Cobalt in PDB 3f4d: Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10

The structure of Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10, PDB code: 3f4d was solved by R.Hawwa, J.Aikens, R.J.Turner, B.Santarsiero, A.Mesecar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.36
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.166, 156.734, 50.209, 90.00, 116.21, 90.00
R / Rfree (%)	17 / 24.9

The binding sites of Cobalt atom in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10 (pdb code 3f4d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10, PDB code: 3f4d:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10


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 Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co401 b:29.0 occ:1.00 O A:HOH569 2.0 46.3 1.0 NE2 A:HIS25 2.1 25.7 1.0 NE2 A:HIS23 2.1 26.8 1.0 OD1 A:ASP266 2.5 24.5 1.0 OQ1 A:KCX145 2.5 34.8 1.0 O A:HOH599 2.9 41.7 1.0 CE1 A:HIS23 3.0 24.9 1.0 CE1 A:HIS25 3.0 25.9 1.0 CD2 A:HIS25 3.1 26.2 1.0 CD2 A:HIS23 3.1 29.1 1.0 CG A:ASP266 3.2 25.8 1.0 CX A:KCX145 3.3 36.4 1.0 CO A:CO402 3.3 48.2 1.0 OD2 A:ASP266 3.3 22.9 1.0 OQ2 A:KCX145 3.5 38.6 1.0 O A:HOH648 3.6 42.1 1.0 ND1 A:HIS23 4.1 28.7 1.0 ND1 A:HIS25 4.1 25.5 1.0 CG A:HIS25 4.2 26.4 1.0 CG A:HIS23 4.2 28.1 1.0 NZ A:KCX145 4.4 35.8 1.0 CE1 A:HIS206 4.5 32.6 1.0 NE2 A:HIS206 4.5 33.9 1.0 CB A:ASP266 4.6 22.4 1.0 CG A:PRO69 4.6 27.6 1.0 O A:HOH750 4.9 68.2 1.0

Cobalt binding site 2 out of 4 in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10


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 Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co402 b:48.2 occ:1.00 O A:HOH569 2.1 46.3 1.0 OQ2 A:KCX145 2.3 38.6 1.0 ND1 A:HIS178 2.3 33.1 1.0 NE2 A:HIS206 2.4 33.9 1.0 O A:HOH599 3.0 41.7 1.0 CX A:KCX145 3.2 36.4 1.0 CE1 A:HIS178 3.2 32.3 1.0 CE1 A:HIS206 3.3 32.6 1.0 OH A:TYR99 3.3 49.2 1.0 OQ1 A:KCX145 3.3 34.8 1.0 CO A:CO401 3.3 29.0 1.0 CG A:HIS178 3.4 29.2 1.0 CD2 A:HIS206 3.4 31.9 1.0 CB A:HIS178 3.7 29.3 1.0 CE1 A:TYR99 4.1 47.7 1.0 CE1 A:HIS23 4.1 24.9 1.0 OD2 A:ASP266 4.1 22.9 1.0 CZ A:TYR99 4.2 47.4 1.0 NH1 A:ARG230 4.2 46.8 1.0 NE2 A:HIS23 4.3 26.8 1.0 O A:HOH750 4.4 68.2 1.0 NE2 A:HIS178 4.4 32.6 1.0 ND1 A:HIS206 4.4 32.5 1.0 NZ A:KCX145 4.4 35.8 1.0 CD2 A:HIS178 4.5 32.4 1.0 CG A:HIS206 4.5 29.9 1.0 CA A:HIS178 4.7 27.8 1.0 CG A:ASP266 4.9 25.8 1.0 OD1 A:ASP266 4.9 24.5 1.0 O A:HOH648 5.0 42.1 1.0

Cobalt binding site 3 out of 4 in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10


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 Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co401 b:31.6 occ:1.00 NE2 B:HIS25 2.1 26.1 1.0 NE2 B:HIS23 2.2 23.1 1.0 OD1 B:ASP266 2.3 38.4 1.0 O B:HOH570 2.3 39.4 1.0 OQ1 B:KCX145 2.4 33.6 1.0 CE1 B:HIS25 3.0 22.4 1.0 CG B:ASP266 3.1 36.2 1.0 CE1 B:HIS23 3.1 25.1 1.0 CX B:KCX145 3.1 38.2 1.0 CD2 B:HIS23 3.2 25.7 1.0 CD2 B:HIS25 3.2 27.2 1.0 OD2 B:ASP266 3.2 37.3 1.0 CO B:CO402 3.3 50.0 1.0 OQ2 B:KCX145 3.3 38.6 1.0 ND1 B:HIS25 4.2 25.9 1.0 NZ B:KCX145 4.2 38.2 1.0 ND1 B:HIS23 4.2 24.1 1.0 CG B:HIS25 4.3 25.4 1.0 CG B:HIS23 4.3 24.6 1.0 CE1 B:HIS206 4.5 35.3 1.0 NE2 B:HIS206 4.5 36.9 1.0 CB B:ASP266 4.5 33.3 1.0 CG B:PRO69 4.8 23.3 1.0 CA B:ASP266 5.0 31.0 1.0

Cobalt binding site 4 out of 4 in the Crystal Structure of Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10


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 Organophosphorus Hydrolase From Geobacillus Stearothermophilus Strain 10 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co402 b:50.0 occ:1.00 OQ2 B:KCX145 2.4 38.6 1.0 ND1 B:HIS178 2.4 39.6 1.0 NE2 B:HIS206 2.4 36.9 1.0 OH B:TYR99 3.1 54.0 1.0 CE1 B:HIS178 3.2 37.4 1.0 O B:HOH570 3.2 39.4 1.0 CO B:CO401 3.3 31.6 1.0 CX B:KCX145 3.3 38.2 1.0 OQ1 B:KCX145 3.4 33.6 1.0 CE1 B:HIS206 3.4 35.3 1.0 CD2 B:HIS206 3.4 36.0 1.0 CG B:HIS178 3.5 37.5 1.0 OD2 B:ASP266 3.8 37.3 1.0 NH2 B:ARG230 3.8 51.2 1.0 CB B:HIS178 3.9 36.8 1.0 CZ B:TYR99 4.1 51.7 1.0 CE1 B:TYR99 4.1 49.6 1.0 NE2 B:HIS23 4.3 23.1 1.0 NE2 B:HIS178 4.4 37.2 1.0 CE1 B:HIS23 4.4 25.1 1.0 NZ B:KCX145 4.5 38.2 1.0 ND1 B:HIS206 4.5 34.8 1.0 CG B:HIS206 4.6 34.2 1.0 CD2 B:HIS178 4.6 37.6 1.0 O B:HOH731 4.7 86.1 1.0 CG B:ASP266 4.7 36.2 1.0 OD1 B:ASP266 4.7 38.4 1.0 CZ B:ARG230 4.8 50.2 1.0 CA B:HIS178 4.9 35.2 1.0 O B:HOH650 4.9 54.5 1.0 NE B:ARG230 5.0 48.1 1.0

R.Hawwa, J.Aikens, R.J.Turner, B.D.Santarsiero, A.D.Mesecar. Structural Basis For Thermostability Revealed Through the Identification and Characterization of A Highly Thermostable Phosphotriesterase-Like Lactonase From Geobacillus Stearothermophilus. Arch.Biochem.Biophys. V. 488 109 2009.
ISSN: ISSN 0003-9861
PubMed: 19615330
DOI: 10.1016/J.ABB.2009.06.005