Cadmium in PDB 4b7b: EG5-3

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

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

Cobalt	(Co)	5 atoms
Chlorine	(Cl)	10 atoms
Calcium	(Ca)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Cadmium atom in the EG5-3 (pdb code 4b7b). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 11 binding sites of Cadmium where determined in the EG5-3, PDB code: 4b7b:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1365 b:60.8 occ:1.00 O A:HOH2177 2.3 33.6 1.0 O A:HOH2178 2.3 34.7 1.0 NE2 A:HIS354 2.6 30.8 1.0 CL A:CL1375 2.9 55.9 1.0 CD2 A:HIS354 3.4 27.5 1.0 O A:HOH2030 3.5 42.8 1.0 CE1 A:HIS354 3.6 29.0 1.0 ND2 A:ASN358 4.0 34.4 1.0 CG A:HIS354 4.6 29.1 1.0 ND1 A:HIS354 4.6 30.2 1.0 OD1 A:ASN358 4.7 34.2 1.0 CG A:ASN358 4.8 34.0 1.0

Cadmium binding site 2 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1366 b:29.8 occ:1.00 O A:HOH2012 2.2 27.3 1.0 SG A:CYS43 2.4 25.3 1.0 CL A:CL1376 2.5 27.4 1.0 SG A:CYS25 2.7 26.1 1.0 O A:HOH2025 3.0 32.6 1.0 CL A:CL1374 3.1 43.9 1.0 CB A:CYS25 3.2 23.3 1.0 CB A:CYS43 3.6 29.5 1.0 CD A:CD1367 3.6 28.8 1.0 CG2 A:VAL41 3.7 23.2 1.0 N A:CYS43 4.0 27.5 1.0 O A:VAL41 4.0 26.3 1.0 O A:HOH2010 4.2 27.0 1.0 CA A:CYS43 4.4 28.9 1.0 O A:HOH2021 4.5 27.2 1.0 C A:VAL41 4.6 25.5 1.0 C A:GLU42 4.7 28.6 1.0 CA A:CA1388 4.7 29.6 1.0 CA A:CYS25 4.7 21.4 1.0 O A:HOH2037 4.9 33.8 1.0 CB A:PRO338 4.9 20.6 1.0 CA A:GLU42 4.9 27.6 1.0

Cadmium binding site 3 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1367 b:28.8 occ:1.00 O A:HOH2011 2.4 25.4 1.0 O A:ARG26 2.5 20.9 1.0 CA A:CA1388 2.6 29.6 1.0 CL A:CL1376 2.6 27.4 1.0 SG A:CYS25 2.7 26.1 1.0 O A:CYS25 3.0 22.4 1.0 C A:ARG26 3.2 21.5 1.0 C A:CYS25 3.3 20.1 1.0 CB A:CYS25 3.4 23.3 1.0 CD A:CD1366 3.6 29.8 1.0 O A:HOH2012 3.6 27.3 1.0 N A:ARG26 3.7 19.3 1.0 N A:PRO27 3.9 22.9 1.0 CA A:CYS25 3.9 21.4 1.0 CA A:ARG26 3.9 20.7 1.0 CA A:PRO27 4.0 23.9 1.0 O A:HOH2191 4.1 22.0 1.0 CB A:PRO338 4.4 20.6 1.0 CG A:PRO338 4.4 21.1 1.0 N A:PHE28 4.7 21.3 1.0 O A:HOH2021 4.7 27.2 1.0 C A:PRO27 4.7 21.9 1.0 CD A:PRO338 4.7 21.5 1.0 O A:HOH2009 4.8 26.5 1.0 CD A:PRO27 5.0 19.7 1.0

Cadmium binding site 4 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1368 b:20.3 occ:1.00 O A:HOH2049 1.9 23.1 1.0 SG A:CYS87 2.5 21.7 1.0 OD1 A:ASP91 2.5 21.2 1.0 OD2 A:ASP91 2.5 21.6 1.0 CO A:CO1383 2.6 35.0 1.0 CG A:ASP91 2.9 20.4 1.0 O A:HOH2050 2.9 24.9 1.0 O A:HOH2048 3.2 24.9 1.0 O A:CYS87 3.3 18.2 1.0 C A:CYS87 3.6 18.4 1.0 CB A:CYS87 3.7 18.1 1.0 N A:PRO88 4.1 18.9 1.0 NZ A:LYS146 4.1 21.8 1.0 CA A:CYS87 4.2 17.6 1.0 O A:HOH2047 4.3 21.8 1.0 CA A:PRO88 4.4 17.6 1.0 CB A:ASP91 4.4 16.9 1.0 O A:HOH2053 4.4 24.3 1.0

Cadmium binding site 5 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1369 b:73.9 occ:1.00 OE2 A:GLU145 2.3 51.2 1.0 CO A:CO1386 2.6 45.9 1.0 OD1 A:ASP149 2.8 35.2 1.0 O A:HOH2093 2.9 40.7 1.0 OD2 A:ASP149 3.0 36.1 1.0 CD A:GLU145 3.0 45.3 1.0 O A:HOH2092 3.1 38.0 1.0 CG A:ASP149 3.3 36.0 1.0 OE1 A:GLU145 3.3 44.7 1.0 CO A:CO1385 3.5 78.9 1.0 CL A:CL1377 4.0 66.3 1.0 CG A:GLU145 4.1 34.3 1.0 O A:HOH2095 4.6 34.3 1.0 O A:GLU145 4.8 28.1 1.0 CB A:ASP149 4.8 31.7 1.0 O A:HOH2094 4.9 29.7 1.0

