Copper in PDB 5b7m: Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease

The structure of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease, PDB code: 5b7m was solved by M.Akter, Y.Higuchi, N.Shibata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.49 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.911, 106.915, 262.892, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Copper atom in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease (pdb code 5b7m). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 12 binding sites of Copper where determined in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease, PDB code: 5b7m:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu601 b:17.0 occ:1.00 ND1 A:HIS505 2.0 16.5 1.0 ND1 A:HIS443 2.0 15.8 1.0 SG A:CYS500 2.2 14.8 1.0 CE1 A:HIS443 3.0 17.5 1.0 CE1 A:HIS505 3.0 16.8 1.0 CG A:HIS505 3.0 16.4 1.0 CG A:HIS443 3.1 15.7 1.0 CB A:CYS500 3.2 14.4 1.0 SD A:MET510 3.2 16.7 1.0 CB A:HIS505 3.4 14.9 1.0 CB A:HIS443 3.5 18.1 1.0 CA A:HIS443 3.7 15.9 1.0 O A:LEU442 3.9 19.0 1.0 CE A:MET510 4.0 16.8 1.0 NE2 A:HIS505 4.1 16.7 1.0 NE2 A:HIS443 4.1 17.7 1.0 CD2 A:HIS505 4.1 14.5 1.0 CB A:LEU502 4.1 14.2 1.0 CD2 A:HIS443 4.2 17.9 1.0 N A:HIS443 4.5 15.9 1.0 C A:LEU442 4.5 19.4 1.0 CA A:CYS500 4.6 15.4 1.0 CG A:MET510 4.7 17.9 1.0 CD1 A:LEU502 4.7 14.6 1.0 CA A:HIS505 4.9 15.6 1.0 C A:HIS443 4.9 15.2 1.0 O A:LEU502 4.9 15.6 1.0 CG A:LEU502 5.0 15.4 1.0

Copper binding site 2 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu602 b:26.8 occ:0.65 NE2 A:HIS499 1.9 16.9 1.0 NE2 A:HIS448 1.9 19.9 1.0 NE2 A:HIS143 2.1 30.8 1.0 O A:HOH936 2.4 37.9 1.0 CE1 A:HIS448 2.8 23.3 1.0 CD2 A:HIS499 2.8 19.2 1.0 CE1 A:HIS499 2.9 17.6 1.0 CD2 A:HIS143 2.9 25.6 1.0 CD2 A:HIS448 3.0 19.6 1.0 CE1 A:HIS143 3.2 30.4 1.0 CU A:CU604 3.5 36.1 0.4 CD2 A:HIS446 3.6 16.4 1.0 NE2 A:HIS101 3.9 24.1 1.0 ND1 A:HIS499 4.0 17.9 1.0 CG A:HIS499 4.0 18.6 1.0 ND1 A:HIS448 4.0 21.6 1.0 CD2 A:HIS101 4.1 21.9 1.0 CG A:HIS143 4.1 24.4 1.0 CG A:HIS448 4.1 18.3 1.0 ND1 A:HIS143 4.2 28.9 1.0 NE2 A:HIS446 4.2 17.8 1.0 CE1 A:HIS101 4.5 22.0 1.0 CB A:MET497 4.6 21.9 1.0 CG A:HIS101 4.7 22.1 1.0 CG A:HIS446 4.7 15.7 1.0 CU A:CU603 4.8 20.1 0.8 ND1 A:HIS101 4.9 23.5 1.0 OE1 A:GLU506 5.0 30.1 1.0

Copper binding site 3 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu603 b:20.1 occ:0.85 ND1 A:HIS103 1.9 15.6 1.0 NE2 A:HIS141 2.0 15.9 1.0 NE2 A:HIS501 2.2 17.9 1.0 O A:HOH936 2.4 37.9 1.0 CE1 A:HIS103 2.9 13.4 1.0 CD2 A:HIS141 3.0 14.3 1.0 CE1 A:HIS141 3.0 18.0 1.0 CG A:HIS103 3.0 14.0 1.0 CD2 A:HIS501 3.1 20.6 1.0 CE1 A:HIS501 3.2 18.5 1.0 CB A:HIS103 3.4 14.3 1.0 CZ2 A:TRP139 3.6 15.1 1.0 CU A:CU604 3.9 36.1 0.4 CE2 A:TRP139 4.0 13.8 1.0 NE2 A:HIS103 4.0 13.9 1.0 ND1 A:HIS141 4.1 16.5 1.0 CD2 A:HIS103 4.1 13.9 1.0 CG A:HIS141 4.1 14.8 1.0 NE1 A:TRP139 4.1 13.3 1.0 CD2 A:HIS101 4.2 21.9 1.0 CG A:HIS501 4.3 18.7 1.0 ND1 A:HIS501 4.3 18.4 1.0 CH2 A:TRP139 4.3 15.5 1.0 CD2 A:HIS446 4.4 16.4 1.0 NE2 A:HIS446 4.5 17.8 1.0 NE2 A:HIS101 4.6 24.1 1.0 CA A:HIS103 4.7 14.3 1.0 CU A:CU602 4.8 26.8 0.7 CD2 A:TRP139 5.0 12.0 1.0

