Cobalt in PDB 3hdi: Crystal Structure of Bacillus Halodurans Metallo Peptidase

The structure of Crystal Structure of Bacillus Halodurans Metallo Peptidase, PDB code: 3hdi was solved by A.Aleshin, S.Gramatikova, A.Y.Strongin, B.Stec, R.C.Liddington, J.W.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.141, 193.981, 125.567, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 26.9

The binding sites of Cobalt atom in the Crystal Structure of Bacillus Halodurans Metallo Peptidase (pdb code 3hdi). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Bacillus Halodurans Metallo Peptidase, PDB code: 3hdi:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Bacillus Halodurans Metallo Peptidase


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 Bacillus Halodurans Metallo Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Co500 b:47.0 occ:1.00 NE2 A:HIS46 2.2 46.3 1.0 NE2 A:HIS50 2.3 50.1 1.0 OE2 A:GLU126 2.3 47.6 1.0 O C:ALA14 2.4 77.8 0.5 OE1 A:GLU126 2.6 35.6 1.0 CD A:GLU126 2.7 40.9 1.0 CE1 A:HIS46 3.0 43.7 1.0 CD2 A:HIS50 3.1 48.9 1.0 CE1 A:HIS50 3.3 49.2 1.0 CD2 A:HIS46 3.3 45.6 1.0 C C:ALA14 3.7 79.5 0.5 O C:ALA13 3.8 77.3 0.5 C C:ALA13 3.8 79.8 0.5 N C:ALA14 4.1 79.2 0.5 ND1 A:HIS46 4.2 43.1 1.0 CG A:GLU126 4.2 41.3 1.0 CA C:ALA13 4.2 80.7 0.5 CG A:HIS50 4.2 46.4 1.0 O C:ALA15 4.3 78.0 0.5 ND1 A:HIS50 4.3 49.1 1.0 OE2 A:GLU49 4.3 54.6 1.0 CG A:HIS46 4.3 43.4 1.0 CE2 B:TYR281 4.4 49.8 1.0 CD2 A:LEU157 4.4 34.4 1.0 CA C:ALA14 4.5 78.9 0.5 OH B:TYR281 4.6 43.4 1.0 N C:ALA15 4.6 81.3 0.5 OE1 A:GLU49 4.7 58.7 1.0 CA C:ALA15 4.7 81.2 0.5 CZ B:TYR281 4.9 48.9 1.0 C C:ALA15 4.9 80.5 0.5 CD A:GLU49 4.9 57.1 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Bacillus Halodurans Metallo Peptidase


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 Bacillus Halodurans Metallo Peptidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Co500 b:46.6 occ:1.00 NE2 B:HIS50 2.1 56.0 1.0 OE1 B:GLU126 2.2 44.9 1.0 NE2 B:HIS46 2.3 44.0 1.0 O D:ALA14 2.4 90.9 0.5 OE2 B:GLU126 2.7 43.5 1.0 CD B:GLU126 2.8 42.7 1.0 N D:ALA14 3.0 92.8 0.5 CE1 B:HIS50 3.0 56.7 1.0 CD2 B:HIS50 3.2 56.8 1.0 CE1 B:HIS46 3.2 45.7 1.0 C D:ALA14 3.2 91.8 0.5 CD2 B:HIS46 3.3 46.1 1.0 C D:ALA13 3.3 93.3 0.5 CA D:ALA14 3.5 92.2 0.5 CA D:ALA13 3.7 93.8 0.5 O D:ALA13 4.0 92.7 0.5 OE2 B:GLU49 4.1 57.3 1.0 ND1 B:HIS50 4.2 60.6 1.0 OH A:TYR281 4.2 57.1 1.0 CG B:HIS50 4.3 58.6 1.0 CG B:GLU126 4.3 41.5 1.0 CE2 A:TYR281 4.3 54.3 1.0 ND1 B:HIS46 4.3 46.9 1.0 CG B:HIS46 4.4 45.7 1.0 N D:ALA15 4.4 92.1 0.5 CD2 B:LEU157 4.5 39.5 1.0 N D:ALA13 4.6 94.0 0.5 OE1 B:GLU49 4.6 56.4 1.0 CZ A:TYR281 4.7 56.2 1.0 CD B:GLU49 4.7 56.0 1.0 CB D:ALA13 4.8 92.3 0.5 CB D:ALA14 5.0 92.3 0.5 CA D:ALA15 5.0 91.3 0.5

A.E.Aleshin, S.Gramatikova, G.L.Hura, A.Bobkov, A.Y.Strongin, B.Stec, J.A.Tainer, R.C.Liddington, J.W.Smith. Crystal and Solution Structures of A Prokaryotic M16B Peptidase: An Open and Shut Case. Structure V. 17 1465 2009.
ISSN: ISSN 0969-2126
PubMed: 19913481
DOI: 10.1016/J.STR.2009.09.009