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Cadmium in PDB 1yj1: X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin

Protein crystallography data

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin, PDB code: 1yj1 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 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.872, 50.395, 92.941, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 21.8

Other elements in 1yj1:

The structure of X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Cadmium atom in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin (pdb code 1yj1). 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 [D-GLN35]Ubiquitin, PDB code: 1yj1:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 17 in 1yj1

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Cadmium binding site 1 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


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Stereo pair view

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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd90

b:12.0
occ:1.00
 CL A:CL91 2.5 9.1 1.0
CL B:CL93 2.5 9.8 1.0
CL A:CL92 2.5 10.3 1.0
O A:HOH95 2.8 16.7 1.0
O C:HOH96 2.9 11.8 1.0
O C:HOH1341 3.0 63.9 1.0
O C:HOH94 3.3 25.6 1.0
O A:HOH97 3.8 24.7 1.0
O B:HOH1257 4.1 6.8 0.5
O B:HOH203 4.6 12.9 1.0
O A:SER20 4.6 4.2 1.0
O A:HOH102 4.7 11.2 1.0
O A:HOH303 4.7 13.0 1.0
ND2 C:ASN25 4.7 3.6 1.0
O B:SER20 4.8 7.6 1.0
ND2 B:ASN25 4.8 4.6 1.0
O C:SER20 4.8 4.8 1.0
ND2 A:ASN25 4.9 4.0 1.0

Cadmium binding site 2 out of 17 in 1yj1

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Cadmium binding site 2 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


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Stereo pair view

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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:8.7
occ:1.00
 O A:HOH102 2.1 11.2 1.0
OE1 B:GLU18 2.2 9.1 1.0
OD1 A:ASP21 2.3 7.9 1.0
O A:HOH103 2.3 4.1 1.0
OD2 A:ASP21 2.4 7.6 1.0
OE2 B:GLU18 2.5 9.6 1.0
CD B:GLU18 2.7 9.3 1.0
CG A:ASP21 2.8 2.6 1.0
CE A:LYS29 4.2 10.8 1.0
ND2 A:ASN25 4.2 4.0 1.0
CG B:GLU18 4.3 7.9 1.0
CB A:ASP21 4.3 4.4 1.0
O A:HOH1109 4.4 11.3 1.0
OE1 A:GLU18 4.5 7.5 1.0
O B:HOH203 4.5 12.9 1.0
N A:GLU18 4.7 3.7 1.0
CL A:CL91 4.7 9.1 1.0
NZ A:LYS29 4.7 16.8 1.0
CB A:ASN25 4.8 2.0 1.0
CG A:GLU18 4.8 5.4 1.0
CG A:ASN25 4.9 2.0 1.0
CB A:GLU18 4.9 4.2 1.0

Cadmium binding site 3 out of 17 in 1yj1

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Cadmium binding site 3 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


Mono view


Stereo pair view

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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd104

b:8.4
occ:1.00
 O A:HOH106 2.1 16.3 1.0
OE2 A:GLU24 2.2 5.9 1.0
OD1 A:ASP52 2.4 8.3 1.0
OE1 A:GLU24 2.4 8.1 1.0
O A:HOH107 2.4 2.0 1.0
O A:HOH105 2.5 3.9 1.0
CD A:GLU24 2.7 7.4 1.0
CG A:ASP52 3.3 8.2 1.0
CB A:ASP52 3.7 6.7 1.0
CG A:GLU24 4.2 4.8 1.0
OD2 A:ASP52 4.3 12.8 1.0
NZ A:LYS27 4.4 9.3 1.0
O A:HOH1152 4.6 18.6 0.5
O B:HOH1240 4.6 27.4 1.0
CD A:LYS27 4.8 5.9 1.0
O B:HOH1161 4.8 16.5 1.0
CB A:GLU24 5.0 5.4 1.0

Cadmium binding site 4 out of 17 in 1yj1

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Cadmium binding site 4 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


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Stereo pair view

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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd108

b:13.8
occ:0.75
 O A:HOH112 2.0 11.1 1.0
O A:HOH113 2.1 15.6 1.0
O A:HOH109 2.2 15.2 1.0
ND1 A:HIS68 2.3 9.9 1.0
O A:HOH110 2.5 4.0 1.0
O A:HOH111 2.5 15.2 1.0
CE1 A:HIS68 3.2 11.1 1.0
CG A:HIS68 3.3 9.4 1.0
CB A:HIS68 3.6 5.8 1.0
NE2 A:HIS68 4.3 12.7 1.0
O A:LEU69 4.4 4.4 1.0
O A:THR7 4.4 5.0 1.0
CD2 A:HIS68 4.4 11.0 1.0
CB A:LYS6 4.4 8.2 1.0
CA A:HIS68 4.5 4.6 1.0
O A:LYS6 4.7 6.3 1.0

Cadmium binding site 5 out of 17 in 1yj1

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Cadmium binding site 5 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd114

b:8.8
occ:0.50
 OD2 A:ASP58 2.3 6.8 1.0
O C:HOH118 2.4 19.6 0.5
OD1 A:ASP58 2.4 6.3 1.0
O A:HOH117 2.5 14.1 1.0
O C:HOH118 2.5 11.0 0.5
O A:HOH116 2.6 11.2 1.0
CG A:ASP58 2.7 5.3 1.0
O A:HOH115 2.8 27.5 1.0
O A:HOH1134 4.1 24.4 1.0
CB A:ASP58 4.2 6.2 1.0
CD A:ARG54 4.3 9.1 1.0
OG1 A:THR55 4.4 6.9 1.0
N A:THR55 4.8 3.7 1.0
NH1 A:ARG54 4.9 8.5 1.0
CG2 A:THR55 4.9 7.7 1.0
NE A:ARG54 5.0 6.7 1.0