Copper binding site 4 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu604 b:36.1 occ:0.40 NE2 A:HIS446 1.9 17.8 1.0 NE2 A:HIS101 1.9 24.1 1.0 CD2 A:HIS446 2.6 16.4 1.0 O A:HOH936 2.8 37.9 1.0 CD2 A:HIS101 2.9 21.9 1.0 CE1 A:HIS101 2.9 22.0 1.0 CE1 A:HIS446 3.0 19.2 1.0 O A:HOH798 3.1 23.2 1.0 NE2 A:HIS448 3.3 19.9 1.0 CD2 A:HIS448 3.3 19.6 1.0 CG A:HIS103 3.4 14.0 1.0 ND1 A:HIS103 3.5 15.6 1.0 CU A:CU602 3.5 26.8 0.7 CA A:HIS103 3.6 14.3 1.0 CB A:HIS103 3.7 14.3 1.0 CG A:HIS446 3.8 15.7 1.0 CU A:CU603 3.9 20.1 0.8 ND1 A:HIS446 4.0 15.5 1.0 ND1 A:HIS101 4.0 23.5 1.0 CG A:HIS101 4.0 22.1 1.0 CE1 A:HIS448 4.0 23.3 1.0 CE1 A:HIS103 4.0 13.4 1.0 CG A:HIS448 4.0 18.3 1.0 CD2 A:HIS103 4.0 13.9 1.0 NE2 A:HIS103 4.3 13.9 1.0 ND1 A:HIS448 4.4 21.6 1.0 N A:GLY104 4.4 15.3 1.0 N A:HIS103 4.5 14.7 1.0 C A:HIS103 4.5 15.3 1.0 NE2 A:HIS499 4.7 16.9 1.0 NE2 A:HIS141 4.9 15.9 1.0 O A:TRP102 4.9 18.2 1.0 CA A:HIS448 4.9 17.9 1.0 C A:TRP102 5.0 17.4 1.0 CB A:HIS448 5.0 18.9 1.0 O A:HOH758 5.0 24.5 1.0

Copper binding site 5 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu601 b:17.2 occ:1.00 ND1 B:HIS505 2.0 14.7 1.0 ND1 B:HIS443 2.1 17.4 1.0 SG B:CYS500 2.2 14.3 1.0 CE1 B:HIS505 3.0 15.8 1.0 CG B:HIS505 3.0 16.2 1.0 CE1 B:HIS443 3.1 17.9 1.0 CG B:HIS443 3.1 15.9 1.0 CB B:CYS500 3.2 13.3 1.0 SD B:MET510 3.2 17.2 1.0 CB B:HIS505 3.4 13.9 1.0 CB B:HIS443 3.4 15.0 1.0 CA B:HIS443 3.7 13.7 1.0 O B:LEU442 3.9 19.5 1.0 CE B:MET510 4.0 20.1 1.0 CB B:LEU502 4.1 12.6 1.0 NE2 B:HIS505 4.1 16.5 1.0 CD2 B:HIS505 4.2 14.5 1.0 NE2 B:HIS443 4.2 16.8 1.0 CD2 B:HIS443 4.2 16.4 1.0 N B:HIS443 4.5 13.9 1.0 C B:LEU442 4.5 19.8 1.0 CA B:CYS500 4.6 12.6 1.0 CD1 B:LEU502 4.7 15.6 1.0 CG B:MET510 4.7 17.4 1.0 CA B:HIS505 4.9 14.8 1.0 CG B:LEU502 4.9 13.7 1.0 C B:HIS443 4.9 16.0 1.0 O B:LEU502 5.0 14.9 1.0

