Nickel in PDB 5hzu: Crystal Structure of Dronpa-NI2+

The structure of Crystal Structure of Dronpa-NI2+, PDB code: 5hzu 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)	29.03 / 1.89
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	105.372, 109.403, 72.087, 71.11, 85.97, 61.30
R / Rfree (%)	15.1 / 19.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 25;

Binding sites:

The binding sites of Nickel atom in the Crystal Structure of Dronpa-NI2+ (pdb code 5hzu). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 25 binding sites of Nickel where determined in the Crystal Structure of Dronpa-NI2+, PDB code: 5hzu:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Nickel binding site 1 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni301 b:36.1 occ:1.00 NE2 A:HIS212 2.1 25.8 1.0 ND1 A:HIS194 2.1 27.8 1.0 O A:HOH501 2.2 42.4 1.0 O A:HOH534 2.2 37.5 1.0 O B:HOH404 2.3 39.0 1.0 O B:HOH408 2.4 32.4 1.0 CE1 A:HIS194 2.9 30.2 1.0 CD2 A:HIS212 3.0 26.7 1.0 CE1 A:HIS212 3.1 26.2 1.0 CG A:HIS194 3.2 27.8 1.0 CB A:HIS194 3.6 23.8 1.0 NE2 A:HIS194 4.1 29.0 1.0 OE2 B:GLU218 4.1 53.4 1.0 OE1 B:GLU218 4.2 53.6 1.0 CG A:HIS212 4.2 23.8 1.0 ND1 A:HIS212 4.2 27.0 1.0 CD2 A:HIS194 4.2 30.6 1.0 CD B:GLU218 4.5 56.1 1.0 O A:HOH553 4.7 33.0 1.0 OE1 A:GLU196 4.8 39.6 1.0 O A:HOH415 4.9 22.7 1.0

Nickel binding site 2 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni302 b:42.2 occ:1.00 O A:HOH540 1.8 36.1 1.0 O A:HOH473 1.9 39.7 1.0 O A:HOH541 2.2 38.2 1.0 O A:HOH543 2.2 41.9 1.0 NE2 A:HIS200 2.3 24.9 1.0 O A:HOH547 2.5 37.2 1.0 CD2 A:HIS200 3.1 24.5 1.0 CE1 A:HIS200 3.3 24.1 1.0 CG A:HIS200 4.3 25.3 1.0 ND1 A:HIS200 4.3 26.4 1.0 O A:HOH496 4.5 33.2 1.0 OH A:TYR204 4.6 30.1 1.0 O A:HOH556 4.9 35.0 1.0

Nickel binding site 3 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni301 b:32.0 occ:1.00 O B:HOH453 2.0 33.6 1.0 O B:HOH504 2.0 38.4 1.0 ND1 B:HIS194 2.1 30.2 1.0 NE2 B:HIS212 2.1 25.3 1.0 O B:HOH529 2.2 28.7 1.0 O B:HOH530 2.3 31.2 1.0 O B:HOH552 2.8 40.9 1.0 CE1 B:HIS194 3.0 30.2 1.0 CE1 B:HIS212 3.1 23.9 1.0 CG B:HIS194 3.1 26.4 1.0 CD2 B:HIS212 3.1 23.1 1.0 CB B:HIS194 3.5 21.3 1.0 NE2 B:HIS194 4.1 28.5 1.0 CD2 B:HIS194 4.2 28.1 1.0 ND1 B:HIS212 4.2 22.6 1.0 CG B:HIS212 4.3 21.5 1.0 O B:HOH537 4.4 25.7 1.0 OE1 B:GLU196 5.0 38.6 1.0

Nickel binding site 4 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni302 b:34.8 occ:1.00 O B:HOH524 1.9 38.9 1.0 O B:HOH501 1.9 46.6 1.0 O B:HOH449 1.9 30.0 1.0 NE2 B:HIS200 2.2 28.3 1.0 O B:HOH540 2.6 38.1 1.0 CD2 B:HIS200 3.0 27.1 1.0 CE1 B:HIS200 3.2 23.6 1.0 CG B:HIS200 4.2 23.5 1.0 ND1 B:HIS200 4.3 26.6 1.0 O B:HOH468 4.3 26.7 1.0 OH B:TYR204 4.4 25.3 1.0 O B:HOH465 4.7 39.0 1.0 O B:HOH516 4.9 34.6 1.0

Nickel binding site 5 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni301 b:36.7 occ:1.00 ND1 C:HIS194 2.1 32.3 1.0 NE2 C:HIS212 2.2 24.8 1.0 O C:HOH543 2.3 35.3 1.0 O C:HOH535 2.4 32.9 1.0 O C:HOH540 2.4 29.0 1.0 O C:HOH518 2.4 34.0 1.0 CE1 C:HIS212 3.0 25.1 1.0 CE1 C:HIS194 3.0 33.8 1.0 CG C:HIS194 3.1 27.8 1.0 CD2 C:HIS212 3.3 25.9 1.0 CB C:HIS194 3.5 22.6 1.0 NE2 C:HIS194 4.2 32.8 1.0 ND1 C:HIS212 4.2 24.3 1.0 CD2 C:HIS194 4.2 33.0 1.0 CG C:HIS212 4.3 22.8 1.0 OE1 C:GLU196 5.0 33.6 1.0

