Atomistry » Copper » PDB 5ce9-5i0y » 5hzt
Atomistry »
  Copper »
    PDB 5ce9-5i0y »
      5hzt »

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

Protein crystallography data

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

Copper Binding Sites:

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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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 5hzt

Go back to Copper Binding Sites List in 5hzt
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

Reference:

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
Page generated: Mon Jul 14 04:38:41 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy