408
DOI: 10.1021/ACS.BIOCHEM.4C00476