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Cadmium in PDB 1yiw: X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin

Protein crystallography data

The structure of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin, PDB code: 1yiw was solved by D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.776, 50.476, 92.649, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 20.7

Other elements in 1yiw:

The structure of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin (pdb code 1yiw). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 17 binding sites of Cadmium where determined in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin, PDB code: 1yiw:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10; 11; 12; 13; 14; 15; 16; 17;

Cadmium binding site 1 out of 17 in 1yiw

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Cadmium binding site 1 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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A full contact list of Cadmium with other atoms in the Cd binding site number 1 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd90

b:17.2
occ:1.00
O A:HOH95 2.4 26.7 1.0
O B:HOH96 2.4 22.2 1.0
CL C:CL91 2.5 13.0 1.0
CL A:CL92 2.5 14.6 1.0
CL B:CL93 2.5 15.1 1.0
O C:HOH94 2.7 25.0 1.0
O A:HOH97 3.8 36.6 1.0
O B:HOH203 4.6 11.9 1.0
O A:SER20 4.6 8.6 1.0
O A:HOH102 4.6 15.2 1.0
ND2 C:ASN25 4.7 6.0 1.0
ND2 B:ASN25 4.7 6.8 1.0
O C:HOH303 4.8 17.3 1.0
O B:SER20 4.8 10.3 1.0
O C:SER20 4.8 8.1 1.0
ND2 A:ASN25 4.8 6.6 1.0

Cadmium binding site 2 out of 17 in 1yiw

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Cadmium binding site 2 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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A full contact list of Cadmium with other atoms in the Cd binding site number 2 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:12.6
occ:1.00
OD1 A:ASP21 2.2 6.0 1.0
OE1 B:GLU18 2.2 12.6 1.0
O A:HOH102 2.2 15.2 1.0
OD2 A:ASP21 2.3 8.6 1.0
O A:HOH103 2.4 6.0 1.0
OE2 B:GLU18 2.5 8.9 1.0
CG A:ASP21 2.7 8.2 1.0
CD B:GLU18 2.7 9.8 1.0
CE A:LYS29 4.1 14.9 1.0
ND2 A:ASN25 4.2 6.6 1.0
CB A:ASP21 4.2 8.2 1.0
CG B:GLU18 4.3 7.3 1.0
O B:HOH1145 4.3 21.1 0.5
O A:HOH1109 4.5 19.9 1.0
O B:HOH203 4.6 11.9 1.0
OE1 A:GLU18 4.6 9.5 1.0
NZ A:LYS29 4.6 19.0 1.0
N A:GLU18 4.6 8.3 1.0
CL C:CL91 4.7 13.0 1.0
CG A:GLU18 4.8 9.4 1.0
CB A:ASN25 4.9 4.8 1.0
CG A:ASN25 4.9 6.7 1.0

Cadmium binding site 3 out of 17 in 1yiw

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Cadmium binding site 3 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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A full contact list of Cadmium with other atoms in the Cd binding site number 3 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:13.2
occ:1.00
O A:HOH106 1.9 18.7 1.0
OE1 A:GLU24 2.3 11.7 1.0
OD1 A:ASP52 2.3 14.5 1.0
OE2 A:GLU24 2.4 13.9 1.0
O A:HOH107 2.4 4.1 1.0
O A:HOH105 2.5 5.7 1.0
CD A:GLU24 2.7 13.8 1.0
CG A:ASP52 3.3 10.9 1.0
CB A:ASP52 3.7 10.8 1.0
CG A:GLU24 4.2 9.0 1.0
OD2 A:ASP52 4.4 16.4 1.0
NZ A:LYS27 4.6 14.1 1.0
O B:HOH1240 4.6 27.6 0.5
O A:HOH1141 4.7 21.8 1.0
CD A:LYS27 4.7 11.0 1.0
O A:HOH1106 5.0 10.1 1.0
CB A:GLU24 5.0 7.8 1.0

