Cobalt in PDB 5hzs: Crystal Structure of Dronpa-CO2+

The structure of Crystal Structure of Dronpa-CO2+, PDB code: 5hzs 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)	29.57 / 2.17
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	72.330, 105.479, 109.776, 115.79, 109.51, 93.95
R / Rfree (%)	16.6 / 22.5

Pages:

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

Binding sites:

The binding sites of Cobalt atom in the Crystal Structure of Dronpa-CO2+ (pdb code 5hzs). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 24 binding sites of Cobalt where determined in the Crystal Structure of Dronpa-CO2+, PDB code: 5hzs:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co301 b:39.6 occ:1.00 O A:HOH501 2.3 44.2 1.0 O A:HOH494 2.4 35.8 1.0 ND1 A:HIS194 2.4 32.1 1.0 NE2 A:HIS212 2.4 31.7 1.0 O A:HOH447 2.5 32.6 1.0 O A:HOH497 2.5 37.5 1.0 CE1 A:HIS194 3.3 35.9 1.0 CE1 A:HIS212 3.4 31.9 1.0 CG A:HIS194 3.4 31.6 1.0 CD2 A:HIS212 3.4 32.4 1.0 CB A:HIS194 3.7 27.8 1.0 NE2 A:HIS194 4.4 37.0 1.0 ND1 A:HIS212 4.5 35.7 1.0 OE1 A:GLU196 4.5 47.7 1.0 CD2 A:HIS194 4.5 33.5 1.0 CG A:HIS212 4.6 30.4 1.0

Cobalt binding site 2 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Co302 b:52.8 occ:1.00 O A:HOH480 1.8 54.6 1.0 O A:HOH475 1.9 27.1 1.0 O A:HOH453 2.2 50.2 1.0 NE2 A:HIS200 2.3 36.3 1.0 O J:HOH455 2.4 33.7 1.0 O J:HOH459 2.9 35.4 1.0 CE1 A:HIS200 3.2 38.4 1.0 CD2 A:HIS200 3.3 37.4 1.0 O A:HOH410 4.1 43.5 1.0 OE1 J:GLU117 4.3 73.4 1.0 ND1 A:HIS200 4.4 33.8 1.0 CG A:HIS200 4.4 36.2 1.0 OH A:TYR204 4.5 38.9 1.0 OE2 J:GLU117 4.5 70.6 1.0 CD J:GLU117 4.8 63.1 1.0

Cobalt binding site 3 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co301 b:37.1 occ:1.00 O B:HOH412 1.9 44.2 1.0 NE2 B:HIS212 2.0 23.8 1.0 ND1 B:HIS194 2.1 32.3 1.0 O B:HOH482 2.2 34.3 1.0 O B:HOH472 2.4 44.5 1.0 CE1 B:HIS194 2.9 34.3 1.0 CE1 B:HIS212 2.9 22.5 1.0 CD2 B:HIS212 3.1 23.4 1.0 CG B:HIS194 3.2 28.6 1.0 CB B:HIS194 3.6 29.4 1.0 NE2 B:HIS194 4.0 32.1 1.0 ND1 B:HIS212 4.1 24.7 1.0 CD2 B:HIS194 4.2 30.4 1.0 CG B:HIS212 4.2 23.1 1.0 OE1 B:GLU196 4.5 42.1 1.0

Cobalt binding site 4 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Co302 b:47.7 occ:1.00 O B:HOH496 1.9 36.8 1.0 O B:HOH503 2.2 46.2 1.0 NE2 B:HIS200 2.3 36.7 1.0 CD2 B:HIS200 3.2 31.5 1.0 CE1 B:HIS200 3.3 31.9 1.0 O B:HOH505 3.9 44.2 1.0 O B:HOH416 4.0 41.0 1.0 CG B:HIS200 4.4 33.1 1.0 ND1 B:HIS200 4.4 32.8 1.0 OH B:TYR204 4.5 29.8 1.0

Cobalt binding site 5 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Co301 b:34.4 occ:1.00 O C:HOH508 2.0 35.2 1.0 O C:HOH420 2.0 30.3 1.0 NE2 C:HIS212 2.3 22.0 1.0 ND1 C:HIS194 2.3 33.3 1.0 CE1 C:HIS212 3.0 21.4 1.0 CE1 C:HIS194 3.2 35.3 1.0 CG C:HIS194 3.3 33.6 1.0 CD2 C:HIS212 3.5 22.8 1.0 CB C:HIS194 3.6 30.1 1.0 ND1 C:HIS212 4.2 21.9 1.0 NE2 C:HIS194 4.3 38.0 1.0 CD2 C:HIS194 4.4 38.0 1.0 CG C:HIS212 4.5 21.2 1.0 OE1 C:GLU196 4.6 42.9 1.0 O C:HOH517 4.7 30.6 1.0