Copper binding site 6 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu602 b:24.5 occ:0.50 NE2 B:HIS499 1.8 18.8 1.0 NE2 B:HIS448 1.9 18.4 1.0 NE2 B:HIS143 2.0 34.9 1.0 O B:HOH931 2.5 35.4 1.0 CE1 B:HIS448 2.8 21.6 1.0 CE1 B:HIS499 2.8 17.4 1.0 CD2 B:HIS143 2.8 32.6 1.0 CD2 B:HIS499 2.9 18.8 1.0 CD2 B:HIS448 3.0 16.2 1.0 CE1 B:HIS143 3.1 34.5 1.0 CU B:CU604 3.4 41.4 0.4 CD2 B:HIS446 3.6 14.7 1.0 O B:HOH860 3.6 36.9 1.0 NE2 B:HIS101 3.9 25.2 1.0 ND1 B:HIS499 3.9 17.5 1.0 ND1 B:HIS448 3.9 19.4 1.0 CG B:HIS499 4.0 17.7 1.0 CD2 B:HIS101 4.0 24.1 1.0 CG B:HIS143 4.0 30.3 1.0 CG B:HIS448 4.1 16.3 1.0 ND1 B:HIS143 4.1 33.7 1.0 NE2 B:HIS446 4.2 15.4 1.0 CE1 B:HIS101 4.5 21.8 1.0 CB B:MET497 4.6 19.0 1.0 CG B:HIS101 4.7 21.5 1.0 CG B:HIS446 4.8 15.6 1.0 CU B:CU603 4.9 18.9 0.8 ND1 B:HIS101 4.9 23.2 1.0 OE1 B:GLU506 5.0 30.9 1.0

Copper binding site 7 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu603 b:18.9 occ:0.81 NE2 B:HIS141 2.0 15.0 1.0 ND1 B:HIS103 2.0 14.6 1.0 NE2 B:HIS501 2.2 16.3 1.0 O B:HOH931 2.5 35.4 1.0 CD2 B:HIS141 2.9 12.9 1.0 CE1 B:HIS103 2.9 12.5 1.0 CE1 B:HIS141 3.0 16.9 1.0 CG B:HIS103 3.0 14.0 1.0 CD2 B:HIS501 3.1 19.2 1.0 CE1 B:HIS501 3.2 18.1 1.0 CB B:HIS103 3.4 14.1 1.0 CZ2 B:TRP139 3.6 11.6 1.0 CU B:CU604 3.8 41.4 0.4 CE2 B:TRP139 3.9 12.6 1.0 O B:HOH860 4.0 36.9 1.0 NE1 B:TRP139 4.0 12.1 1.0 ND1 B:HIS141 4.0 16.8 1.0 CG B:HIS141 4.1 13.8 1.0 NE2 B:HIS103 4.1 12.8 1.0 CD2 B:HIS103 4.1 12.7 1.0 CD2 B:HIS101 4.1 24.1 1.0 CG B:HIS501 4.3 17.5 1.0 ND1 B:HIS501 4.3 16.8 1.0 CH2 B:TRP139 4.4 13.8 1.0 CD2 B:HIS446 4.4 14.7 1.0 NE2 B:HIS446 4.5 15.4 1.0 NE2 B:HIS101 4.5 25.2 1.0 CA B:HIS103 4.7 14.2 1.0 CU B:CU602 4.9 24.5 0.5 CD2 B:TRP139 4.9 11.9 1.0

Copper binding site 8 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu604 b:41.4 occ:0.40 NE2 B:HIS101 1.9 25.2 1.0 NE2 B:HIS446 1.9 15.4 1.0 CD2 B:HIS446 2.6 14.7 1.0 CD2 B:HIS101 2.8 24.1 1.0 CE1 B:HIS101 2.9 21.8 1.0 O B:HOH931 3.0 35.4 1.0 CE1 B:HIS446 3.1 16.3 1.0 NE2 B:HIS448 3.2 18.4 1.0 O B:HOH810 3.2 21.3 1.0 CD2 B:HIS448 3.2 16.2 1.0 CU B:CU602 3.4 24.5 0.5 ND1 B:HIS103 3.5 14.6 1.0 CG B:HIS103 3.6 14.0 1.0 CA B:HIS103 3.7 14.2 1.0 CB B:HIS103 3.8 14.1 1.0 CG B:HIS446 3.8 15.6 1.0 CU B:CU603 3.8 18.9 0.8 CE1 B:HIS448 3.9 21.6 1.0 CG B:HIS101 3.9 21.5 1.0 ND1 B:HIS101 3.9 23.2 1.0 CG B:HIS448 4.0 16.3 1.0 ND1 B:HIS446 4.0 15.9 1.0 CE1 B:HIS103 4.0 12.5 1.0 CD2 B:HIS103 4.2 12.7 1.0 ND1 B:HIS448 4.4 19.4 1.0 NE2 B:HIS103 4.4 12.8 1.0 NE2 B:HIS499 4.6 18.8 1.0 N B:GLY104 4.6 15.8 1.0 N B:HIS103 4.6 14.6 1.0 C B:HIS103 4.7 14.6 1.0 NE2 B:HIS141 4.8 15.0 1.0 CD2 B:HIS143 4.9 32.6 1.0 CA B:HIS448 4.9 16.0 1.0 NE2 B:HIS143 4.9 34.9 1.0 O B:TRP102 5.0 16.8 1.0 CB B:HIS448 5.0 16.9 1.0

