Cadmium in PDB 4a1i: Ykud From B.Subtilis

The structure of Ykud From B.Subtilis, PDB code: 4a1i was solved by M.Blaise, S.Fuglsang Midtgaard, S.Roi Midtgaard, T.Boesen, S.Thirup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	51.302 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.450, 91.850, 123.700, 90.00, 90.25, 90.00
R / Rfree (%)	17.29 / 21.81

The structure of Ykud From B.Subtilis also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Cadmium atom in the Ykud From B.Subtilis (pdb code 4a1i). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Ykud From B.Subtilis, PDB code: 4a1i:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1169 b:14.0 occ:0.82 O A:HOH2184 2.2 21.3 1.0 NE2 H:HIS119 2.3 9.3 1.0 SG A:CYS139 2.4 13.7 1.0 CL A:CL1170 2.5 17.4 1.0 O2 A:SO41165 2.6 18.5 1.0 O1 A:SO41165 2.7 12.2 0.9 CE1 H:HIS119 3.1 8.7 1.0 S A:SO41165 3.2 13.8 0.8 CB A:CYS139 3.3 13.2 1.0 CD2 H:HIS119 3.3 11.7 1.0 O A:HIS119 3.8 12.0 1.0 O4 A:SO41165 3.9 13.3 0.8 N A:CYS139 4.0 10.1 1.0 CA A:CYS139 4.2 11.1 1.0 ND1 H:HIS119 4.3 9.8 1.0 O3 A:SO41165 4.4 13.8 0.9 CG H:HIS119 4.4 10.2 1.0 CH2 A:TRP112 4.4 15.9 1.0 ND1 A:HIS119 4.4 11.3 1.0 NE2 A:HIS123 4.5 13.7 1.0 CZ3 A:TRP112 4.5 16.8 1.0 CE1 A:HIS119 4.7 12.0 1.0 CD2 A:HIS123 4.8 12.9 1.0 CB A:LYS137 4.8 15.4 1.0

Cadmium binding site 2 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1167 b:14.4 occ:0.83 O B:HOH2170 2.1 14.9 1.0 SG B:CYS139 2.4 13.3 1.0 CL B:CL1168 2.5 14.9 0.9 O4 B:SO41165 2.6 17.9 0.8 O3 B:SO41165 2.7 13.6 1.0 S B:SO41165 3.2 15.1 1.0 CB B:CYS139 3.3 13.1 1.0 O B:HIS119 3.8 9.7 1.0 O2 B:SO41165 3.9 15.3 1.0 N B:CYS139 4.0 10.0 1.0 CA B:CYS139 4.2 11.3 1.0 O1 B:SO41165 4.4 16.5 1.0 CH2 B:TRP112 4.5 16.0 1.0 ND1 B:HIS119 4.5 13.7 1.0 NE2 B:HIS123 4.5 13.9 1.0 CZ3 B:TRP112 4.5 16.3 1.0 CD2 B:HIS123 4.8 12.7 1.0 CE1 B:HIS119 4.8 13.6 1.0 C B:HIS119 5.0 10.2 1.0 CB B:LYS137 5.0 14.5 1.0

Cadmium binding site 3 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Cd1168 b:15.0 occ:0.85 O C:HOH2173 2.2 16.0 1.0 NE2 F:HIS119 2.3 12.5 1.0 SG C:CYS139 2.4 13.8 1.0 CL C:CL1169 2.5 10.8 0.8 O2 C:SO41165 2.6 19.5 1.0 O4 C:SO41165 2.7 16.2 1.0 CE1 F:HIS119 3.1 11.8 1.0 S C:SO41165 3.2 17.2 1.0 CB C:CYS139 3.3 12.0 1.0 CD2 F:HIS119 3.4 13.5 1.0 O C:HIS119 3.9 14.6 1.0 O3 C:SO41165 4.0 20.2 1.0 N C:CYS139 4.0 10.2 1.0 CA C:CYS139 4.2 11.7 1.0 ND1 F:HIS119 4.3 11.1 1.0 O1 C:SO41165 4.4 18.0 1.0 CG F:HIS119 4.4 11.8 1.0 NE2 C:HIS123 4.5 12.5 1.0 CH2 C:TRP112 4.5 18.9 1.0 CZ3 C:TRP112 4.5 18.5 1.0 ND1 C:HIS119 4.5 11.6 1.0 O F:HOH2128 4.5 26.5 1.0 CE1 C:HIS119 4.7 13.3 1.0 CD2 C:HIS123 4.8 13.8 1.0 CB C:LYS137 4.9 13.9 1.0

