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Cadmium in PDB 1vel: Mycobacterium Smegmatis Dps Tetragonal Form

Protein crystallography data

The structure of Mycobacterium Smegmatis Dps Tetragonal Form, PDB code: 1vel was solved by S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.21 / 2.99
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.643, 123.643, 262.328, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21

Other elements in 1vel:

The structure of Mycobacterium Smegmatis Dps Tetragonal Form also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Mycobacterium Smegmatis Dps Tetragonal Form (pdb code 1vel). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Mycobacterium Smegmatis Dps Tetragonal Form, PDB code: 1vel:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 1vel

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Cadmium binding site 1 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:48.8
occ:1.00
 NE2 A:HIS39 2.5 41.8 1.0
O A:HOH448 2.6 28.7 1.0
CD2 A:HIS39 3.1 41.8 1.0
CE1 A:HIS39 3.6 41.8 1.0
NE2 A:HIS51 4.2 42.8 1.0
CE1 A:HIS51 4.2 42.8 1.0
CG A:HIS39 4.4 41.8 1.0
OD2 A:ASP55 4.4 54.0 1.0
ND1 A:HIS39 4.6 41.8 1.0
NE1 A:TRP40 4.7 55.9 1.0
CD1 A:TRP40 4.7 55.9 1.0
OD1 A:ASP55 4.7 54.0 1.0
CE A:LYS36 4.9 60.1 1.0

Cadmium binding site 2 out of 10 in 1vel

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Cadmium binding site 2 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:39.4
occ:0.75
 OD1 B:ASP136 2.4 76.8 1.0
OD1 C:ASP136 2.5 64.0 1.0
OD1 A:ASP136 2.6 71.1 1.0
OD2 B:ASP136 3.0 76.8 1.0
OD2 A:ASP136 3.0 71.1 1.0
CG B:ASP136 3.0 76.8 1.0
CG A:ASP136 3.1 71.1 1.0
CG C:ASP136 3.2 64.0 1.0
OD2 C:ASP136 3.2 64.0 1.0
CB A:ASP136 4.5 71.1 1.0
CB B:ASP136 4.5 76.8 1.0
CB C:ASP136 4.6 64.0 1.0

Cadmium binding site 3 out of 10 in 1vel

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Cadmium binding site 3 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:41.1
occ:1.00
 NE2 B:HIS39 2.5 51.7 1.0
O B:HOH405 2.6 26.8 1.0
CD2 B:HIS39 3.3 51.7 1.0
CE1 B:HIS39 3.6 51.7 1.0
NZ B:LYS36 3.9 36.2 1.0
NE2 B:HIS51 4.2 52.3 1.0
CE1 B:HIS51 4.2 52.3 1.0
OD2 B:ASP55 4.4 48.9 1.0
NE1 B:TRP40 4.5 41.0 1.0
CG B:HIS39 4.5 51.7 1.0
CE B:LYS36 4.6 36.2 1.0
ND1 B:HIS39 4.6 51.7 1.0
OD1 B:ASP55 4.7 48.9 1.0
CD1 B:TRP40 4.7 41.0 1.0
O B:HOH524 4.8 76.7 1.0

Cadmium binding site 4 out of 10 in 1vel

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Cadmium binding site 4 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd205

b:41.6
occ:1.00
 OD2 C:ASP66 2.3 47.3 1.0
OD1 C:ASP66 2.4 47.3 1.0
OE1 C:GLU70 2.5 52.9 1.0
NE2 E:HIS39 2.5 46.7 1.0
O C:HOH445 2.7 24.9 1.0
CG C:ASP66 2.7 47.3 1.0
CD C:GLU70 3.0 52.9 1.0
OE2 C:GLU70 3.0 52.9 1.0
CD2 E:HIS39 3.2 46.7 1.0
CE1 E:HIS39 3.7 46.7 1.0
NE2 E:HIS51 3.9 43.7 1.0
CE1 E:HIS51 4.1 43.7 1.0
CG C:GLU70 4.2 52.9 1.0
CB C:ASP66 4.3 47.3 1.0
O C:HOH334 4.3 67.5 1.0
NZ E:LYS36 4.5 38.1 1.0
CG E:HIS39 4.5 46.7 1.0
NE1 E:TRP40 4.5 44.2 1.0
O C:HOH509 4.6 67.5 1.0
ND1 E:HIS39 4.6 46.7 1.0
OD2 E:ASP55 4.7 47.8 1.0
CD1 E:TRP40 4.8 44.2 1.0
CE E:LYS36 4.9 38.1 1.0
O C:ASP66 5.0 55.8 1.0
OD1 E:ASP55 5.0 47.8 1.0

Cadmium binding site 5 out of 10 in 1vel

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Cadmium binding site 5 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


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Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd210

b:32.6
occ:0.40
 OE1 C:GLU118 2.3 93.0 1.0
O C:HOH494 2.6 38.2 1.0
OE2 C:GLU118 2.8 93.0 1.0
O C:HOH493 2.9 26.2 1.0
CD C:GLU118 2.9 93.0 1.0
CG C:GLU118 4.4 93.0 1.0

