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

Protein crystallography data

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

Cobalt Binding Sites:

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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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 5hzs

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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

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 10:47:32 2020

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