Copper in PDB 5hzt: Crystal Structure of Dronpa-CU2+

The structure of Crystal Structure of Dronpa-CU2+, PDB code: 5hzt was solved by K.Y.Hwang, K.H.Nam, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.94 / 2.84
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.268, 105.961, 108.030, 115.89, 107.68, 94.12
R / Rfree (%)	21.4 / 24.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Copper atom in the Crystal Structure of Dronpa-CU2+ (pdb code 5hzt). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 24 binding sites of Copper where determined in the Crystal Structure of Dronpa-CU2+, PDB code: 5hzt:
Jump to Copper binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Copper binding site 1 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:81.2 occ:1.00 NE2 A:HIS210 2.2 68.3 1.0 NE2 A:HIS212 2.6 66.5 1.0 CE1 A:HIS212 2.7 66.7 1.0 O A:HOH407 2.8 29.1 1.0 CD2 A:HIS210 3.1 62.9 1.0 CE1 A:HIS210 3.3 64.8 1.0 CD2 A:HIS212 3.8 70.0 1.0 ND1 A:HIS212 3.9 69.5 1.0 CG A:HIS210 4.3 57.7 1.0 ND1 A:HIS210 4.3 62.5 1.0 CD A:LYS37 4.5 92.3 1.0 CG A:HIS212 4.5 63.9 1.0 CE A:LYS37 4.6 98.6 1.0 O A:HOH402 4.9 54.1 1.0 CG A:LYS37 5.0 81.6 1.0

Copper binding site 2 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu302 b:82.5 occ:1.00 NE2 A:HIS200 2.1 53.5 1.0 CE1 A:HIS200 2.8 52.8 1.0 CD2 A:HIS200 3.3 53.2 1.0 OH A:TYR204 3.9 39.5 1.0 ND1 A:HIS200 4.0 50.9 1.0 OE2 J:GLU117 4.1 90.8 1.0 CG A:HIS200 4.2 53.6 1.0 OE1 J:GLU117 4.5 74.2 1.0 CD J:GLU117 4.5 76.6 1.0 CZ A:TYR204 4.9 30.4 1.0

Copper binding site 3 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:99.1 occ:1.00 CE1 B:HIS210 2.5 0.1 1.0 NE2 B:HIS210 3.0 0.1 1.0 NE2 B:HIS212 3.0 0.8 1.0 CE1 B:HIS212 3.1 0.5 1.0 ND1 B:HIS210 3.2 0.8 1.0 NZ B:LYS37 3.3 79.7 1.0 CD2 B:HIS210 3.8 0.5 1.0 CG B:HIS210 4.0 0.5 1.0 CD2 B:HIS212 4.1 0.2 1.0 ND1 B:HIS212 4.1 0.4 1.0 CE B:LYS37 4.6 84.9 1.0 CG B:HIS212 4.6 0.4 1.0

Copper binding site 4 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu302 b:0.3 occ:1.00 NE2 B:HIS200 2.2 92.1 1.0 CE1 B:HIS200 3.2 90.3 1.0 CD2 B:HIS200 3.2 87.8 1.0 OH B:TYR204 4.3 74.7 1.0 ND1 B:HIS200 4.3 83.8 1.0 CG B:HIS200 4.4 81.0 1.0

Copper binding site 5 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 5 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu301 b:0.8 occ:1.00 O C:HOH403 2.2 66.3 1.0 NE2 C:HIS212 2.3 83.2 1.0 NE2 C:HIS210 2.4 74.4 1.0 O C:HOH402 3.0 46.9 1.0 CE1 C:HIS210 3.2 75.1 1.0 CE1 C:HIS212 3.3 86.4 1.0 CD2 C:HIS212 3.3 86.1 1.0 CD2 C:HIS210 3.5 74.1 1.0 CD C:LYS37 3.5 94.4 1.0 CE C:LYS37 3.8 98.5 1.0 CG C:LYS37 4.2 92.2 1.0 ND1 C:HIS212 4.4 85.2 1.0 ND1 C:HIS210 4.4 81.4 1.0 CG C:HIS212 4.4 80.7 1.0 CG C:HIS210 4.6 74.5 1.0 CB C:LYS37 4.9 86.7 1.0