Cadmium binding site 4 out of 17 in 1yiw

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Cadmium binding site 4 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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A full contact list of Cadmium with other atoms in the Cd binding site number 4 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd108

b:14.1
occ:0.50
O A:HOH109 2.2 19.1 1.0
O A:HOH113 2.2 26.8 1.0
O A:HOH112 2.2 16.3 1.0
ND1 A:HIS68 2.3 14.5 1.0
O A:HOH110 2.4 9.8 1.0
O A:HOH111 2.5 22.1 1.0
CE1 A:HIS68 3.2 13.9 1.0
CG A:HIS68 3.3 10.2 1.0
CB A:HIS68 3.6 9.0 1.0
NE2 A:HIS68 4.3 13.9 1.0
CB A:LYS6 4.4 9.9 1.0
CD2 A:HIS68 4.4 15.8 1.0
O A:THR7 4.4 11.0 1.0
O A:LEU69 4.4 8.9 1.0
CA A:HIS68 4.5 8.6 1.0
O A:LYS6 4.7 9.7 1.0

Cadmium binding site 5 out of 17 in 1yiw

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Cadmium binding site 5 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd114

b:15.4
occ:0.50
OD1 A:ASP58 2.2 10.6 1.0
O A:HOH118 2.3 18.1 0.5
O A:HOH117 2.3 20.6 1.0
OD2 A:ASP58 2.5 12.2 1.0
O A:HOH116 2.5 16.6 1.0
O A:HOH118 2.5 18.0 0.5
O A:HOH115 2.6 40.7 1.0
CG A:ASP58 2.7 10.5 1.0
O A:HOH1154 3.9 16.2 0.5
CB A:ASP58 4.2 8.2 1.0
CD A:ARG54 4.3 11.6 1.0
OG1 A:THR55 4.4 10.8 1.0
O A:HOH1134 4.8 23.4 1.0
CG2 A:THR55 4.8 9.8 1.0
N A:THR55 4.8 7.6 1.0
NH1 A:ARG54 4.9 14.2 1.0
O A:HOH1140 5.0 22.1 1.0

Cadmium binding site 6 out of 17 in 1yiw

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Cadmium binding site 6 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd119

b:21.1
occ:0.50
O A:HOH123 2.1 18.7 1.0
O A:HOH120 2.1 19.5 1.0
O A:HOH122 2.4 42.8 1.0
O A:HOH124 2.7 22.8 1.0
O A:HOH121 3.4 39.4 1.0
NE2 A:HIS68 3.6 13.9 1.0
CD2 A:HIS68 3.6 15.8 1.0
O A:HOH1155 3.7 17.9 0.5
N A:ALA46 4.1 11.3 1.0
O A:THR66 4.4 11.5 1.0
CA A:ALA46 4.5 12.7 1.0
CE1 A:HIS68 4.9 13.9 1.0
CG A:HIS68 4.9 10.2 1.0

Cadmium binding site 7 out of 17 in 1yiw

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Cadmium binding site 7 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:13.4
occ:1.00
O C:HOH303 2.0 17.3 1.0
OE1 A:GLU18 2.2 9.5 1.0
OD1 C:ASP21 2.2 6.5 1.0
O C:HOH302 2.4 7.0 1.0
OD2 C:ASP21 2.5 10.1 1.0
OE2 A:GLU18 2.6 9.0 1.0
CD A:GLU18 2.7 10.3 1.0
CG C:ASP21 2.7 10.3 1.0
ND2 C:ASN25 4.1 6.0 1.0
CE C:LYS29 4.2 17.8 1.0
CG A:GLU18 4.2 9.4 1.0
CB C:ASP21 4.3 7.4 1.0
O A:HOH102 4.4 15.2 1.0
OE2 C:GLU18 4.4 11.0 1.0
O B:HOH1145 4.5 21.1 0.5
N C:GLU18 4.6 8.2 1.0
NZ C:LYS29 4.7 22.9 1.0
CL B:CL93 4.7 15.1 1.0
CB C:ASN25 4.8 4.8 1.0
CG C:GLU18 4.8 9.0 1.0
CG C:ASN25 4.8 7.4 1.0
CB C:GLU18 4.9 8.7 1.0

