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Cadmium in PDB 3c7m: Crystal Structure of Reduced Dsbl

Protein crystallography data

The structure of Crystal Structure of Reduced Dsbl, PDB code: 3c7m was solved by C.U.Stirnimann, J.P.A.Grimshaw, R.Glockshuber, M.G.Grutter, G.Capitani, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.74 / 1.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.945, 66.634, 77.891, 90.00, 107.02, 90.00
R / Rfree (%) 16.4 / 18.9

Other elements in 3c7m:

The structure of Crystal Structure of Reduced Dsbl also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Reduced Dsbl (pdb code 3c7m). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Reduced Dsbl, PDB code: 3c7m:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 1 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd196

b:11.3
occ:0.92
 OD1 A:ASP113 2.2 13.2 1.0
OE2 A:GLU63 2.3 9.7 0.5
CL A:CL202 2.3 14.4 0.5
OD1 B:ASP156 2.4 12.3 1.0
OD2 B:ASP156 2.5 12.4 1.0
O A:HOH543 2.5 25.6 1.0
OE2 A:GLU63 2.6 10.2 0.5
CL A:CL202 2.7 10.0 0.5
OE1 A:GLU63 2.7 9.4 0.5
OE1 A:GLU63 2.7 9.2 0.5
CG B:ASP156 2.8 10.9 1.0
CD A:GLU63 2.8 10.2 0.5
CD A:GLU63 2.9 9.8 0.5
CG A:ASP113 3.2 12.7 1.0
CB A:ASP113 3.5 11.3 1.0
NZ B:LYS159 4.0 19.9 1.0
CA A:ASP113 4.1 11.2 1.0
O A:HOH510 4.2 4.7 0.5
OD2 A:ASP113 4.3 17.4 1.0
O A:HOH510 4.3 5.5 0.5
CB B:ASP156 4.3 10.1 1.0
CG A:GLU63 4.3 9.7 0.5
O A:HOH220 4.3 10.7 1.0
CG A:GLU63 4.3 9.6 0.5
CD1 B:TYR155 4.4 10.9 1.0
O A:HOH360 4.7 33.5 1.0
CE1 B:TYR155 4.8 11.2 1.0
O A:HOH223 4.8 12.8 1.0
O B:HOH500 4.8 24.8 1.0
CD A:ARG110 4.8 10.2 1.0
CE B:LYS159 4.9 19.3 1.0
O A:HOH219 4.9 11.6 1.0
CG A:ARG110 4.9 9.5 1.0
NZ B:LYS12 4.9 14.8 0.5
O B:HOH318 4.9 15.3 1.0
CB A:ARG110 4.9 9.3 1.0
C A:ASP113 5.0 11.1 1.0

Cadmium binding site 2 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 2 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd197

b:10.9
occ:0.94
 OE2 A:GLU109 2.3 9.6 1.0
CL A:CL200 2.6 12.1 0.9
OE1 A:GLU109 2.6 11.8 1.0
CD A:GLU109 2.8 9.6 1.0
O A:HOH256 4.0 10.4 1.0
CG A:GLU109 4.3 9.9 1.0
N A:TRP111 4.4 8.6 1.0
CA A:TRP111 4.4 8.4 1.0
O A:HOH273 4.5 17.9 1.0
O A:HOH456 4.5 23.3 1.0
O A:HOH332 4.8 21.2 1.0

Cadmium binding site 3 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 3 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd198

b:11.2
occ:0.95
 OD1 A:ASP183 2.3 11.1 1.0
OD2 A:ASP187 2.3 11.9 1.0
OD1 A:ASP187 2.5 11.7 1.0
CL A:CL201 2.5 11.9 0.9
CG A:ASP187 2.7 10.8 1.0
CG A:ASP183 3.0 12.1 1.0
OD2 A:ASP183 3.0 13.3 1.0
CB A:ASP187 4.3 11.0 1.0
O A:ASP183 4.3 10.4 1.0
O A:HOH275 4.3 27.0 1.0
CB A:ASP183 4.4 11.0 1.0
O A:HOH404 4.6 32.4 1.0
O A:HOH377 4.6 30.9 1.0
C A:ASP183 4.7 10.7 1.0

