Copper in PDB 1s4c: Yhch Protein (HI0227) Copper Complex

The structure of Yhch Protein (HI0227) Copper Complex, PDB code: 1s4c was solved by A.Teplyakov, G.Obmolova, J.Toedt, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.20
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.900, 153.900, 53.800, 90.00, 112.90, 90.00
R / Rfree (%)	17.6 / 24.6

The binding sites of Copper atom in the Yhch Protein (HI0227) Copper Complex (pdb code 1s4c). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Yhch Protein (HI0227) Copper Complex, PDB code: 1s4c:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in the Yhch Protein (HI0227) Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Yhch Protein (HI0227) Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu201 b:44.0 occ:1.00 OD2 A:ASP70 1.9 40.4 1.0 OXT A:ACT205 2.1 54.4 1.0 NE2 A:HIS65 2.2 27.1 1.0 NE2 A:HIS130 2.3 33.3 1.0 O A:ACT205 2.9 68.9 1.0 C A:ACT205 2.9 66.8 1.0 CG A:ASP70 3.0 52.2 1.0 CD2 A:HIS130 3.1 25.4 1.0 CD2 A:HIS65 3.1 38.0 1.0 CE1 A:HIS65 3.3 28.2 1.0 CE1 A:HIS130 3.3 26.7 1.0 OD1 A:ASP70 3.5 36.6 1.0 NE2 A:GLN72 3.7 35.7 1.0 NZ A:LYS149 3.9 38.9 1.0 OE1 A:GLU63 4.1 63.2 1.0 CD A:GLU63 4.1 68.6 1.0 CG A:GLU63 4.1 48.4 1.0 CB A:ASP70 4.3 33.6 1.0 CG A:HIS65 4.3 27.7 1.0 CG A:HIS130 4.3 39.4 1.0 ND1 A:HIS65 4.3 33.5 1.0 CH3 A:ACT205 4.4 64.6 1.0 ND1 A:HIS130 4.4 44.0 1.0 OE2 A:GLU63 4.7 62.9 1.0

Copper binding site 2 out of 4 in the Yhch Protein (HI0227) Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Yhch Protein (HI0227) Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu202 b:46.2 occ:1.00 OD2 B:ASP70 1.9 44.4 1.0 NE2 B:HIS65 2.0 37.7 1.0 NE2 B:HIS130 2.2 27.2 1.0 O B:HOH227 2.3 54.6 1.0 OE2 B:GLU63 2.7 73.3 1.0 CG B:ASP70 2.9 48.8 1.0 CD2 B:HIS65 3.0 42.3 1.0 CE1 B:HIS65 3.0 37.2 1.0 CE1 B:HIS130 3.0 37.2 1.0 CD2 B:HIS130 3.3 37.5 1.0 OD1 B:ASP70 3.4 44.3 1.0 NE2 B:GLN72 3.7 41.0 1.0 CD B:GLU63 3.8 88.8 1.0 NZ B:LYS149 3.8 50.3 1.0 ND1 B:HIS65 4.1 49.7 1.0 CG B:HIS65 4.1 34.3 1.0 CG B:GLU63 4.1 63.0 1.0 CB B:ASP70 4.2 33.9 1.0 ND1 B:HIS130 4.2 42.6 1.0 CG B:HIS130 4.4 39.4 1.0 OE1 B:GLU63 4.9 80.5 1.0 CE B:LYS149 4.9 47.2 1.0

Copper binding site 3 out of 4 in the Yhch Protein (HI0227) Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Yhch Protein (HI0227) Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu203 b:47.9 occ:1.00 OD2 C:ASP70 2.0 47.4 1.0 NE2 C:HIS65 2.1 36.1 1.0 NE2 C:HIS130 2.2 37.8 1.0 O C:HOH215 2.6 43.8 1.0 CD2 C:HIS65 3.0 26.2 1.0 CG C:ASP70 3.1 47.0 1.0 CE1 C:HIS130 3.2 37.7 1.0 CE1 C:HIS65 3.2 30.2 1.0 CD2 C:HIS130 3.2 40.1 1.0 OE2 C:GLU63 3.3 95.0 1.0 CD C:GLU63 3.4 72.2 1.0 OD1 C:ASP70 3.6 42.4 1.0 OE1 C:GLU63 3.8 61.8 1.0 CG C:GLU63 3.8 66.2 1.0 NE2 C:GLN72 3.8 53.9 1.0 NZ C:LYS149 4.0 43.1 1.0 CG C:HIS65 4.2 42.1 1.0 ND1 C:HIS65 4.2 31.0 1.0 CB C:ASP70 4.3 27.6 1.0 ND1 C:HIS130 4.3 34.5 1.0 CG C:HIS130 4.3 29.7 1.0

Copper binding site 4 out of 4 in the Yhch Protein (HI0227) Copper Complex


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Yhch Protein (HI0227) Copper Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu204 b:53.2 occ:1.00 NE2 D:HIS65 2.1 65.2 1.0 OD2 D:ASP70 2.2 52.7 1.0 NE2 D:HIS130 2.2 46.0 1.0 O D:HOH232 2.6 54.2 1.0 CG D:ASP70 2.9 49.4 1.0 CE1 D:HIS65 3.0 54.1 1.0 CE1 D:HIS130 3.0 39.1 1.0 OD1 D:ASP70 3.1 50.4 1.0 CD2 D:HIS65 3.1 39.8 1.0 CD2 D:HIS130 3.3 54.5 1.0 NE2 D:GLN72 3.7 47.6 1.0 NZ D:LYS149 4.0 58.2 1.0 ND1 D:HIS65 4.1 64.5 1.0 CB D:ASP70 4.2 40.2 1.0 CG D:GLU63 4.2 72.4 1.0 ND1 D:HIS130 4.2 38.2 1.0 CG D:HIS65 4.2 64.1 1.0 CG D:HIS130 4.4 31.6 1.0 OE1 D:GLU63 4.9 81.0 1.0 CD D:GLU63 4.9 95.2 1.0 CE D:LYS149 4.9 46.2 1.0 CD D:GLN72 5.0 74.4 1.0

A.Teplyakov, G.Obmolova, J.Toedt, M.Y.Galperin, G.L.Gilliland. Crystal Structure of the Bacterial Yhch Protein Indicates A Role in Sialic Acid Catabolism. J.Bacteriol. V. 187 5520 2005.
ISSN: ISSN 0021-9193
PubMed: 16077096
DOI: 10.1128/JB.187.16.5520-5527.2005