Cadmium binding site 6 out of 10 in 1vel

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Cadmium binding site 6 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd204

b:43.9
occ:1.00
 NE2 D:HIS39 2.4 42.9 1.0
O D:HOH447 2.4 36.6 1.0
CD2 D:HIS39 3.2 42.9 1.0
CE1 D:HIS39 3.5 42.9 1.0
NE2 D:HIS51 3.9 43.3 1.0
CE1 D:HIS51 4.1 43.3 1.0
OD2 D:ASP55 4.4 57.1 1.0
CG D:HIS39 4.4 42.9 1.0
ND1 D:HIS39 4.5 42.9 1.0
NE1 D:TRP40 4.6 60.9 1.0
NZ D:LYS36 4.6 42.3 1.0
OD1 D:ASP55 4.7 57.1 1.0
CD1 D:TRP40 4.8 60.9 1.0
CG D:ASP55 5.0 57.1 1.0

Cadmium binding site 7 out of 10 in 1vel

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Cadmium binding site 7 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd208

b:31.8
occ:0.75
 OD1 D:ASP136 2.4 63.2 1.0
OD1 E:ASP136 2.5 57.1 1.0
OD2 F:ASP136 2.5 67.1 1.0
OD2 D:ASP136 3.0 63.2 1.0
CG D:ASP136 3.0 63.2 1.0
OD1 F:ASP136 3.0 67.1 1.0
CG F:ASP136 3.1 67.1 1.0
OD2 E:ASP136 3.2 57.1 1.0
CG E:ASP136 3.2 57.1 1.0
CB D:ASP136 4.4 63.2 1.0
CB F:ASP136 4.5 67.1 1.0
CB E:ASP136 4.6 57.1 1.0

Cadmium binding site 8 out of 10 in 1vel

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Cadmium binding site 8 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd209

b:48.5
occ:0.40
 OD1 D:ASP129 2.2 80.3 1.0
O D:HOH496 2.6 68.2 1.0
CG D:ASP129 3.0 80.3 1.0
OD2 D:ASP129 3.2 80.3 1.0
CB D:ASP129 4.4 80.3 1.0
CA D:ASP129 4.9 57.2 1.0
CG D:GLU128 4.9 90.6 1.0

Cadmium binding site 9 out of 10 in 1vel

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Cadmium binding site 9 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cd203

b:41.9
occ:1.00
 OD2 E:ASP66 2.4 42.0 1.0
OD1 E:ASP66 2.5 42.0 1.0
NE2 C:HIS39 2.5 49.5 1.0
OE1 E:GLU70 2.6 56.3 1.0
O E:HOH444 2.6 29.1 1.0
CG E:ASP66 2.8 42.0 1.0
CD E:GLU70 3.1 56.3 1.0
OE2 E:GLU70 3.1 56.3 1.0
CD2 C:HIS39 3.3 49.5 1.0
CE1 C:HIS39 3.6 49.5 1.0
NZ C:LYS36 3.9 39.7 1.0
NE2 C:HIS51 4.1 51.4 1.0
CE1 C:HIS51 4.2 51.4 1.0
OD2 C:ASP55 4.2 49.1 1.0
CB E:ASP66 4.3 42.0 1.0
CG E:GLU70 4.4 56.3 1.0
CG C:HIS39 4.5 49.5 1.0
NE1 C:TRP40 4.6 48.7 1.0
ND1 C:HIS39 4.6 49.5 1.0
CD1 C:TRP40 4.7 48.7 1.0
OD1 C:ASP55 4.8 49.1 1.0
CE C:LYS36 4.8 39.7 1.0
CG C:ASP55 4.9 49.1 1.0

Cadmium binding site 10 out of 10 in 1vel

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Cadmium binding site 10 out of 10 in the Mycobacterium Smegmatis Dps Tetragonal Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Mycobacterium Smegmatis Dps Tetragonal Form within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cd206

b:40.5
occ:1.00
 O F:HOH449 2.5 35.0 1.0
NE2 F:HIS39 2.7 39.8 1.0
CD2 F:HIS39 3.3 39.8 1.0
CE1 F:HIS39 3.9 39.8 1.0
NZ F:LYS36 4.0 38.7 1.0
NE2 F:HIS51 4.1 47.4 1.0
CE1 F:HIS51 4.1 47.4 1.0
OD2 F:ASP55 4.3 58.0 1.0
NE1 F:TRP40 4.6 42.8 1.0
CG F:HIS39 4.6 39.8 1.0
CD1 F:TRP40 4.7 42.8 1.0
ND1 F:HIS39 4.9 39.8 1.0
OD1 F:ASP55 4.9 58.0 1.0

Reference:

S.Roy, S.Gupta, S.Das, K.Sekar, D.Chatterji, M.Vijayan. X-Ray Analysis of Mycobacterium Smegmatis Dps and A Comparative Study Involving Other Dps and Dps-Like Molecules J.Mol.Biol. V. 339 1103 2004.
ISSN: ISSN 0022-2836
PubMed: 15178251
DOI: 10.1016/J.JMB.2004.04.042
Page generated: Thu Jul 10 11:22:38 2025

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