Cadmium binding site 8 out of 17 in 1yiw

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Cadmium binding site 8 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:14.1
occ:1.00
O B:HOH203 2.1 11.9 1.0
OD1 B:ASP21 2.3 8.4 1.0
O B:HOH202 2.3 7.2 1.0
OE2 C:GLU18 2.4 11.0 1.0
OE1 C:GLU18 2.4 10.0 1.0
OD2 B:ASP21 2.5 11.8 1.0
CD C:GLU18 2.7 9.2 1.0
CG B:ASP21 2.8 9.6 1.0
CE B:LYS29 4.0 13.6 1.0
ND2 B:ASN25 4.2 6.8 1.0
O B:HOH1145 4.2 21.1 0.5
CG C:GLU18 4.3 9.0 1.0
CB B:ASP21 4.3 6.6 1.0
OE1 B:GLU18 4.5 12.6 1.0
NZ B:LYS29 4.6 15.8 1.0
O C:HOH303 4.7 17.3 1.0
N B:GLU18 4.7 6.9 1.0
CL A:CL92 4.7 14.6 1.0
CG B:GLU18 4.8 7.3 1.0
CB B:ASN25 4.8 4.3 1.0
CG B:ASN25 4.8 5.5 1.0

Cadmium binding site 9 out of 17 in 1yiw

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Cadmium binding site 9 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:14.5
occ:1.00
OE2 B:GLU24 2.2 15.7 1.0
O B:HOH205 2.4 22.0 1.0
OD1 B:ASP52 2.4 17.8 1.0
O B:HOH206 2.4 5.3 1.0
O B:HOH207 2.5 4.2 1.0
OE1 B:GLU24 2.5 16.8 1.0
CD B:GLU24 2.7 12.2 1.0
CG B:ASP52 3.3 13.4 1.0
CB B:ASP52 3.8 9.7 1.0
CG B:GLU24 4.2 8.3 1.0
NZ B:LYS27 4.4 13.3 1.0
OD2 B:ASP52 4.4 16.8 1.0
O B:HOH1244 4.7 28.0 0.5
O B:HOH1229 4.7 23.9 1.0
CD B:LYS27 4.8 9.5 1.0
O C:HOH1335 4.9 32.3 1.0
CB B:GLU24 4.9 8.5 1.0
O B:HOH1210 5.0 12.8 1.0

Cadmium binding site 10 out of 17 in 1yiw

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Cadmium binding site 10 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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A full contact list of Cadmium with other atoms in the Cd binding site number 10 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd208

b:15.8
occ:0.50
O B:HOH213 2.3 16.0 1.0
NE2 B:HIS68 2.5 16.6 1.0
O B:HOH212 2.5 12.4 0.5
O B:HOH209 2.5 31.6 1.0
O B:HOH211 2.6 27.7 1.0
O B:HOH212 2.6 14.8 0.5
O B:HOH210 2.7 13.1 1.0
CD2 B:HIS68 3.2 16.8 1.0
CE1 B:HIS68 3.6 13.2 1.0
N B:ALA46 4.2 9.8 1.0
CG B:HIS68 4.4 11.1 1.0
O B:THR66 4.5 10.4 1.0
ND1 B:HIS68 4.5 13.7 1.0
CA B:ALA46 4.6 10.1 1.0
O B:HOH1245 4.9 17.0 0.5

Cadmium binding site 11 out of 17 in 1yiw

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Cadmium binding site 11 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 11 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd214

b:28.0
occ:0.50
O B:HOH216 2.3 23.9 1.0
OD1 B:ASP58 2.3 7.5 1.0
OD2 B:ASP58 2.4 11.3 1.0
O B:HOH217 2.4 23.6 1.0
CG B:ASP58 2.7 11.1 1.0
O B:HOH218 2.8 30.1 1.0
O B:HOH215 3.1 38.3 1.0
CB B:ASP58 4.2 8.3 1.0
O B:HOH1234 4.2 22.6 1.0
CD B:ARG54 4.4 12.5 1.0
OG1 B:THR55 4.4 9.1 1.0
CG2 B:THR55 4.7 9.3 1.0
NH1 B:ARG54 4.8 18.0 1.0
N B:THR55 4.9 6.6 1.0
NE B:ARG54 5.0 16.0 1.0