Cadmium binding site 4 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Cd1166 b:15.4 occ:0.86 O D:HOH2175 2.2 17.9 1.0 NE2 E:HIS119 2.3 11.1 1.0 SG D:CYS139 2.4 15.2 1.0 CL D:CL1167 2.5 17.3 1.0 O3 D:SO41165 2.6 15.8 0.9 O4 D:SO41165 2.8 14.7 1.0 CE1 E:HIS119 3.0 13.2 1.0 S D:SO41165 3.2 16.4 0.9 CB D:CYS139 3.3 15.3 1.0 CD2 E:HIS119 3.4 12.5 1.0 O D:HIS119 3.8 11.7 1.0 N D:CYS139 4.0 9.8 1.0 O1 D:SO41165 4.0 18.8 1.0 CA D:CYS139 4.2 11.7 1.0 ND1 E:HIS119 4.2 12.3 1.0 O2 D:SO41165 4.4 18.5 1.0 CG E:HIS119 4.4 11.6 1.0 ND1 D:HIS119 4.4 12.1 1.0 CH2 D:TRP112 4.5 13.4 1.0 NE2 D:HIS123 4.5 13.9 1.0 CZ3 D:TRP112 4.6 14.0 1.0 CE1 D:HIS119 4.7 14.3 1.0 CD2 D:HIS123 4.8 15.2 1.0 CB D:LYS137 4.8 17.8 1.0 O E:HOH2115 4.9 28.8 1.0 CE1 D:PHE108 4.9 23.4 1.0

Cadmium binding site 5 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Cd1168 b:14.7 occ:0.77 O E:HOH2144 2.0 9.1 1.0 NE2 D:HIS119 2.2 15.6 1.0 SG E:CYS139 2.4 13.7 1.0 CL E:CL1169 2.4 10.1 0.8 O1 E:SO41165 2.6 22.9 1.0 O4 E:SO41165 2.9 15.3 1.0 CE1 D:HIS119 2.9 14.3 1.0 S E:SO41165 3.3 14.7 1.0 CD2 D:HIS119 3.4 15.8 1.0 CB E:CYS139 3.4 10.6 1.0 O E:HIS119 3.9 12.5 1.0 N E:CYS139 4.1 8.9 1.0 O2 E:SO41165 4.1 14.1 1.0 ND1 D:HIS119 4.1 12.1 1.0 CA E:CYS139 4.3 10.8 1.0 NE2 E:HIS123 4.4 10.3 1.0 CH2 E:TRP112 4.4 17.4 1.0 CG D:HIS119 4.4 12.4 1.0 O3 E:SO41165 4.5 14.9 1.0 CZ3 E:TRP112 4.5 17.8 1.0 ND1 E:HIS119 4.5 12.3 1.0 O E:HOH2115 4.5 28.8 1.0 O E:HOH2169 4.5 37.4 1.0 CE1 E:HIS119 4.7 13.2 1.0 CD2 E:HIS123 4.7 11.2 1.0 CB E:LYS137 4.8 15.5 1.0

