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Cadmium in PDB 2gbr: Crystal Structure of the 35-36 Moad Insertion Mutant of Ubiquitin

Protein crystallography data

The structure of Crystal Structure of the 35-36 Moad Insertion Mutant of Ubiquitin, PDB code: 2gbr was solved by D.M.Ferraro, D.J.Ferraro, S.Ramaswamy, A.D.Robertson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 4.99 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 44.465, 54.807, 92.627, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 29

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of the 35-36 Moad Insertion Mutant of Ubiquitin (pdb code 2gbr). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 13 binding sites of Cadmium where determined in the Crystal Structure of the 35-36 Moad Insertion Mutant of Ubiquitin, PDB code: 2gbr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 13 in 2gbr

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Cadmium binding site 1 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:34.8
occ:0.50
O A:HOH317 2.2 26.9 1.0
OE1 A:GLU24 2.3 32.6 1.0
OE2 A:GLU24 2.6 35.5 1.0
OD2 A:ASP57 2.6 29.8 1.0
CD A:GLU24 2.7 30.4 1.0
CG A:ASP57 3.0 29.2 1.0
CB A:ASP57 3.5 26.4 1.0
OD1 A:ASP57 3.7 33.8 1.0
O A:HOH343 4.1 35.4 1.0
CG A:GLU24 4.3 24.4 1.0
CB A:GLU24 4.9 22.7 1.0
NZ A:LYS27 4.9 29.2 1.0
O A:HOH352 5.0 56.2 1.0
CA A:ASP57 5.0 25.9 1.0

Cadmium binding site 2 out of 13 in 2gbr

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Cadmium binding site 2 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd308

b:37.7
occ:0.50
O A:HOH337 2.3 29.4 1.0
OD2 A:ASP63 2.3 24.9 1.0
OD1 A:ASP63 2.4 24.5 1.0
CG A:ASP63 2.7 22.7 1.0
CD A:ARG59 4.0 25.1 1.0
CB A:ASP63 4.1 23.4 1.0
OG1 A:THR60 4.4 20.6 1.0
NE A:ARG59 4.6 26.7 1.0
NH1 A:ARG59 4.7 29.5 1.0
N A:THR60 4.8 22.4 1.0
O A:HOH323 4.9 34.5 1.0
CZ A:ARG59 5.0 27.6 1.0
CA A:ASP63 5.0 22.9 1.0

Cadmium binding site 3 out of 13 in 2gbr

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Cadmium binding site 3 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd313

b:87.7
occ:1.00
OD1 A:ASP32 2.2 25.8 1.0
O A:HOH328 2.4 34.1 1.0
O A:HOH347 2.6 39.4 1.0
CG A:ASP32 3.1 26.2 1.0
OD2 A:ASP32 3.3 26.3 1.0
O A:HOH370 3.6 40.7 1.0
O A:ALA28 4.4 20.9 1.0
CB A:ASP32 4.5 25.9 1.0
N A:ASP32 4.8 24.8 1.0
CA A:ASP32 4.8 26.1 1.0

Cadmium binding site 4 out of 13 in 2gbr

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Cadmium binding site 4 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd301

b:30.7
occ:1.00
O B:HOH318 2.3 17.5 1.0
O B:HOH315 2.3 20.1 1.0
OD1 B:ASP21 2.3 25.1 1.0
OD2 B:ASP21 2.5 25.4 1.0
CG B:ASP21 2.7 24.4 1.0
CB B:ASP21 4.2 23.1 1.0
ND2 B:ASN25 4.3 19.1 1.0
CE B:LYS29 4.3 26.1 1.0
OE2 B:GLU18 4.5 22.2 1.0
N B:GLU18 4.5 23.0 1.0
CG B:GLU18 4.7 22.8 1.0
O C:HOH312 4.8 27.1 1.0
CB B:ASN25 4.9 20.1 1.0
CB B:GLU18 4.9 23.1 1.0
CG B:ASN25 5.0 19.8 1.0
O C:HOH332 5.0 17.8 1.0

Cadmium binding site 5 out of 13 in 2gbr

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Cadmium binding site 5 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd303

b:28.5
occ:1.00
O C:HOH311 2.3 14.3 1.0
OE2 B:GLU18 2.3 22.2 1.0
OD1 C:ASP21 2.3 20.6 1.0
OD2 C:ASP21 2.5 23.5 1.0
OE1 B:GLU18 2.6 22.4 1.0
CD B:GLU18 2.8 23.7 1.0
CG C:ASP21 2.8 21.9 1.0
CE C:LYS29 3.9 27.6 1.0
ND2 C:ASN25 4.2 20.5 1.0
CG B:GLU18 4.3 22.8 1.0
NZ C:LYS29 4.3 30.4 1.0
CB C:ASP21 4.3 20.7 1.0
OE1 C:GLU18 4.4 22.1 1.0
O B:HOH315 4.4 20.1 1.0
N C:GLU18 4.6 21.4 1.0
CB C:ASN25 4.8 20.1 1.0
CG C:ASN25 4.9 20.0 1.0
CB C:GLU18 4.9 21.6 1.0
CG C:GLU18 4.9 21.5 1.0

