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Cadmium 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:

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

Cadmium Binding Sites:

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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

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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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

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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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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 4b7b

Go back to Cadmium Binding Sites List in 4b7b
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

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 08:24:02 2020

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