Cadmium binding site 6 out of 17 in 1yj1

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Cadmium binding site 6 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd119

b:14.1
occ:0.50
 O A:HOH123 2.1 20.4 1.0
O A:HOH121 2.4 24.1 1.0
O A:HOH120 2.5 14.0 1.0
O A:HOH124 2.6 13.1 1.0
O A:HOH122 2.7 25.1 1.0
NE2 A:HIS68 3.8 12.7 1.0
CD2 A:HIS68 3.8 11.0 1.0
N A:ALA46 4.1 9.1 1.0
O A:THR66 4.3 8.1 1.0
CA A:ALA46 4.4 10.0 1.0
CE1 A:HIS68 5.0 11.1 1.0

Cadmium binding site 7 out of 17 in 1yj1

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Cadmium binding site 7 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


Mono view


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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:8.9
occ:1.00
 O A:HOH303 1.9 13.0 1.0
OE1 A:GLU18 2.2 7.5 1.0
OD1 C:ASP21 2.3 5.9 1.0
O C:HOH302 2.3 4.7 1.0
OE2 A:GLU18 2.4 8.0 1.0
OD2 C:ASP21 2.5 7.5 1.0
CD A:GLU18 2.7 6.9 1.0
CG C:ASP21 2.8 8.1 1.0
CE C:LYS29 4.1 12.9 1.0
ND2 C:ASN25 4.2 3.6 1.0
CG A:GLU18 4.3 5.4 1.0
CB C:ASP21 4.3 3.9 1.0
O A:HOH102 4.5 11.2 1.0
OE2 C:GLU18 4.6 8.5 1.0
NZ C:LYS29 4.7 13.9 1.0
N C:GLU18 4.7 4.1 1.0
CL B:CL93 4.7 9.8 1.0
CG C:GLU18 4.8 6.5 1.0
CB C:ASN25 4.8 2.6 1.0
CG C:ASN25 4.8 2.3 1.0
CB C:GLU18 5.0 2.9 1.0

Cadmium binding site 8 out of 17 in 1yj1

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Cadmium binding site 8 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


Mono view


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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd201

b:9.6
occ:1.00
 O B:HOH203 2.1 12.9 1.0
OE2 C:GLU18 2.1 8.5 1.0
OD1 B:ASP21 2.2 7.3 1.0
O B:HOH202 2.4 3.4 1.0
OD2 B:ASP21 2.5 7.4 1.0
OE1 C:GLU18 2.6 7.2 1.0
CD C:GLU18 2.7 6.6 1.0
CG B:ASP21 2.7 7.0 1.0
CE B:LYS29 4.0 9.5 1.0
ND2 B:ASN25 4.2 4.6 1.0
CB B:ASP21 4.3 4.9 1.0
CG C:GLU18 4.3 6.5 1.0
OE1 B:GLU18 4.5 9.1 1.0
NZ B:LYS29 4.5 13.3 1.0
CL A:CL92 4.7 10.3 1.0
N B:GLU18 4.7 4.2 1.0
CB B:ASN25 4.8 2.0 1.0
O A:HOH303 4.8 13.0 1.0
CG B:ASN25 4.8 3.1 1.0
CG B:GLU18 4.9 7.9 1.0
CB B:GLU18 5.0 5.3 1.0

Cadmium binding site 9 out of 17 in 1yj1

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Cadmium binding site 9 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


Mono view


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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd204

b:9.9
occ:1.00
 O B:HOH205 2.0 15.2 1.0
OE2 B:GLU24 2.3 10.2 1.0
OD1 B:ASP52 2.4 10.4 1.0
O B:HOH206 2.4 4.0 1.0
OE1 B:GLU24 2.4 8.3 1.0
O B:HOH207 2.5 4.3 1.0
CD B:GLU24 2.7 9.9 1.0
CG B:ASP52 3.3 10.2 1.0
CB B:ASP52 3.8 7.5 1.0
CG B:GLU24 4.2 6.5 1.0
OD2 B:ASP52 4.3 13.0 1.0
O C:HOH1338 4.4 21.5 1.0
NZ B:LYS27 4.5 11.8 1.0
O B:HOH1229 4.6 18.2 1.0
CD B:LYS27 4.8 5.4 1.0
CB B:GLU24 4.9 5.8 1.0
O B:HOH1210 5.0 12.6 1.0

Cadmium binding site 10 out of 17 in 1yj1

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Cadmium binding site 10 out of 17 in the X-Ray Crystal Structure of A Chemically Synthesized [D-GLN35]Ubiquitin


Mono view


Stereo pair view

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 [D-GLN35]Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd208

b:12.2
occ:0.75
 O B:HOH209 2.2 15.3 1.0
NE2 B:HIS68 2.3 9.8 1.0
O B:HOH213 2.3 14.1 1.0
O B:HOH212 2.4 6.9 0.5
O B:HOH211 2.5 15.7 1.0
O B:HOH210 2.6 7.2 1.0
O B:HOH212 2.6 14.4 0.5
CD2 B:HIS68 3.2 10.3 1.0
CE1 B:HIS68 3.3 6.5 1.0
O B:HOH1250 3.4 17.1 0.5
O B:HOH1234 3.8 31.7 1.0
N B:ALA46 4.2 7.2 1.0
CG B:HIS68 4.4 8.0 1.0
ND1 B:HIS68 4.4 7.0 1.0
CA B:ALA46 4.5 7.2 1.0
O B:THR66 4.5 7.9 1.0
O B:HOH1261 4.7 12.9 0.5

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: Sat Dec 12 08:16:01 2020

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