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Cadmium in PDB 3h7p: Crystal Structure of K63-Linked Di-Ubiquitin

Protein crystallography data

The structure of Crystal Structure of K63-Linked Di-Ubiquitin, PDB code: 3h7p was solved by S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.21 / 1.90
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 105.530, 105.530, 105.530, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 23.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of K63-Linked Di-Ubiquitin (pdb code 3h7p). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of K63-Linked Di-Ubiquitin, PDB code: 3h7p:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 3h7p

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Cadmium binding site 1 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd77

b:42.2
occ:0.83
 N A:MET1 2.0 32.8 1.0
OE1 A:GLU16 2.6 41.9 1.0
OE2 A:GLU16 2.6 45.2 1.0
CD A:GLU16 2.9 44.0 1.0
CA A:MET1 3.1 29.8 1.0
C A:MET1 3.4 30.3 1.0
O A:MET1 3.5 40.1 1.0
NH1 A:ARG63 4.1 55.7 1.0
N A:GLN2 4.2 34.7 1.0
O A:HOH99 4.3 43.4 1.0
CB A:MET1 4.3 38.3 1.0
CG A:GLU16 4.4 41.2 1.0
O A:HOH123 4.4 61.1 1.0
O A:HOH111 4.8 46.3 1.0
O A:VAL17 4.8 31.2 1.0
CG A:GLN2 4.9 53.3 1.0

Cadmium binding site 2 out of 10 in 3h7p

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Cadmium binding site 2 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd78

b:27.9
occ:0.41
 CD A:CD78 0.0 27.9 0.4
CD A:CD78 1.4 32.5 0.6
OE1 A:GLU18 2.5 27.9 1.0
O A:HOH136 2.8 39.2 0.5
O A:HOH82 3.0 29.4 1.0
CD A:GLU18 3.4 38.8 1.0
OE2 A:GLU18 3.6 41.3 1.0
CG A:GLU18 4.8 26.1 1.0
O A:HOH109 4.8 60.7 1.0

Cadmium binding site 3 out of 10 in 3h7p

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Cadmium binding site 3 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd78

b:32.5
occ:0.59
 CD A:CD78 0.0 32.5 0.6
CD A:CD78 1.4 27.9 0.4
O A:HOH82 2.3 29.4 1.0
OE1 A:GLU18 2.4 27.9 1.0
OE2 A:GLU18 2.5 41.3 1.0
CD A:GLU18 2.8 38.8 1.0
O A:HOH136 3.5 39.2 0.5
CG A:GLU18 4.2 26.1 1.0
O A:HOH109 4.3 60.7 1.0

Cadmium binding site 4 out of 10 in 3h7p

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Cadmium binding site 4 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd79

b:44.2
occ:0.58
 OD2 A:ASP52 2.3 57.2 1.0
OE1 A:GLU24 2.5 50.5 1.0
O A:HOH125 2.5 44.9 1.0
OE2 A:GLU24 2.6 47.6 1.0
O A:HOH88 2.6 60.4 1.0
CD A:GLU24 2.9 49.6 1.0
CG A:ASP52 3.2 50.6 1.0
CB A:ASP52 3.5 40.6 1.0
CG A:GLU24 4.4 38.2 1.0
OD1 A:ASP52 4.4 55.1 1.0
NZ A:LYS27 4.6 40.9 1.0
CD A:LYS27 4.9 28.1 1.0
CA A:ASP52 5.0 34.8 1.0

Cadmium binding site 5 out of 10 in 3h7p

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Cadmium binding site 5 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd80

b:43.7
occ:0.53
 CD A:CD80 0.0 43.7 0.5
CD A:CD80 1.9 43.3 0.5
OE1 A:GLU64 2.5 42.5 1.0
CD A:GLU64 3.3 44.2 1.0
OE2 A:GLU64 3.4 50.4 1.0
O A:HOH141 3.5 54.2 1.0
O A:HOH121 3.8 51.8 1.0
O A:HOH116 4.6 52.2 1.0
CG A:GLU64 4.7 39.8 1.0
O A:HOH144 4.8 65.5 1.0