Cadmium binding site 4 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 4 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd199

b:14.8
occ:0.53
 O A:HOH512 2.4 27.6 1.0
ND1 A:HIS105 2.4 11.4 1.0
CL A:CL205 2.5 19.4 0.5
CL A:CL204 2.5 14.6 0.5
CE1 A:HIS105 3.3 12.4 1.0
CG A:HIS105 3.4 11.5 1.0
CB A:HIS105 3.7 11.8 1.0
CA A:HIS105 3.9 11.6 1.0
CB A:PRO30 4.1 15.4 1.0
NZ A:LYS108 4.3 10.7 0.5
CE1 A:TYR104 4.3 10.8 1.0
O A:HIS105 4.5 13.4 1.0
NE2 A:HIS105 4.5 11.0 1.0
CD1 A:TYR104 4.5 9.6 1.0
CD2 A:HIS105 4.5 11.6 1.0
C A:HIS105 4.7 12.5 1.0
O A:HOH535 4.7 37.5 1.0
CA A:PRO30 4.7 15.2 1.0
CG A:PRO30 4.7 15.4 1.0
N A:HIS105 4.9 10.9 1.0
CD A:PRO30 4.9 15.4 1.0
O A:TYR104 5.0 10.8 1.0

Cadmium binding site 5 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 5 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd196

b:11.1
occ:0.90
 OD1 B:ASP113 2.3 12.7 1.0
OE2 B:GLU63 2.4 11.2 1.0
OD1 A:ASP156 2.4 11.1 1.0
O B:HOH257 2.4 25.1 1.0
CL A:CL203 2.4 17.2 0.9
OD2 A:ASP156 2.5 11.7 1.0
OE1 B:GLU63 2.7 11.0 1.0
CG A:ASP156 2.8 9.4 1.0
CD B:GLU63 2.8 10.8 1.0
CG B:ASP113 3.1 12.9 1.0
CB B:ASP113 3.5 11.4 1.0
NZ A:LYS159 4.1 19.3 1.0
CA B:ASP113 4.1 11.2 1.0
OD2 B:ASP113 4.2 17.6 1.0
O B:HOH325 4.3 9.5 1.0
CB A:ASP156 4.3 9.6 1.0
CG B:GLU63 4.3 9.4 1.0
O B:HOH622 4.4 14.5 1.0
CD1 A:TYR155 4.4 10.8 1.0
O A:HOH215 4.5 40.1 1.0
O A:HOH523 4.6 39.2 1.0
O B:HOH294 4.7 13.2 1.0
CE1 A:TYR155 4.7 11.8 1.0
O A:HOH400 4.8 32.2 1.0
CE A:LYS159 4.8 19.4 1.0
CD B:ARG110 4.8 10.0 1.0
CG B:ARG110 4.9 9.3 1.0
O B:HOH265 4.9 10.6 1.0
O A:HOH250 4.9 15.3 1.0
CB B:ARG110 4.9 8.9 1.0
C B:ASP113 5.0 11.1 1.0

Cadmium binding site 6 out of 6 in 3c7m

Go back to Cadmium Binding Sites List in 3c7m
Cadmium binding site 6 out of 6 in the Crystal Structure of Reduced Dsbl


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 Reduced Dsbl within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd197

b:14.7
occ:0.51
 O B:HOH570 2.3 29.0 1.0
ND1 B:HIS105 2.4 12.9 1.0
CL B:CL198 2.5 13.2 0.5
CL B:CL199 2.5 21.5 0.5
CE1 B:HIS105 3.4 13.9 1.0
CG B:HIS105 3.4 12.4 1.0
CB B:HIS105 3.7 12.1 1.0
CA B:HIS105 3.9 11.8 1.0
CB B:PRO30 4.1 14.7 1.0
CE1 B:TYR104 4.3 11.5 1.0
NZ B:LYS108 4.3 18.5 1.0
O B:HIS105 4.4 12.9 1.0
CD1 B:TYR104 4.5 10.5 1.0
NE2 B:HIS105 4.5 12.5 1.0
CD2 B:HIS105 4.6 13.0 1.0
C B:HIS105 4.7 12.4 1.0
CA B:PRO30 4.7 14.3 1.0
CG B:PRO30 4.7 14.5 1.0
CD B:PRO30 4.9 14.5 1.0
N B:HIS105 4.9 10.9 1.0
O B:TYR104 4.9 10.9 1.0

Reference:

J.P.Grimshaw, C.U.Stirnimann, M.S.Brozzo, G.Malojcic, M.G.Grutter, G.Capitani, R.Glockshuber. Dsbl and Dsbi Form A Specific Dithiol Oxidase System For Periplasmic Arylsulfate Sulfotransferase in Uropathogenic Escherichia Coli. J.Mol.Biol. V. 380 667 2008.
ISSN: ISSN 0022-2836
PubMed: 18565543
DOI: 10.1016/J.JMB.2008.05.031
Page generated: Sun Jan 24 09:43:58 2021

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