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Cadmium in PDB 3tlr: Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant

Protein crystallography data

The structure of Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant, PDB code: 3tlr was solved by M.Colombo, S.Ricagno, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.92 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 29.930, 98.200, 142.380, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.6

Other elements in 3tlr:

The structure of Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant (pdb code 3tlr). 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 the Tetrameric Beta-2 Microglobulin DIMC20 Mutant, PDB code: 3tlr:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 3tlr

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Cadmium binding site 1 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd100

b:50.3
occ:1.00
 O C:HOH108 2.1 20.6 1.0
OD2 C:ASP34 2.3 57.6 1.0
NE2 A:HIS31 2.3 41.8 1.0
O A:MET0 2.4 63.6 1.0
N A:MET0 2.5 61.5 1.0
OD1 C:ASP34 2.8 50.5 1.0
CG C:ASP34 2.9 50.4 1.0
C A:MET0 3.2 63.7 1.0
CD2 A:HIS31 3.2 42.1 1.0
CA A:MET0 3.3 61.4 1.0
CE1 A:HIS31 3.4 41.3 1.0
CB A:MET0 4.3 64.2 1.0
CB C:ASP34 4.3 39.7 1.0
CG A:HIS31 4.4 40.5 1.0
N A:ILE1 4.5 58.8 1.0
ND1 A:HIS31 4.5 42.1 1.0

Cadmium binding site 2 out of 10 in 3tlr

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Cadmium binding site 2 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd101

b:47.1
occ:1.00
 NE2 D:HIS13 2.3 36.6 1.0
OE1 A:GLU69 2.4 43.9 1.0
OE1 A:GLU50 2.4 68.2 1.0
OE2 A:GLU50 2.6 60.1 1.0
OE2 A:GLU69 2.8 50.9 1.0
CD A:GLU50 2.9 67.7 1.0
CD A:GLU69 3.0 54.4 1.0
CD2 D:HIS13 3.2 36.8 1.0
CE1 D:HIS13 3.4 36.3 1.0
O D:HOH121 3.5 37.0 1.0
CG D:ARG12 4.1 36.2 1.0
CG D:HIS13 4.4 34.9 1.0
CG A:GLU50 4.4 47.2 1.0
CG A:GLU69 4.4 38.4 1.0
ND1 D:HIS13 4.5 36.9 1.0
CE1 A:PHE22 4.5 41.0 1.0
CE1 A:TYR67 4.7 44.4 1.0
CZ A:PHE22 4.7 40.4 1.0
O A:HOH125 5.0 85.1 1.0
NE D:ARG12 5.0 62.0 1.0
CB D:ARG12 5.0 29.2 1.0

Cadmium binding site 3 out of 10 in 3tlr

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Cadmium binding site 3 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd102

b:72.3
occ:1.00
 OE2 A:GLU16 2.3 78.1 1.0
OE1 A:GLU16 2.7 70.2 1.0
CD A:GLU16 2.9 78.3 1.0
CG A:GLU16 4.3 53.8 1.0
NZ A:LYS19 4.4 62.4 1.0
CE A:LYS19 4.8 62.4 1.0
CD A:LYS19 4.9 58.3 1.0

Cadmium binding site 4 out of 10 in 3tlr

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Cadmium binding site 4 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd100

b:77.8
occ:1.00
 OE1 C:GLU69 2.2 57.7 1.0
O B:HOH123 2.3 20.9 1.0
NE2 B:HIS13 2.6 48.9 1.0
CD C:GLU69 3.1 72.8 1.0
CE1 B:HIS13 3.3 48.6 1.0
OE2 C:GLU69 3.5 70.2 1.0
CD2 B:HIS13 3.5 49.1 1.0
OG1 C:THR68 4.1 54.5 1.0
ND1 B:HIS13 4.4 49.2 1.0
CG B:HIS13 4.4 47.4 1.0
CG C:GLU69 4.5 52.6 1.0
N C:GLU69 4.6 42.8 1.0
CA C:THR68 4.8 44.6 1.0
CB C:THR68 5.0 53.1 1.0
CB C:GLU69 5.0 43.1 1.0

Cadmium binding site 5 out of 10 in 3tlr

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Cadmium binding site 5 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd101

b:49.3
occ:1.00
 N B:MET0 2.2 52.5 1.0
O D:HOH108 2.2 33.5 1.0
OD2 D:ASP34 2.3 58.1 1.0
O B:MET0 2.3 55.3 1.0
NE2 B:HIS31 2.4 37.4 1.0
OD1 D:ASP34 2.7 49.4 1.0
CG D:ASP34 2.8 50.3 1.0
C B:MET0 3.0 55.6 1.0
CA B:MET0 3.1 52.6 1.0
CD2 B:HIS31 3.3 37.8 1.0
CE1 B:HIS31 3.4 37.1 1.0
CB B:MET0 3.9 55.4 1.0
CB D:ASP34 4.3 39.4 1.0
N B:ILE1 4.3 51.4 1.0
CG B:HIS31 4.5 36.5 1.0
ND1 B:HIS31 4.6 38.1 1.0

