Cobalt in PDB 6lkb: Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71.

All present enzymatic activity of Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71.:
5.2.1.8;

The structure of Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71., PDB code: 6lkb was solved by S.Lakhanpal, C.Jobichen, K.Swaminathan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.48 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.954, 60.928, 127.044, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.3

The binding sites of Cobalt atom in the Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71. (pdb code 6lkb). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71., PDB code: 6lkb:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71.


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 the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co702 b:18.1 occ:1.00 ND1 B:HIS481 2.1 17.6 1.0 ND1 A:HIS481 2.1 18.8 1.0 OD1 B:ASP486 2.1 17.3 1.0 OD1 A:ASP486 2.1 17.5 1.0 OD2 A:ASP486 2.2 20.4 1.0 OD2 B:ASP486 2.3 20.2 1.0 CG A:ASP486 2.5 19.8 1.0 CG B:ASP486 2.5 17.9 1.0 CE1 A:HIS481 3.0 17.2 1.0 CE1 B:HIS481 3.0 17.4 1.0 CG B:HIS481 3.1 15.8 1.0 CG A:HIS481 3.1 15.7 1.0 CB B:HIS481 3.5 16.6 1.0 CB A:HIS481 3.5 16.0 1.0 CB A:ASP486 4.0 19.2 1.0 CB B:ASP486 4.0 19.7 1.0 NE2 A:HIS481 4.1 18.0 1.0 NE2 B:HIS481 4.1 18.5 1.0 CA B:HIS481 4.2 17.0 1.0 CA A:HIS481 4.2 16.2 1.0 CD2 B:HIS481 4.2 17.7 1.0 CD2 A:HIS481 4.2 16.6 1.0 HO3 A:GOL701 4.4 45.8 1.0 O B:HOH828 4.7 23.1 1.0 CA A:ASP486 4.7 18.1 1.0 CA B:ASP486 4.8 18.6 1.0 O3 A:GOL701 4.8 38.1 1.0 O A:HOH845 4.8 23.0 1.0 N A:ASP486 4.8 18.6 1.0 N B:ASP486 4.9 18.3 1.0 C A:GLY485 5.0 18.4 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71.


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 the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co704 b:47.6 occ:1.00 O A:HOH938 2.2 33.7 1.0 ND1 A:HIS506 2.8 20.2 1.0 CE1 A:HIS506 3.4 22.3 1.0 ND2 A:ASN509 3.6 22.3 1.0 CB A:ASN509 3.8 19.2 1.0 CB A:TYR511 3.9 19.6 1.0 CD1 A:TYR511 3.9 22.4 1.0 CA A:HIS506 3.9 15.7 1.0 CG A:HIS506 4.0 16.9 1.0 CG A:TYR511 4.2 18.0 1.0 O A:HOH919 4.2 35.0 1.0 CG A:ASN509 4.2 22.3 1.0 O A:THR505 4.4 18.4 1.0 CG2 A:ILE541 4.5 19.3 1.0 N A:HIS506 4.5 16.0 1.0 CB A:HIS506 4.5 16.0 1.0 NE2 A:HIS506 4.6 21.1 1.0 C A:THR505 4.7 20.8 1.0 O A:HIS506 4.7 19.3 1.0 O A:HOH902 4.7 44.0 1.0 C A:HIS506 4.8 16.6 1.0 CG2 A:THR505 4.8 21.5 1.0 CE1 A:TYR511 4.8 21.3 1.0 CA A:TYR511 4.9 18.8 1.0 CD2 A:HIS506 4.9 21.6 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71.


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 the Peptidylprolyl Isomerase Domain of Arabidopsis Thaliana CYP71. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co703 b:70.6 occ:1.00 OD1 B:ASP601 2.1 35.5 1.0 CG B:ASP601 3.1 35.2 1.0 N B:ASP601 3.1 24.4 1.0 N B:MET600 3.1 22.3 1.0 N B:GLY599 3.5 21.0 1.0 C B:GLY599 3.6 21.3 1.0 CA B:GLY599 3.6 19.6 1.0 CB B:ASP601 3.7 26.9 1.0 CA B:MET600 3.9 23.2 1.0 O B:HOH875 3.9 37.2 1.0 C B:MET600 4.0 22.8 1.0 CA B:ASP601 4.0 25.3 1.0 CB B:MET600 4.0 23.7 1.0 O B:HOH955 4.0 56.4 1.0 OD2 B:ASP601 4.0 41.2 1.0 CE B:MET600 4.1 27.1 1.0 SD B:MET600 4.4 27.1 1.0 O B:GLY599 4.6 20.2 1.0 C B:LYS598 4.7 21.6 1.0 CG B:MET600 4.8 25.2 1.0

S.Lakhanpal, J.S.Fan, S.Luan, K.Swaminathan. Structural and Functional Analyses of the Ppiase Domain of Arabidopsis Thaliana CYP71 Reveal Its Catalytic Activity Toward Histone H3. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 33098102
DOI: 10.1002/1873-3468.13965