Cadmium binding site 6 out of 10 in 3h7p

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Cadmium binding site 6 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd80

b:43.3
occ:0.47
 CD A:CD80 0.0 43.3 0.5
CD A:CD80 1.9 43.7 0.5
OE2 A:GLU64 2.2 50.4 1.0
O A:HOH121 2.5 51.8 1.0
OE1 A:GLU64 2.6 42.5 1.0
CD A:GLU64 2.7 44.2 1.0
O A:HOH116 2.8 52.2 1.0
CG A:GLU64 4.2 39.8 1.0
O A:HOH141 4.6 54.2 1.0
O A:HOH144 4.8 65.5 1.0
NE A:ARG63 4.8 50.1 1.0

Cadmium binding site 7 out of 10 in 3h7p

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Cadmium binding site 7 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd77

b:65.1
occ:0.54
 N B:MET1 2.4 56.5 1.0
OE2 B:GLU16 2.5 72.0 1.0
OE1 B:GLU16 2.9 62.7 1.0
CA B:MET1 3.0 57.3 1.0
CD B:GLU16 3.1 67.2 1.0
O B:HOH112 3.2 54.3 1.0
C B:MET1 3.6 48.4 1.0
O B:MET1 3.9 53.7 1.0
O B:HOH118 4.3 49.7 1.0
N B:GLN2 4.4 42.1 1.0
CB B:MET1 4.4 60.8 1.0
CG B:GLU16 4.6 62.5 1.0
O B:VAL17 4.7 40.0 1.0

Cadmium binding site 8 out of 10 in 3h7p

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Cadmium binding site 8 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd78

b:50.9
occ:0.45
 CD B:CD78 0.0 50.9 0.5
CD B:CD78 1.5 49.2 0.6
OD1 B:ASP21 2.3 51.1 1.0
OE2 B:GLU18 2.8 50.2 1.0
CG B:ASP21 3.1 41.5 1.0
OD2 B:ASP21 3.3 44.6 1.0
CD B:GLU18 3.7 55.9 1.0
CG B:GLU18 3.9 43.8 1.0
CB B:GLU18 4.1 38.4 1.0
ND2 B:ASN25 4.1 40.6 1.0
O B:HOH100 4.5 41.1 1.0
CB B:ASP21 4.5 34.7 1.0
CA B:ASP21 4.8 41.0 1.0
N B:GLU18 4.9 37.8 1.0
OE1 B:GLU18 4.9 59.5 1.0

Cadmium binding site 9 out of 10 in 3h7p

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Cadmium binding site 9 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd78

b:49.2
occ:0.55
 CD B:CD78 0.0 49.2 0.6
CD B:CD78 1.5 50.9 0.5
OD1 B:ASP21 2.3 51.1 1.0
OD2 B:ASP21 2.7 44.6 1.0
CG B:ASP21 2.9 41.5 1.0
OE2 B:GLU18 3.8 50.2 1.0
NZ B:LYS29 4.0 48.7 1.0
CE B:LYS29 4.0 48.9 1.0
ND2 B:ASN25 4.2 40.6 1.0
CG B:GLU18 4.3 43.8 1.0
CB B:ASP21 4.4 34.7 1.0
CD B:GLU18 4.5 55.9 1.0
N B:GLU18 4.6 37.8 1.0
CB B:GLU18 4.6 38.4 1.0
CG B:ASN25 4.9 39.1 1.0
CB B:ASN25 4.9 30.8 1.0

Cadmium binding site 10 out of 10 in 3h7p

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Cadmium binding site 10 out of 10 in the Crystal Structure of K63-Linked Di-Ubiquitin


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of K63-Linked Di-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd79

b:52.9
occ:0.71
 O B:HOH83 2.2 42.9 1.0
OD2 B:ASP52 2.5 53.5 1.0
OE1 B:GLU24 2.6 66.0 1.0
CG B:ASP52 3.3 49.4 1.0
CB B:ASP52 3.7 43.0 1.0
CD B:GLU24 3.8 67.7 1.0
OD1 B:ASP52 4.3 48.1 1.0
OE2 B:GLU24 4.7 70.8 1.0
CG B:GLU24 4.7 54.3 1.0
CB B:GLU24 5.0 44.4 1.0

Reference:

S.D.Weeks, K.C.Grasty, L.Hernandez-Cuebas, P.J.Loll. Crystal Structures of Lys-63-Linked Tri- and Di-Ubiquitin Reveal A Highly Extended Chain Architecture. Proteins V. 77 753 2009.
ISSN: ISSN 0887-3585
PubMed: 19731378
DOI: 10.1002/PROT.22568
Page generated: Thu Jul 10 12:40:22 2025

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