Cadmium binding site 6 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ F:Cd1168 b:15.3 occ:0.82 O F:HOH2162 2.2 17.4 1.0 NE2 C:HIS119 2.3 13.8 1.0 SG F:CYS139 2.4 14.5 1.0 CL F:CL1169 2.5 16.8 0.9 O1 F:SO41165 2.6 18.6 1.0 O3 F:SO41165 2.7 14.6 1.0 CE1 C:HIS119 3.1 13.3 1.0 S F:SO41165 3.2 17.0 0.9 CB F:CYS139 3.3 17.8 1.0 CD2 C:HIS119 3.3 13.3 1.0 O F:HIS119 3.8 13.5 1.0 O4 F:SO41165 4.0 20.5 1.0 N F:CYS139 4.0 12.8 1.0 CA F:CYS139 4.2 13.2 1.0 ND1 C:HIS119 4.3 11.6 1.0 O2 F:SO41165 4.4 17.9 1.0 CG C:HIS119 4.4 11.1 1.0 ND1 F:HIS119 4.4 11.1 1.0 NE2 F:HIS123 4.5 16.6 1.0 CH2 F:TRP112 4.5 15.8 1.0 CZ3 F:TRP112 4.5 16.2 1.0 O F:HOH2192 4.6 38.6 1.0 CE1 F:HIS119 4.6 11.8 1.0 O F:HOH2128 4.6 26.5 1.0 CD2 F:HIS123 4.8 17.9 1.0 CB F:LYS137 4.9 19.5 1.0 CE1 F:PHE108 4.9 24.4 1.0

Cadmium binding site 7 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ G:Cd1168 b:13.3 occ:0.74 O G:HOH2133 2.0 9.6 1.0 SG G:CYS139 2.4 13.4 1.0 CL G:CL1169 2.5 15.4 0.9 O1 G:SO41165 2.6 17.1 1.0 O2 G:SO41165 2.7 7.6 0.9 S G:SO41165 3.2 11.3 0.9 CB G:CYS139 3.3 11.7 1.0 O G:HIS119 3.9 9.1 1.0 O3 G:SO41165 4.0 11.3 0.9 N G:CYS139 4.0 10.3 1.0 CA G:CYS139 4.2 8.8 1.0 NE2 G:HIS123 4.3 11.7 1.0 O4 G:SO41165 4.4 10.8 0.9 CZ3 G:TRP112 4.4 15.4 1.0 CH2 G:TRP112 4.5 16.9 1.0 O G:HOH2102 4.5 26.7 1.0 ND1 G:HIS119 4.5 11.2 1.0 CD2 G:HIS123 4.7 13.4 1.0 CE1 G:HIS119 4.7 12.1 1.0 CB G:LYS137 4.8 14.2 1.0 O G:HOH2161 4.9 38.7 1.0 CE1 G:PHE108 5.0 25.0 1.0

Cadmium binding site 8 out of 8 in the Ykud From B.Subtilis


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ H:Cd1168 b:15.5 occ:0.84 O H:HOH2136 2.2 14.8 1.0 NE2 A:HIS119 2.2 12.4 1.0 SG H:CYS139 2.4 14.9 1.0 CL H:CL1169 2.6 9.2 0.7 O1 H:SO41165 2.7 13.6 0.7 O2 H:SO41165 2.7 15.7 1.0 CE1 A:HIS119 3.1 12.0 1.0 S H:SO41165 3.2 13.7 0.9 CB H:CYS139 3.3 12.9 1.0 CD2 A:HIS119 3.3 11.6 1.0 O H:HIS119 3.9 9.8 1.0 N H:CYS139 4.0 11.8 1.0 O3 H:SO41165 4.0 14.6 0.8 CA H:CYS139 4.2 11.0 1.0 ND1 A:HIS119 4.2 11.3 1.0 O4 H:SO41165 4.4 12.2 0.8 CG A:HIS119 4.4 10.1 1.0 CH2 H:TRP112 4.4 14.9 1.0 NE2 H:HIS123 4.4 12.0 1.0 ND1 H:HIS119 4.4 9.8 1.0 CZ3 H:TRP112 4.5 16.8 1.0 CE1 H:HIS119 4.6 8.7 1.0 CD2 H:HIS123 4.8 12.1 1.0 CB H:LYS137 4.8 18.1 1.0

M.Blaise, S.Fuglsang Midtgaard, S.Roi Midtgaard, T.Boesen, S.Thirup. Structures of Three New Crystal Forms of the Ykud L,D-Transpeptidase From B. Subtilis. To Be Published.