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Cobalt in PDB 4b7b: EG5-3

Protein crystallography data

The structure of EG5-3, PDB code: 4b7b was solved by S.K.Talapatra, F.Kozielski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.911 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 81.500, 81.500, 114.921, 90.00, 90.00, 120.00
R / Rfree (%) 17.92 / 25.04

Other elements in 4b7b:

The structure of EG5-3 also contains other interesting chemical elements:

Cadmium (Cd) 11 atoms
Chlorine (Cl) 10 atoms
Calcium (Ca) 1 atom

Cobalt Binding Sites:

The binding sites of Cobalt atom in the EG5-3 (pdb code 4b7b). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the EG5-3, PDB code: 4b7b:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in 4b7b

Go back to Cobalt Binding Sites List in 4b7b
Cobalt binding site 1 out of 5 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of EG5-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1383

b:35.0
occ:1.00
O A:HOH2050 2.3 24.9 1.0
CD A:CD1368 2.6 20.3 1.0
O A:HOH2053 3.1 24.3 1.0
NZ A:LYS146 3.1 21.8 1.0
OD1 A:ASP91 3.5 21.2 1.0
O A:HOH2188 3.6 26.0 1.0
O A:HOH2048 3.9 24.9 1.0
CE A:LYS146 3.9 21.7 1.0
OD2 A:ASP91 4.1 21.6 1.0
CG A:ASP91 4.2 20.4 1.0
SG A:CYS87 4.2 21.7 1.0
O A:HOH2049 4.2 23.1 1.0

Cobalt binding site 2 out of 5 in 4b7b

Go back to Cobalt Binding Sites List in 4b7b
Cobalt binding site 2 out of 5 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of EG5-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1384

b:55.3
occ:1.00
OD2 A:ASP186 2.5 43.8 1.0
O A:HOH2189 2.5 38.6 1.0
CG A:ASP186 3.3 38.2 1.0
CB A:ASP186 3.6 36.2 1.0
OD1 A:ASP186 4.3 38.8 1.0
O A:HOH2111 4.9 33.5 1.0
NH1 A:ARG312 5.0 36.7 1.0

Cobalt binding site 3 out of 5 in 4b7b

Go back to Cobalt Binding Sites List in 4b7b
Cobalt binding site 3 out of 5 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of EG5-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1385

b:78.9
occ:1.00
OE1 A:GLU145 2.6 44.7 1.0
O A:HOH2190 2.6 50.1 1.0
CL A:CL1377 2.9 66.3 1.0
O A:HOH2092 3.4 38.0 1.0
CD A:CD1369 3.5 73.9 1.0
CD A:GLU145 3.6 45.3 1.0
OE2 A:GLU145 3.8 51.2 1.0
NZ A:LYS207 3.8 39.9 1.0
OD1 A:ASP149 4.9 35.2 1.0
CG A:GLU145 5.0 34.3 1.0
CE A:LYS207 5.0 27.9 1.0

Cobalt binding site 4 out of 5 in 4b7b

Go back to Cobalt Binding Sites List in 4b7b
Cobalt binding site 4 out of 5 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of EG5-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1386

b:45.9
occ:1.00
OD2 A:ASP149 2.1 36.1 1.0
O A:HOH2095 2.3 34.3 1.0
CD A:CD1369 2.6 73.9 1.0
OE2 A:GLU145 2.7 51.2 1.0
O A:HOH2093 2.9 40.7 1.0
O A:HOH2094 3.1 29.7 1.0
CG A:ASP149 3.3 36.0 1.0
CD A:GLU145 3.5 45.3 1.0
CG A:GLU145 3.7 34.3 1.0
OD1 A:ASP149 3.8 35.2 1.0
OE1 A:GLU145 4.5 44.7 1.0
CB A:ASP149 4.5 31.7 1.0
O A:GLU145 4.8 28.1 1.0

Cobalt binding site 5 out of 5 in 4b7b

Go back to Cobalt Binding Sites List in 4b7b
Cobalt binding site 5 out of 5 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of EG5-3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1387

b:52.6
occ:1.00
O A:HOH2159 2.3 29.2 1.0
O A:HOH2158 2.3 25.4 1.0
O A:HOH2106 2.8 34.4 1.0
CA A:GLU166 3.7 34.4 1.0
CB A:SER291 3.7 26.6 1.0
N A:GLU166 3.9 36.1 1.0
OG A:SER291 4.0 31.0 1.0
CB A:GLU166 4.0 33.4 1.0
CG2 A:ILE163 4.0 26.4 1.0
CG A:LYS315 4.2 26.9 1.0
CB A:LYS315 4.3 23.2 1.0
N A:LYS315 4.3 20.1 1.0
CB A:SER314 4.7 21.8 1.0
NE2 A:HIS236 4.7 22.8 1.0
CD2 A:HIS236 4.9 21.3 1.0
CA A:LYS315 4.9 20.6 1.0
CA A:SER291 4.9 26.3 1.0
C A:GLU166 4.9 32.8 1.0

Reference:

S.K.Talapatra, N.G.Anthony, S.P.Mackay, F.Kozielski. The Mitotic Kinesin EG5 Overcomes Inhibition to the Phase I/II Clinical Candidate SB743921 By An Allosteric Resistance Mechanism. J.Med.Chem. V. 56 6317 2013.
ISSN: ISSN 0022-2623
PubMed: 23875972
DOI: 10.1021/JM4006274
Page generated: Sun Dec 13 10:43:50 2020

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