Copper binding site 6 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 6 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu302 b:90.6 occ:1.00 NE2 C:HIS200 2.1 64.1 1.0 CE1 C:HIS200 3.0 64.2 1.0 CD2 C:HIS200 3.1 62.9 1.0 OH C:TYR204 3.7 50.0 1.0 ND1 C:HIS200 4.1 60.9 1.0 CG C:HIS200 4.2 63.1 1.0 CZ C:TYR204 4.7 46.8 1.0

Copper binding site 7 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 7 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu301 b:83.9 occ:1.00 NE2 D:HIS212 2.1 64.5 1.0 NE2 D:HIS210 2.3 58.6 1.0 CE1 D:HIS212 2.6 64.2 1.0 CD2 D:HIS210 3.0 55.8 1.0 CD2 D:HIS212 3.3 62.8 1.0 O D:HOH402 3.4 46.1 1.0 CE1 D:HIS210 3.5 56.7 1.0 ND1 D:HIS212 3.8 62.2 1.0 CG D:HIS212 4.1 58.8 1.0 CG D:HIS210 4.2 51.0 1.0 ND1 D:HIS210 4.4 55.7 1.0 CD D:LYS37 4.6 78.7 1.0 NZ D:LYS198 5.0 89.5 1.0

Copper binding site 8 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 8 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Cu302 b:79.3 occ:1.00 NE2 D:HIS200 1.9 64.0 1.0 CE1 D:HIS200 2.6 64.2 1.0 CD2 D:HIS200 3.2 62.2 1.0 ND1 D:HIS200 3.9 61.2 1.0 OH D:TYR204 4.0 49.4 1.0 CG D:HIS200 4.1 59.5 1.0 CZ D:TYR204 4.9 46.2 1.0

Copper binding site 9 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 9 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu301 b:81.8 occ:1.00 NE2 E:HIS210 2.1 56.2 1.0 NE2 E:HIS212 2.5 47.6 1.0 O E:HOH404 2.6 51.3 1.0 CE1 E:HIS212 2.6 47.2 1.0 CD2 E:HIS210 3.0 51.8 1.0 CE1 E:HIS210 3.1 56.8 1.0 CD2 E:HIS212 3.7 46.3 1.0 ND1 E:HIS212 3.8 44.0 1.0 CD E:LYS37 4.1 69.6 1.0 CG E:HIS210 4.2 51.4 1.0 ND1 E:HIS210 4.2 55.2 1.0 CG E:HIS212 4.3 41.5 1.0 CE E:LYS37 4.4 73.0 1.0 CG E:LYS37 4.7 56.3 1.0

Copper binding site 10 out of 24 in the Crystal Structure of Dronpa-CU2+


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 10 of Crystal Structure of Dronpa-CU2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Cu302 b:76.8 occ:1.00 NE2 E:HIS200 2.0 43.6 1.0 CE1 E:HIS200 2.8 42.5 1.0 CD2 E:HIS200 3.1 41.1 1.0 OH E:TYR204 3.8 33.6 1.0 ND1 E:HIS200 4.0 41.2 1.0 CG E:HIS200 4.2 41.6 1.0 CZ E:TYR204 4.8 33.0 1.0

I.J.Kim, S.Kim, J.Park, I.Eom, S.Kim, J.H.Kim, S.C.Ha, Y.G.Kim, K.Y.Hwang, K.H.Nam. Crystal Structures of Dronpa Complexed with Quenchable Metal Ions Provide Insight Into Metal Biosensor Development Febs Lett. V. 590 2982 2016.
ISSN: ISSN 1873-3468
PubMed: 27433793
DOI: 10.1002/1873-3468.12316