Cobalt binding site 6 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Co302 b:49.5 occ:1.00 O C:HOH428 1.9 43.0 1.0 NE2 C:HIS200 2.1 30.3 1.0 CD2 C:HIS200 3.0 27.2 1.0 CE1 C:HIS200 3.3 26.8 1.0 CG C:HIS200 4.2 26.1 1.0 ND1 C:HIS200 4.3 27.7 1.0 OH C:TYR204 4.4 33.0 1.0 O C:HOH470 4.4 30.6 1.0

Cobalt binding site 7 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Co301 b:41.3 occ:1.00 O D:HOH475 1.8 41.2 1.0 ND1 D:HIS194 2.0 36.7 1.0 NE2 D:HIS212 2.3 28.3 1.0 O D:HOH455 2.3 38.9 1.0 O D:HOH500 2.4 32.0 1.0 O D:HOH503 2.4 31.3 1.0 CE1 D:HIS194 2.8 42.5 1.0 CG D:HIS194 3.1 37.1 1.0 CE1 D:HIS212 3.2 29.0 1.0 CD2 D:HIS212 3.4 29.6 1.0 CB D:HIS194 3.6 32.3 1.0 NE2 D:HIS194 4.0 39.6 1.0 CD2 D:HIS194 4.1 38.6 1.0 OE1 D:GLU196 4.4 45.6 1.0 ND1 D:HIS212 4.4 32.7 1.0 CG D:HIS212 4.5 29.7 1.0 O E:GLU218 4.7 63.2 1.0

Cobalt binding site 8 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Co302 b:49.0 occ:1.00 O D:HOH508 2.0 41.8 1.0 O D:HOH501 2.1 43.3 1.0 NE2 D:HIS200 2.4 36.3 1.0 CD2 D:HIS200 3.3 36.3 1.0 CE1 D:HIS200 3.4 32.8 1.0 O D:HOH427 4.2 42.2 1.0 O D:HOH509 4.2 36.0 1.0 O D:HOH504 4.4 51.8 1.0 CG D:HIS200 4.5 34.1 1.0 OH D:TYR204 4.5 39.0 1.0 ND1 D:HIS200 4.5 35.9 1.0

Cobalt binding site 9 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Co301 b:32.3 occ:1.00 O E:HOH491 1.9 25.7 1.0 ND1 E:HIS194 2.1 31.1 1.0 NE2 E:HIS212 2.2 27.4 1.0 O E:HOH496 2.3 40.1 1.0 O E:HOH503 2.3 22.2 1.0 O E:HOH514 2.5 30.8 1.0 CE1 E:HIS194 2.9 31.8 1.0 CG E:HIS194 3.2 24.4 1.0 CE1 E:HIS212 3.2 23.6 1.0 CD2 E:HIS212 3.2 26.1 1.0 CB E:HIS194 3.6 23.6 1.0 NE2 E:HIS194 4.1 27.6 1.0 CD2 E:HIS194 4.2 27.0 1.0 ND1 E:HIS212 4.3 24.5 1.0 CG E:HIS212 4.4 26.2 1.0 OE1 E:GLU196 4.5 30.3 1.0 O E:HOH507 4.7 25.0 1.0

Cobalt binding site 10 out of 24 in the Crystal Structure of Dronpa-CO2+


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystal Structure of Dronpa-CO2+ within 5.0Å range: probe atom residue distance (Å) B Occ E:Co302 b:45.6 occ:1.00 NE2 E:HIS200 2.0 45.2 1.0 O E:HOH436 2.2 41.1 1.0 O E:HOH511 2.6 36.8 1.0 CD2 E:HIS200 2.8 41.0 1.0 O E:HOH519 2.9 37.6 1.0 CE1 E:HIS200 3.1 40.5 1.0 CG E:HIS200 4.0 37.9 1.0 O E:HOH404 4.0 29.9 1.0 ND1 E:HIS200 4.1 38.5 1.0 OH E:TYR204 4.4 36.4 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