Cadmium binding site 12 out of 17 in 1yiw

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Cadmium binding site 12 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 12 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd225

b:31.7
occ:0.50
OE1 B:GLU64 2.2 25.6 1.0
OE2 B:GLU64 2.6 24.3 1.0
CD B:GLU64 2.7 19.9 1.0
CG B:GLU64 4.2 17.5 1.0

Cadmium binding site 13 out of 17 in 1yiw

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Cadmium binding site 13 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 13 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd229

b:42.8
occ:0.25
OD1 B:ASP39 2.5 16.1 1.0
OD2 B:ASP39 2.7 19.5 1.0
CG B:ASP39 3.0 17.1 1.0
OE1 B:GLN40 3.7 17.8 0.5
OE1 B:GLN40 4.0 19.0 0.5
O B:HOH1223 4.3 17.2 1.0
CB B:PRO37 4.4 11.6 1.0
CB B:ASP39 4.5 12.6 1.0
CD B:GLN40 4.6 13.3 0.5
CG B:GLN40 4.7 14.0 1.0
CD B:GLN40 4.8 14.3 0.5
CG B:PRO37 5.0 12.9 1.0

Cadmium binding site 14 out of 17 in 1yiw

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Cadmium binding site 14 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 14 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd304

b:12.6
occ:1.00
OE2 C:GLU24 2.3 10.5 1.0
O C:HOH306 2.3 18.5 1.0
OE1 C:GLU24 2.4 13.1 1.0
O C:HOH307 2.4 7.2 1.0
O C:HOH305 2.4 6.9 1.0
OD1 C:ASP52 2.4 14.8 1.0
CD C:GLU24 2.7 11.4 1.0
CG C:ASP52 3.4 16.0 1.0
CB C:ASP52 3.8 9.6 1.0
CG C:GLU24 4.2 8.4 1.0
NZ C:LYS27 4.4 11.5 1.0
OD2 C:ASP52 4.4 21.0 1.0
O C:HOH1359 4.6 28.3 0.5
O A:HOH1334 4.7 35.6 1.0
O C:HOH1311 4.7 22.1 1.0
CD C:LYS27 4.8 9.2 1.0
CB C:GLU24 5.0 6.5 1.0
O C:HOH1302 5.0 11.4 1.0

Cadmium binding site 15 out of 17 in 1yiw

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Cadmium binding site 15 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 15 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd308

b:8.1
occ:0.50
NE2 C:HIS68 2.3 14.2 1.0
O C:HOH309 2.3 17.0 1.0
O C:HOH311 2.5 10.7 1.0
O C:HOH310 2.6 10.2 1.0
CD2 C:HIS68 3.2 12.5 1.0
CE1 C:HIS68 3.3 14.7 1.0
O C:HOH1319 4.1 18.6 1.0
ND1 C:HIS68 4.3 14.3 1.0
CG C:HIS68 4.4 10.7 1.0

Cadmium binding site 16 out of 17 in 1yiw

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Cadmium binding site 16 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 16 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd314

b:40.4
occ:1.00
OD1 C:ASP58 2.3 8.7 1.0
O C:HOH316 2.3 29.1 1.0
OD2 C:ASP58 2.4 8.8 1.0
O C:HOH318 2.5 28.6 1.0
O C:HOH315 2.7 29.5 1.0
CG C:ASP58 2.7 9.3 1.0
O C:HOH317 2.8 31.7 1.0
CB C:ASP58 4.2 7.3 1.0
O B:HOH1237 4.3 26.0 1.0
OG1 C:THR55 4.4 9.6 1.0
CD C:ARG54 4.4 8.6 1.0
O C:HOH1314 4.4 20.6 1.0
CG2 C:THR55 4.6 11.3 1.0
N C:THR55 4.9 7.1 1.0

Cadmium binding site 17 out of 17 in 1yiw

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Cadmium binding site 17 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 17 of X-Ray Crystal Structure of A Chemically Synthesized Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd325

b:28.4
occ:0.50
OE1 C:GLU64 2.2 23.7 1.0
OE2 C:GLU64 2.6 23.2 1.0
O C:HOH326 2.7 31.0 1.0
CD C:GLU64 2.7 20.3 1.0
CG C:GLU64 4.2 18.7 1.0
CB C:GLU64 5.0 15.2 1.0

Reference:

D.Bang, G.I.Makhatadze, V.Tereshko, A.A.Kossiakoff, S.B.Kent. X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin Angew.Chem.Int.Ed.Engl. V. 44 3852 2005.
ISSN: ISSN 1433-7851
PubMed: 15834850
DOI: 10.1002/ANIE.200463040
Page generated: Wed Oct 28 09:58:07 2020
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