Cadmium binding site 6 out of 13 in 2gbr

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Cadmium binding site 6 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd304

b:28.3
occ:0.50
OD1 B:ASP32 2.1 33.3 1.0
O B:HOH342 2.5 33.2 1.0
CG B:ASP32 3.1 30.2 1.0
OD2 B:ASP32 3.4 34.3 1.0
CB B:ASP32 4.5 27.7 1.0
O B:ALA28 4.5 23.3 1.0
OE1 B:GLN31 4.5 31.6 1.0
CA B:ASP32 4.8 27.4 1.0
N B:ASP32 4.8 26.5 1.0

Cadmium binding site 7 out of 13 in 2gbr

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Cadmium binding site 7 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd307

b:31.6
occ:0.50
O B:HOH332 1.9 30.4 1.0
OD2 B:ASP57 2.1 36.1 1.0
OE1 B:GLU24 2.5 35.3 1.0
CG B:ASP57 3.1 30.1 1.0
CB B:ASP57 3.5 28.0 1.0
CD B:GLU24 3.7 32.3 1.0
OD2 B:ASP44 4.0 41.2 1.0
OD1 B:ASP57 4.3 32.7 1.0
NZ B:LYS27 4.4 27.9 1.0
O B:HOH375 4.4 56.6 1.0
O B:HOH343 4.4 40.1 1.0
CG B:GLU24 4.5 25.2 1.0
OE2 B:GLU24 4.6 36.9 1.0
CB B:GLU24 4.8 23.5 1.0
CG B:ASP44 4.8 38.2 1.0
CA B:ASP57 5.0 27.6 1.0

Cadmium binding site 8 out of 13 in 2gbr

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Cadmium binding site 8 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd309

b:49.2
occ:0.50
O C:HOH312 2.5 27.1 1.0
O B:HOH314 2.5 15.7 1.0
O B:HOH330 2.7 33.3 1.0
O C:HOH318 3.1 36.3 1.0
O B:HOH315 4.3 20.1 1.0
O B:SER20 4.7 20.7 1.0
ND2 C:ASN25 4.7 20.5 1.0
ND2 B:ASN25 4.8 19.1 1.0
O C:SER20 4.9 19.9 1.0
O C:HOH332 4.9 17.8 1.0

Cadmium binding site 9 out of 13 in 2gbr

Go back to Cadmium Binding Sites List in 2gbr
Cadmium binding site 9 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd311

b:35.3
occ:0.50
O A:HOH320 2.4 29.4 1.0
O B:HOH320 2.5 22.7 1.0
O B:HOH341 2.5 35.1 1.0
O A:HOH334 2.8 38.9 1.0
O B:HOH356 3.2 42.7 1.0
CD2 B:HIS73 3.8 28.0 1.0
CE A:LYS6 3.9 29.9 1.0
CG2 B:ILE49 4.2 28.8 1.0
NE2 B:HIS73 4.2 27.5 1.0
CG B:HIS73 4.3 26.4 1.0
CD A:LYS6 4.4 29.1 1.0
NZ A:LYS6 4.5 29.6 1.0
CG A:LYS6 4.8 27.3 1.0
O A:HOH373 4.8 42.8 1.0
CB B:HIS73 4.8 26.2 1.0
CE1 B:HIS73 4.9 29.5 1.0
CB B:ILE49 4.9 28.2 1.0
N B:GLY52 4.9 31.8 1.0
ND1 B:HIS73 4.9 28.6 1.0
CE1 A:HIS73 5.0 31.1 1.0

Cadmium binding site 10 out of 13 in 2gbr

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Cadmium binding site 10 out of 13 in the Crystal Structure of the 35-36 Moad Insertion Mutant of 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 the 35-36 Moad Insertion Mutant of Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd312

b:44.8
occ:0.50
O A:HOH321 2.2 33.3 1.0
O B:HOH351 2.6 45.5 1.0
NZ B:LYS6 3.1 33.3 1.0
CD2 A:HIS73 3.8 29.5 1.0
NE2 A:HIS73 4.1 29.0 1.0
CG A:HIS73 4.2 27.9 1.0
CE B:LYS6 4.4 31.4 1.0
CG2 A:ILE49 4.4 29.7 1.0
CE1 A:HIS73 4.6 31.1 1.0
ND1 A:HIS73 4.7 29.2 1.0
CB A:HIS73 4.7 27.2 1.0
CD B:LYS6 4.8 30.2 1.0
CE1 B:HIS73 4.8 29.5 1.0
CG B:LYS6 4.9 28.4 1.0
O B:HOH370 4.9 31.3 1.0

Reference:

D.M.Ferraro, D.J.Ferraro, S.Ramaswamy, A.D.Robertson. Structures of Ubiquitin Insertion Mutants Support Site-Specific Reflex Response to Insertions Hypothesis. J.Mol.Biol. V. 359 390 2006.
ISSN: ISSN 0022-2836
PubMed: 16647719
DOI: 10.1016/J.JMB.2006.03.047
Page generated: Sat Dec 12 08:17:11 2020

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