Nickel binding site 6 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 6 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni302 b:38.6 occ:1.00 O C:HOH495 1.9 42.6 1.0 O C:HOH414 2.0 32.1 1.0 O C:HOH541 2.3 38.8 1.0 NE2 C:HIS200 2.3 28.0 1.0 O C:HOH550 2.3 43.7 1.0 CD2 C:HIS200 3.1 27.0 1.0 CE1 C:HIS200 3.4 27.7 1.0 O C:HOH476 4.1 29.7 1.0 CG C:HIS200 4.3 25.2 1.0 ND1 C:HIS200 4.4 27.7 1.0 OH C:TYR204 4.5 29.6 1.0

Nickel binding site 7 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 7 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni301 b:41.1 occ:1.00 O D:HOH434 1.8 38.3 1.0 O D:HOH529 1.9 33.5 1.0 O D:HOH555 2.2 49.8 1.0 O D:HOH541 2.2 44.3 1.0 NE2 D:HIS200 2.2 27.0 1.0 O D:HOH532 2.3 41.8 1.0 O D:HOH528 2.9 40.9 1.0 CD2 D:HIS200 3.1 26.6 1.0 CE1 D:HIS200 3.2 25.4 1.0 O D:HOH478 4.1 34.4 1.0 CG D:HIS200 4.3 24.8 1.0 ND1 D:HIS200 4.3 26.7 1.0 OH D:TYR204 4.7 32.6 1.0

Nickel binding site 8 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 8 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni302 b:35.9 occ:1.00 ND1 D:HIS194 2.0 31.3 1.0 NE2 D:HIS212 2.1 29.7 1.0 O D:HOH504 2.2 35.1 1.0 O D:HOH508 2.2 40.4 1.0 O D:HOH506 2.3 37.2 1.0 O D:HOH530 2.3 48.2 1.0 CE1 D:HIS194 2.9 34.5 1.0 CD2 D:HIS212 3.0 27.6 1.0 CG D:HIS194 3.1 28.1 1.0 CE1 D:HIS212 3.2 26.5 1.0 CB D:HIS194 3.6 23.7 1.0 NE2 D:HIS194 4.0 32.5 1.0 CD2 D:HIS194 4.2 30.5 1.0 CG D:HIS212 4.2 26.4 1.0 ND1 D:HIS212 4.2 29.0 1.0 O D:HOH542 4.4 38.8 1.0 OE2 D:GLU196 4.6 50.4 1.0

Nickel binding site 9 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 9 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni301 b:37.9 occ:1.00 O E:HOH533 2.2 49.9 1.0 ND1 E:HIS194 2.2 31.4 1.0 NE2 E:HIS212 2.2 29.5 1.0 O E:HOH541 2.3 45.0 1.0 O E:HOH519 2.4 35.4 1.0 O E:HOH506 2.4 40.3 1.0 CE1 E:HIS212 2.9 25.7 1.0 CE1 E:HIS194 3.1 32.8 1.0 CG E:HIS194 3.2 27.1 1.0 CD2 E:HIS212 3.4 26.1 1.0 CB E:HIS194 3.5 22.9 1.0 ND1 E:HIS212 4.2 30.0 1.0 NE2 E:HIS194 4.2 33.9 1.0 CD2 E:HIS194 4.3 33.8 1.0 CG E:HIS212 4.4 26.4 1.0 O E:HOH552 4.5 25.6 1.0 O E:HOH549 4.6 33.7 1.0 OE1 E:GLU196 4.8 39.9 1.0

Nickel binding site 10 out of 25 in the Crystal Structure of Dronpa-NI2+


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 10 of Crystal Structure of Dronpa-NI2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni302 b:31.8 occ:1.00 O E:HOH512 1.8 37.1 1.0 O E:HOH494 1.9 32.7 1.0 NE2 E:HIS200 2.1 21.2 1.0 O E:HOH542 2.2 30.8 1.0 O J:HOH526 2.2 34.0 1.0 O E:HOH532 2.2 36.3 1.0 CE1 E:HIS200 3.0 22.2 1.0 CD2 E:HIS200 3.2 20.8 1.0 ND1 E:HIS200 4.1 21.2 1.0 O E:HOH502 4.1 32.5 1.0 O J:HOH546 4.3 32.2 1.0 CG E:HIS200 4.3 22.3 1.0 O E:HOH446 4.3 28.6 1.0 O E:HOH544 4.3 29.6 1.0 OH E:TYR204 4.3 24.7 1.0 OE2 J:GLU117 4.5 48.0 1.0 OE1 J:GLU117 4.5 46.1 1.0 CD J:GLU117 4.8 44.0 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