Cadmium binding site 6 out of 10 in 3tlr

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Cadmium binding site 6 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd102

b:0.0
occ:1.00
 OE1 B:GLU69 2.2 77.5 1.0
OE2 B:GLU47 2.2 20.0 1.0
O C:HOH113 2.6 21.2 1.0
NE2 C:HIS13 2.6 51.0 1.0
CE1 C:HIS13 3.2 50.6 1.0
CD B:GLU69 3.2 80.1 1.0
CD B:GLU47 3.4 20.0 1.0
CD2 C:HIS13 3.5 51.1 1.0
OE2 B:GLU69 3.6 75.7 1.0
OG1 B:THR68 3.8 52.3 1.0
OE1 B:GLU47 4.0 20.0 1.0
ND1 C:HIS13 4.2 51.0 1.0
CG C:HIS13 4.3 49.1 1.0
N B:GLU69 4.5 40.8 1.0
CG B:GLU69 4.5 53.5 1.0
CG B:GLU47 4.6 20.0 1.0
CA B:THR68 4.6 43.4 1.0
CB B:THR68 4.7 51.6 1.0

Cadmium binding site 7 out of 10 in 3tlr

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Cadmium binding site 7 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd103

b:83.0
occ:1.00
 OE1 B:GLU16 2.2 73.6 1.0
OE2 B:GLU16 2.4 74.3 1.0
CD B:GLU16 2.6 79.6 1.0
O B:HOH111 3.0 37.7 1.0
CG B:GLU16 4.1 57.8 1.0
CD B:LYS19 4.9 62.6 1.0
CE B:LYS19 4.9 76.1 1.0

Cadmium binding site 8 out of 10 in 3tlr

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Cadmium binding site 8 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd100

b:45.6
occ:1.00
 O C:MET0 2.2 54.2 1.0
O A:HOH112 2.3 28.3 1.0
OD2 A:ASP34 2.3 64.9 1.0
NE2 C:HIS31 2.4 39.6 1.0
N C:MET0 2.4 53.3 1.0
OD1 A:ASP34 2.6 55.0 1.0
CG A:ASP34 2.7 55.3 1.0
C C:MET0 3.1 55.1 1.0
CA C:MET0 3.2 53.2 1.0
CD2 C:HIS31 3.3 39.8 1.0
CE1 C:HIS31 3.5 39.4 1.0
CB C:MET0 4.1 56.0 1.0
CB A:ASP34 4.2 41.6 1.0
N C:ILE1 4.3 50.5 1.0
CG C:HIS31 4.5 38.4 1.0
ND1 C:HIS31 4.6 40.1 1.0

Cadmium binding site 9 out of 10 in 3tlr

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Cadmium binding site 9 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd100

b:57.4
occ:1.00
 OD2 B:ASP34 2.3 55.2 1.0
NE2 D:HIS31 2.3 39.8 1.0
O D:MET0 2.4 65.4 1.0
N D:MET0 2.5 64.0 1.0
OD1 B:ASP34 2.7 50.0 1.0
CG B:ASP34 2.9 49.4 1.0
O B:HOH109 2.9 24.6 1.0
C D:MET0 3.3 65.6 1.0
CD2 D:HIS31 3.3 39.9 1.0
CA D:MET0 3.4 63.8 1.0
CE1 D:HIS31 3.4 39.4 1.0
CB D:MET0 4.1 66.5 1.0
CB B:ASP34 4.4 38.8 1.0
CG D:HIS31 4.4 38.4 1.0
ND1 D:HIS31 4.5 40.1 1.0
N D:ILE1 4.6 60.2 1.0
O B:HOH124 4.8 49.9 1.0

Cadmium binding site 10 out of 10 in 3tlr

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Cadmium binding site 10 out of 10 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd101

b:46.5
occ:1.00
 OE1 D:GLU69 2.4 48.0 1.0
OE2 D:GLU50 2.4 63.2 1.0
NE2 A:HIS13 2.5 39.5 1.0
OE2 D:GLU69 2.6 37.0 1.0
OE1 D:GLU50 2.7 66.2 1.0
O D:HOH109 2.7 33.7 1.0
CD D:GLU69 2.8 50.5 1.0
CD D:GLU50 2.9 71.6 1.0
O A:HOH113 3.1 42.0 1.0
CD2 A:HIS13 3.4 39.8 1.0
CE1 A:HIS13 3.6 39.2 1.0
CG A:ARG12 4.1 36.3 1.0
CG D:GLU69 4.3 37.1 1.0
CG D:GLU50 4.4 56.3 1.0
CG A:HIS13 4.6 38.1 1.0
CE2 D:PHE22 4.6 41.3 1.0
ND1 A:HIS13 4.7 39.8 1.0
NE A:ARG12 4.9 60.5 1.0
CB A:ARG12 5.0 30.6 1.0

Reference:

M.Colombo, M.De Rosa, V.Bellotti, S.Ricagno, M.Bolognesi. A Recurrent D-Strand Association Interface Is Observed in Beta-2 Microglobulin Oligomers. Febs J. V. 279 1131 2012.
ISSN: ISSN 1742-464X
PubMed: 22289140
DOI: 10.1111/J.1742-4658.2012.08510.X
Page generated: Fri Jul 19 16:33:38 2024

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