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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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: Sun Dec 13 11:17:47 2020

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