Copper binding site 9 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu601 b:30.4 occ:1.00 ND1 C:HIS505 2.0 30.5 1.0 ND1 C:HIS443 2.1 32.6 1.0 SG C:CYS500 2.3 29.1 1.0 CG C:HIS505 3.0 29.3 1.0 CE1 C:HIS505 3.0 30.5 1.0 CE1 C:HIS443 3.0 33.7 1.0 CG C:HIS443 3.1 33.1 1.0 CB C:CYS500 3.1 28.6 1.0 SD C:MET510 3.3 30.8 1.0 CB C:HIS505 3.3 28.8 1.0 CB C:HIS443 3.4 33.6 1.0 CA C:HIS443 3.7 32.3 1.0 O C:LEU442 3.9 34.8 1.0 CB C:LEU502 4.1 26.2 1.0 NE2 C:HIS505 4.1 31.4 1.0 CD2 C:HIS505 4.1 29.5 1.0 NE2 C:HIS443 4.2 36.9 1.0 CE C:MET510 4.2 32.9 1.0 CD2 C:HIS443 4.2 38.4 1.0 N C:HIS443 4.5 35.5 1.0 C C:LEU442 4.5 39.0 1.0 CA C:CYS500 4.6 26.8 1.0 CG C:MET510 4.7 29.1 1.0 CD1 C:LEU502 4.8 26.7 1.0 CA C:HIS505 4.8 26.5 1.0 C C:HIS443 4.9 30.8 1.0 CD C:PRO444 4.9 32.3 1.0 O C:LEU502 4.9 26.4 1.0 CG C:LEU502 5.0 27.7 1.0 N C:LEU502 5.0 26.6 1.0

Copper binding site 10 out of 12 in the Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Structure of Perdeuterated Cueo - the Signal Peptide Was Truncated By HRV3C Protease within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu602 b:34.5 occ:0.62 NE2 C:HIS499 2.0 23.9 1.0 NE2 C:HIS448 2.0 22.3 1.0 NE2 C:HIS143 2.1 40.6 1.0 O C:HOH837 2.4 52.5 1.0 CD2 C:HIS143 2.8 35.2 1.0 CE1 C:HIS448 2.9 28.2 1.0 CE1 C:HIS499 2.9 25.4 1.0 CD2 C:HIS499 2.9 25.6 1.0 CD2 C:HIS448 3.1 25.5 1.0 CU C:CU604 3.1 96.5 0.7 CE1 C:HIS143 3.3 41.6 1.0 CD2 C:HIS446 3.5 27.2 1.0 NE2 C:HIS101 3.8 33.0 1.0 CD2 C:HIS101 4.0 28.9 1.0 ND1 C:HIS448 4.0 26.2 1.0 ND1 C:HIS499 4.0 25.0 1.0 CG C:HIS499 4.1 27.1 1.0 CG C:HIS143 4.1 34.9 1.0 NE2 C:HIS446 4.1 28.2 1.0 CG C:HIS448 4.1 24.5 1.0 ND1 C:HIS143 4.3 39.7 1.0 CE1 C:HIS101 4.4 30.4 1.0 CB C:MET497 4.6 24.9 1.0 CG C:HIS101 4.6 29.9 1.0 CG C:HIS446 4.7 29.9 1.0 CU C:CU603 4.8 28.5 0.8 ND1 C:HIS101 4.8 28.8 1.0 CD2 C:HIS501 4.9 29.4 1.0 OE1 C:GLU506 4.9 46.7 1.0

M.Akter, C.Inoue, H.Komori, N.Matsuda, T.Sakurai, K.Kataoka, Y.Higuchi, N.Shibata. Biochemical, Spectroscopic and X-Ray Structural Analysis of Deuterated Multicopper Oxidase Cueo Prepared From A New Expression Construct For Neutron Crystallography Acta Crystallogr.,Sect.F V. 72 788 2016.
ISSN: ESSN 2053-230X
PubMed: 27710945
DOI: 10.1107/S2053230X1601400X