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Cadmium in PDB 4as7: EG5 Complex 1

Protein crystallography data

The structure of EG5 Complex 1, PDB code: 4as7 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) 28.936 / 2.40
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 81.070, 81.070, 123.961, 90.00, 90.00, 120.00
R / Rfree (%) 15.89 / 21.24

Other elements in 4as7:

The structure of EG5 Complex 1 also contains other interesting chemical elements:

Cobalt (Co) 1 atom
Chlorine (Cl) 5 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the EG5 Complex 1 (pdb code 4as7). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the EG5 Complex 1, PDB code: 4as7:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 1 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1369

b:26.6
occ:1.00
OE2 A:GLU128 2.3 27.1 1.0
OD1 A:ASP208 2.4 24.5 1.0
OD2 A:ASP208 2.6 25.8 1.0
O A:HOH2105 2.6 29.6 1.0
CG A:ASP208 2.8 24.4 1.0
CD A:GLU128 3.2 24.9 1.0
OE1 A:GLU128 3.5 25.0 1.0
O A:HOH2165 4.2 19.5 1.0
NE1 A:TRP127 4.3 24.0 1.0
CB A:ASP208 4.3 19.9 1.0
NZ A:LYS207 4.4 24.4 1.0
CD A:LYS207 4.4 24.9 1.0
CG A:GLU128 4.5 27.4 1.0
CE2 A:TRP127 4.9 23.1 1.0
CE A:LYS207 4.9 23.8 1.0
CD1 A:TRP127 5.0 22.8 1.0
CA A:ASP208 5.0 21.0 1.0

Cadmium binding site 2 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 2 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1370

b:16.8
occ:1.00
OD2 A:ASP91 2.4 15.4 1.0
SG A:CYS87 2.5 16.2 1.0
OD1 A:ASP91 2.6 16.3 1.0
CL A:CL1366 2.6 21.6 1.0
CG A:ASP91 2.8 17.2 1.0
O A:CYS87 3.2 15.7 1.0
C A:CYS87 3.5 13.5 1.0
CB A:CYS87 3.7 14.7 1.0
O A:HOH2069 3.8 26.4 1.0
N A:PRO88 4.0 12.8 1.0
CA A:CYS87 4.1 14.3 1.0
O A:HOH2066 4.3 19.4 1.0
CB A:ASP91 4.3 17.7 1.0
CA A:PRO88 4.3 15.0 1.0
O A:HOH2068 4.5 29.6 1.0
NZ A:LYS146 4.8 20.7 1.0

Cadmium binding site 3 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 3 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1371

b:27.8
occ:1.00
OD1 A:ASP149 2.3 25.6 1.0
OD2 A:ASP149 2.7 27.1 1.0
O A:HOH2116 2.8 25.8 1.0
CG A:ASP149 2.8 26.8 1.0
O A:HOH2117 4.1 32.0 1.0
O A:HOH2123 4.3 32.7 1.0
CB A:ASP149 4.3 23.1 1.0
OE1 A:GLU145 4.3 32.5 1.0
O A:GLU145 4.7 22.6 1.0
CA A:ASP149 5.0 23.2 1.0

Cadmium binding site 4 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 4 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1372

b:35.9
occ:1.00
OE2 A:GLU209 2.2 29.8 1.0
ND1 A:HIS205 2.3 18.1 1.0
O A:HOH2168 2.6 24.1 1.0
OE1 A:GLU209 2.6 26.3 1.0
O A:HOH2163 2.7 26.3 1.0
CD A:GLU209 2.7 28.2 1.0
O A:HOH2160 2.8 25.9 1.0
CG A:HIS205 3.3 23.9 1.0
CE1 A:HIS205 3.3 20.8 1.0
CB A:HIS205 3.5 21.6 1.0
O A:HOH2062 3.9 32.2 1.0
O A:HOH2167 3.9 32.6 1.0
N A:HIS205 4.1 21.4 1.0
CG A:GLU209 4.2 23.3 1.0
O A:THR203 4.4 23.1 1.0
NE2 A:HIS205 4.4 20.0 1.0
CD2 A:HIS205 4.4 21.7 1.0
CA A:HIS205 4.5 22.1 1.0
CB A:GLU209 4.8 23.2 1.0
OD1 A:ASN206 4.9 19.9 1.0

Cadmium binding site 5 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 5 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1373

b:35.5
occ:1.00
O1B A:ADP601 2.3 15.6 1.0
O A:HOH2096 2.4 14.7 1.0
O A:HOH2254 2.4 13.7 1.0
OG1 A:THR112 2.5 17.4 1.0
O A:HOH2095 2.5 23.7 1.0
O A:HOH2256 2.6 15.8 1.0
CB A:THR112 3.1 17.7 1.0
PB A:ADP601 3.4 13.7 1.0
O3B A:ADP601 3.5 16.5 1.0
N A:THR112 4.0 17.4 1.0
O1A A:ADP601 4.1 18.8 1.0
OD2 A:ASP265 4.2 18.0 1.0
CA A:THR112 4.2 17.1 1.0
CG2 A:THR112 4.2 18.5 1.0
O A:HOH2176 4.3 14.7 1.0
O3A A:ADP601 4.4 13.7 1.0
O A:HOH2092 4.4 16.3 1.0
O2B A:ADP601 4.4 14.0 1.0
O A:SER232 4.5 31.1 1.0
OD1 A:ASP265 4.5 14.7 1.0
PA A:ADP601 4.6 15.9 1.0
O A:HOH2173 4.7 32.5 1.0
CG A:ASP265 4.8 14.4 1.0
O A:HOH2093 4.8 20.1 1.0
O2A A:ADP601 4.9 19.8 1.0
CB A:LYS111 4.9 12.5 1.0
NZ A:LYS111 5.0 13.1 1.0
CE A:LYS111 5.0 13.1 1.0

Cadmium binding site 6 out of 6 in 4as7

Go back to Cadmium Binding Sites List in 4as7
Cadmium binding site 6 out of 6 in the EG5 Complex 1


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of EG5 Complex 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1374

b:16.1
occ:1.00
CL A:CL1376 2.4 18.9 1.0
CL A:CL1367 2.4 13.6 1.0
OE2 A:GLU313 2.4 21.1 1.0
OE1 A:GLU313 2.5 16.4 1.0
CD A:GLU313 2.8 20.2 1.0
CG A:GLU313 4.2 17.9 1.0
NH1 A:ARG297 4.3 17.6 1.0
CE1 A:HIS308 4.3 14.9 1.0
CB A:PRO310 4.4 15.0 1.0
NE2 A:HIS308 4.7 14.1 1.0
CG A:PRO310 5.0 15.3 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: Sat Dec 12 08:23:58 2020

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