Cobalt in PDB 5xsv: Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form

All present enzymatic activity of Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form:
3.2.1.14;

The structure of Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form, PDB code: 5xsv was solved by Y.Nishitani, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.80 / 3.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	126.925, 104.730, 156.463, 90.00, 113.43, 90.00
R / Rfree (%)	27.8 / 29.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form (pdb code 5xsv). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 14 binding sites of Cobalt where determined in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form, PDB code: 5xsv:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1001 b:85.4 occ:1.00 NE2 A:HIS787 2.0 88.4 1.0 CE1 A:HIS787 2.7 88.4 1.0 OE2 A:GLU785 2.8 93.5 1.0 CD2 A:HIS787 3.2 88.4 1.0 CD A:GLU785 3.2 93.5 1.0 OE1 A:GLU785 3.7 93.5 1.0 O A:MET780 3.8 90.0 1.0 ND1 A:HIS787 3.9 88.4 1.0 CG A:GLU785 4.0 93.5 1.0 CG A:HIS787 4.2 88.4 1.0 C A:MET780 4.8 90.0 1.0

Cobalt binding site 2 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1002 b:73.6 occ:1.00 NE2 C:HIS799 1.9 95.3 1.0 NE2 A:HIS396 2.0 87.3 1.0 OD2 A:ASP794 2.1 85.4 1.0 CE1 A:HIS396 2.3 87.3 1.0 OD1 A:ASP794 2.4 85.4 1.0 CG A:ASP794 2.5 85.4 1.0 CE1 C:HIS799 2.8 95.3 1.0 CD2 C:HIS799 2.9 95.3 1.0 CD2 A:HIS396 3.3 87.3 1.0 ND1 A:HIS396 3.6 87.3 1.0 ND1 C:HIS799 3.9 95.3 1.0 OD1 C:ASP795 4.0 90.2 1.0 CB A:ASP794 4.0 85.4 1.0 CG C:HIS799 4.0 95.3 1.0 CG A:HIS396 4.0 87.3 1.0 CG2 A:ILE394 4.5 84.4 1.0 CA A:ASP794 4.9 85.4 1.0 CG C:ASP795 4.9 90.2 1.0 N A:ASP794 4.9 85.4 1.0

Cobalt binding site 3 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1003 b:99.0 occ:0.61 OD1 A:ASP670 2.3 0.6 1.0 OG A:SER669 2.8 98.6 1.0 CG A:ASP670 3.2 0.6 1.0 NZ A:LYS666 3.3 94.8 1.0 OD2 A:ASP670 3.4 0.6 1.0 CE A:LYS666 3.7 94.8 1.0 CB A:SER669 4.1 98.6 1.0 CD A:LYS666 4.1 94.8 1.0 CB A:ASP670 4.6 0.6 1.0 N A:ASP670 4.7 0.6 1.0

Cobalt binding site 4 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1004 b:0.5 occ:0.70 NE2 A:HIS765 2.2 0.1 1.0 CD2 A:HIS765 2.5 0.1 1.0 OD2 A:ASP764 2.6 0.8 1.0 CE1 A:HIS765 3.5 0.1 1.0 CG A:ASP764 3.7 0.8 1.0 CG A:HIS765 3.9 0.1 1.0 OD1 A:ASP764 4.1 0.8 1.0 ND1 A:HIS765 4.3 0.1 1.0 OD1 A:ASN715 4.7 97.1 1.0 O A:TRP761 4.8 97.4 1.0 CB A:ASP764 4.9 0.8 1.0

Cobalt binding site 5 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Co1007 b:83.9 occ:1.00 NE2 A:HIS799 1.7 85.8 1.0 OD2 C:ASP794 1.9 87.4 1.0 OD1 C:ASP794 1.9 87.4 1.0 CG C:ASP794 2.1 87.4 1.0 NE2 C:HIS396 2.2 91.1 1.0 CE1 C:HIS396 2.6 91.1 1.0 CD2 A:HIS799 2.7 85.8 1.0 CE1 A:HIS799 2.8 85.8 1.0 CD2 C:HIS396 3.5 91.1 1.0 CB C:ASP794 3.6 87.4 1.0 OD1 A:ASP795 3.8 87.1 1.0 CG A:HIS799 3.8 85.8 1.0 ND1 A:HIS799 3.9 85.8 1.0 ND1 C:HIS396 3.9 91.1 1.0 CG C:HIS396 4.3 91.1 1.0 CG2 C:ILE394 4.4 88.5 1.0 CA C:ASP794 4.5 87.4 1.0 CG A:ASP795 4.6 87.1 1.0 N C:ASP794 4.7 87.4 1.0 CA A:ASP795 4.8 87.1 1.0 O A:ASP795 4.9 87.1 1.0 CB A:ASP795 4.9 87.1 1.0