Cadmium binding site 6 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1370 b:31.1 occ:1.00 O A:HOH2086 2.4 30.3 1.0 O A:HOH2083 2.4 27.7 1.0 OD1 A:ASP208 2.4 23.7 1.0 NE2 A:HIS141 2.6 21.0 1.0 CG A:ASP208 3.3 25.9 1.0 OD2 A:ASP208 3.5 31.8 1.0 CD2 A:HIS141 3.5 18.6 1.0 CE1 A:HIS141 3.5 19.8 1.0 OH A:TYR211 4.3 19.7 1.0 CE2 A:TYR211 4.5 23.5 1.0 ND1 A:HIS141 4.6 20.6 1.0 CB A:ASP208 4.7 21.0 1.0 CG A:HIS141 4.7 19.4 1.0 CB A:LYS207 4.7 22.9 1.0 CZ A:TYR211 4.9 22.9 1.0

Cadmium binding site 7 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1371 b:22.5 occ:1.00 OE2 A:GLU313 2.1 26.1 1.0 CL A:CL1380 2.4 18.9 1.0 CL A:CL1379 2.4 24.4 1.0 CD A:GLU313 2.7 24.6 1.0 OE1 A:GLU313 2.8 26.2 1.0 NH2 A:ARG297 4.1 25.1 1.0 CG A:GLU313 4.1 22.6 1.0 CE1 A:HIS308 4.4 20.0 1.0 CB A:PRO310 4.5 20.1 1.0 O A:HOH2157 4.5 34.4 1.0 NE A:ARG297 4.7 23.6 1.0 NE2 A:HIS308 4.8 19.1 1.0 CZ A:ARG297 4.8 23.6 1.0

Cadmium binding site 8 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1372 b:41.0 occ:1.00 O A:HOH2072 2.2 17.0 1.0 O1B A:ADP1364 2.3 20.2 1.0 OG1 A:THR112 2.4 18.8 1.0 O A:HOH2184 2.5 22.9 1.0 O A:HOH2185 2.6 21.8 1.0 CB A:THR112 3.1 17.8 1.0 PB A:ADP1364 3.4 19.8 1.0 O2B A:ADP1364 3.5 17.3 1.0 N A:THR112 3.9 15.8 1.0 OD2 A:ASP265 3.9 17.7 1.0 O2A A:ADP1364 4.1 20.3 1.0 CA A:THR112 4.1 17.4 1.0 O A:HOH2073 4.2 28.3 1.0 CG2 A:THR112 4.3 18.1 1.0 O3A A:ADP1364 4.3 18.7 1.0 OD1 A:ASP265 4.4 18.2 1.0 O A:HOH2131 4.4 20.6 1.0 O A:HOH2071 4.5 17.4 1.0 O3B A:ADP1364 4.5 17.3 1.0 PA A:ADP1364 4.6 17.7 1.0 CG A:ASP265 4.6 17.9 1.0 O1A A:ADP1364 4.7 19.5 1.0 O A:HOH2074 4.7 31.4 1.0 O A:HOH2183 4.9 21.3 1.0 CB A:LYS111 4.9 16.0 1.0 C A:LYS111 5.0 17.9 1.0

Cadmium binding site 9 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1373 b:28.1 occ:1.00 OE2 A:GLU209 2.3 22.8 1.0 ND1 A:HIS205 2.3 24.0 1.0 CL A:CL1382 2.5 34.9 1.0 OE1 A:GLU209 2.5 21.8 1.0 CL A:CL1381 2.5 36.6 1.0 O A:THR203 2.6 21.9 1.0 CD A:GLU209 2.7 22.0 1.0 CE1 A:HIS205 3.1 24.6 1.0 CG A:HIS205 3.4 22.6 1.0 N A:HIS205 3.7 21.2 1.0 C A:THR203 3.8 20.5 1.0 O A:HOH2187 3.8 31.8 1.0 CB A:HIS205 3.8 21.1 1.0 CG A:GLU209 4.2 21.1 1.0 CA A:VAL204 4.3 19.4 1.0 NE2 A:HIS205 4.3 21.7 1.0 C A:VAL204 4.4 20.2 1.0 CA A:HIS205 4.4 19.9 1.0 CD2 A:HIS205 4.4 20.0 1.0 N A:VAL204 4.5 19.8 1.0 CG2 A:ILE202 4.6 23.5 1.0 CL A:CL1391 4.8 39.3 1.0 CA A:THR203 4.8 21.3 1.0 O A:HOH2119 4.9 24.6 1.0 CB A:THR203 5.0 21.5 1.0

Cadmium binding site 10 out of 11 in the EG5-3


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of EG5-3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1389 b:42.8 occ:1.00 O A:HOH2192 2.2 16.5 1.0 O A:HOH2113 2.6 27.8 1.0 NH2 A:ARG189 4.2 42.8 1.0

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