Cobalt binding site 6 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1001 b:84.0 occ:1.00 NE2 B:HIS787 2.2 88.1 1.0 CE1 B:HIS787 2.7 88.1 1.0 OE2 B:GLU785 2.8 91.1 1.0 CD B:GLU785 3.2 91.1 1.0 CD2 B:HIS787 3.4 88.1 1.0 OE1 B:GLU785 3.6 91.1 1.0 O B:MET780 3.6 89.9 1.0 ND1 B:HIS787 4.0 88.1 1.0 CG B:GLU785 4.0 91.1 1.0 CG B:HIS787 4.3 88.1 1.0 C B:MET780 4.6 89.9 1.0 CA B:LYS781 4.9 92.2 1.0

Cobalt binding site 7 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1002 b:79.9 occ:1.00 OD2 B:ASP794 1.9 88.2 1.0 NE2 B:HIS396 1.9 89.5 1.0 NE2 D:HIS799 1.9 0.2 1.0 OD1 B:ASP794 2.2 88.2 1.0 CE1 B:HIS396 2.2 89.5 1.0 CG B:ASP794 2.3 88.2 1.0 CE1 D:HIS799 2.9 0.2 1.0 CD2 D:HIS799 2.9 0.2 1.0 CD2 B:HIS396 3.2 89.5 1.0 OD1 D:ASP795 3.5 0.3 1.0 ND1 B:HIS396 3.5 89.5 1.0 CB B:ASP794 3.8 88.2 1.0 CG B:HIS396 4.0 89.5 1.0 ND1 D:HIS799 4.0 0.2 1.0 CG D:HIS799 4.1 0.2 1.0 CG2 B:ILE394 4.2 86.0 1.0 CG D:ASP795 4.4 0.3 1.0 CA B:ASP794 4.7 88.2 1.0 N B:ASP794 4.7 88.2 1.0 CA D:ASP795 4.8 0.3 1.0 CB D:ASP795 4.8 0.3 1.0 O D:ASP795 5.0 0.3 1.0

Cobalt binding site 8 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1003 b:0.4 occ:0.69 OD1 B:ASP670 2.9 0.8 1.0 OD2 B:ASP670 3.1 0.8 1.0 CG B:ASP670 3.4 0.8 1.0 NZ B:LYS666 3.4 0.8 1.0 CE B:LYS666 3.5 0.8 1.0 OG B:SER669 3.7 0.6 1.0 CD B:LYS666 4.1 0.8 1.0 CB B:ASP670 4.9 0.8 1.0 CB B:SER669 5.0 0.6 1.0

Cobalt binding site 9 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1004 b:0.4 occ:1.00 NE2 B:HIS765 2.3 99.9 1.0 CD2 B:HIS765 2.8 99.9 1.0 OD2 B:ASP764 3.1 0.1 1.0 CE1 B:HIS765 3.5 99.9 1.0 CG B:ASP764 4.1 0.1 1.0 CG B:HIS765 4.1 99.9 1.0 ND1 B:HIS765 4.4 99.9 1.0 OD1 B:ASP764 4.4 0.1 1.0 OD1 B:ASN715 4.7 96.5 1.0 O B:TRP761 4.9 98.9 1.0

Cobalt binding site 10 out of 14 in the Crystal Structure of An Archaeal Chitinase in the Ligand-Free Form


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 An Archaeal Chitinase in the Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Co1001 b:0.9 occ:0.79 NE2 C:HIS787 2.0 0.5 1.0 CE1 C:HIS787 2.3 0.5 1.0 OE2 C:GLU785 3.0 0.3 1.0 O C:MET780 3.2 0.2 1.0 CD C:GLU785 3.2 0.3 1.0 CD2 C:HIS787 3.3 0.5 1.0 OE1 C:GLU785 3.6 0.3 1.0 ND1 C:HIS787 3.6 0.5 1.0 CG C:GLU785 3.8 0.3 1.0 CG C:HIS787 4.1 0.5 1.0 C C:MET780 4.2 0.2 1.0 CA C:LYS781 4.7 1.0 1.0 N C:LYS781 4.8 1.0 1.0 CB C:MET780 4.9 0.2 1.0

Y.Nishitani, A.Horiuchi, M.Aslam, T.Kanai, H.Atomi, K.Miki. Crystal Structures of An Archaeal Chitinase Chid and Its Ligand Complexes. Glycobiology V. 28 418 2018.
ISSN: ESSN 1460-2423
PubMed: 29800365
DOI: 10.1093/GLYCOB/CWY024