Chlorine 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:

Cadmium

(Cd)

8 atoms

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

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl1170 b:17.4 occ:1.00 CD A:CD1169 2.5 14.0 0.8 O A:HOH2184 2.7 21.3 1.0 CE1 A:HIS119 3.3 12.0 1.0 O2 A:SO41165 3.4 18.5 1.0 CE1 A:PHE108 3.5 20.9 1.0 ND1 A:HIS119 3.5 11.3 1.0 NE2 H:HIS119 3.5 9.3 1.0 CE1 H:HIS119 3.6 8.7 1.0 CZ3 A:TRP112 3.7 16.8 1.0 CH2 A:TRP112 3.8 15.9 1.0 CD H:LYS137 3.8 23.3 1.0 CZ A:PHE108 3.9 22.0 1.0 O A:HIS119 4.0 12.0 1.0 SG A:CYS139 4.1 13.7 1.0 CE H:LYS137 4.2 27.2 1.0 CL H:CL1169 4.6 9.2 0.7 NE2 A:HIS119 4.6 12.4 1.0 CD1 A:PHE108 4.6 20.1 1.0 S A:SO41165 4.7 13.8 0.8 CD2 H:HIS119 4.7 11.7 1.0 ND1 H:HIS119 4.7 9.8 1.0 O1 A:SO41165 4.8 12.2 0.9 CG A:HIS119 4.9 10.1 1.0 CE3 A:TRP112 5.0 18.0 1.0 CZ2 A:TRP112 5.0 17.1 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl1168 b:14.9 occ:0.90 CD B:CD1167 2.5 14.4 0.8 O B:HOH2170 2.6 14.9 1.0 CE1 B:PHE108 3.5 21.5 1.0 O4 B:SO41165 3.5 17.9 0.8 CE1 B:HIS119 3.5 13.6 1.0 ND1 B:HIS119 3.6 13.7 1.0 CZ3 B:TRP112 3.8 16.3 1.0 CH2 B:TRP112 3.8 16.0 1.0 CZ B:PHE108 3.9 23.0 1.0 O B:HIS119 3.9 9.7 1.0 SG B:CYS139 4.1 13.3 1.0 CD1 B:PHE108 4.5 19.4 1.0 S B:SO41165 4.8 15.1 1.0 NE2 B:HIS119 4.8 15.7 1.0 O3 B:SO41165 4.9 13.6 1.0 CE3 B:TRP112 5.0 15.9 1.0 CG B:HIS119 5.0 12.7 1.0 CZ2 B:TRP112 5.0 14.9 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl1169 b:10.8 occ:0.77 CD C:CD1168 2.5 15.0 0.8 O C:HOH2173 2.6 16.0 1.0 O F:HOH2128 3.0 26.5 1.0 CE1 C:HIS119 3.4 13.3 1.0 CE1 C:PHE108 3.4 23.3 1.0 O2 C:SO41165 3.5 19.5 1.0 NE2 F:HIS119 3.5 12.5 1.0 CE1 F:HIS119 3.6 11.8 1.0 ND1 C:HIS119 3.6 11.6 1.0 CZ3 C:TRP112 3.7 18.5 1.0 CH2 C:TRP112 3.8 18.9 1.0 CD F:LYS137 3.8 25.6 1.0 CZ C:PHE108 3.9 24.8 1.0 O C:HIS119 4.0 14.6 1.0 SG C:CYS139 4.1 13.8 1.0 CE F:LYS137 4.2 28.7 1.0 CD1 C:PHE108 4.5 22.3 1.0 CL F:CL1169 4.6 16.8 0.9 NE2 C:HIS119 4.6 13.8 1.0 CD2 F:HIS119 4.7 13.5 1.0 ND1 F:HIS119 4.7 11.1 1.0 S C:SO41165 4.7 17.2 1.0 O4 C:SO41165 4.8 16.2 1.0 CE3 C:TRP112 4.9 17.3 1.0 CG C:HIS119 5.0 11.1 1.0 CZ2 C:TRP112 5.0 16.8 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl1167 b:17.3 occ:1.00 CD D:CD1166 2.5 15.4 0.9 O D:HOH2175 2.7 17.9 1.0 O E:HOH2115 3.2 28.8 1.0 CE1 D:HIS119 3.4 14.3 1.0 CE1 D:PHE108 3.4 23.4 1.0 ND1 D:HIS119 3.5 12.1 1.0 O3 D:SO41165 3.5 15.8 0.9 CE1 E:HIS119 3.6 13.2 1.0 NE2 E:HIS119 3.6 11.1 1.0 CZ3 D:TRP112 3.7 14.0 1.0 CH2 D:TRP112 3.7 13.4 1.0 CD E:LYS137 3.7 22.1 1.0 CZ D:PHE108 3.8 25.6 1.0 O D:HIS119 3.9 11.7 1.0 CE E:LYS137 4.1 23.4 1.0 SG D:CYS139 4.1 15.2 1.0 CD1 D:PHE108 4.5 19.8 1.0 CL E:CL1169 4.6 10.1 0.8 NE2 D:HIS119 4.7 15.6 1.0 ND1 E:HIS119 4.7 12.3 1.0 O E:HOH2169 4.8 37.4 1.0 CD2 E:HIS119 4.8 12.5 1.0 S D:SO41165 4.8 16.4 0.9 CG D:HIS119 4.9 12.4 1.0 CZ2 D:TRP112 4.9 12.7 1.0 CE3 D:TRP112 4.9 11.1 1.0 O4 D:SO41165 5.0 14.7 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl1169 b:10.1 occ:0.75 CD E:CD1168 2.4 14.7 0.8 O E:HOH2144 2.5 9.1 1.0 O E:HOH2115 3.1 28.8 1.0 CE1 E:HIS119 3.4 13.2 1.0 CE1 E:PHE108 3.4 26.8 1.0 CE1 D:HIS119 3.5 14.3 1.0 O1 E:SO41165 3.5 22.9 1.0 ND1 E:HIS119 3.6 12.3 1.0 NE2 D:HIS119 3.6 15.6 1.0 CZ3 E:TRP112 3.6 17.8 1.0 CH2 E:TRP112 3.7 17.4 1.0 CD D:LYS137 3.8 21.8 1.0 CZ E:PHE108 3.9 27.7 1.0 O E:HIS119 4.0 12.5 1.0 O E:HOH2169 4.1 37.4 1.0 SG E:CYS139 4.1 13.7 1.0 CE D:LYS137 4.3 26.4 1.0 CD1 E:PHE108 4.5 24.0 1.0 CL D:CL1167 4.6 17.3 1.0 ND1 D:HIS119 4.6 12.1 1.0 NE2 E:HIS119 4.6 11.1 1.0 CD2 D:HIS119 4.8 15.8 1.0 S E:SO41165 4.8 14.7 1.0 CE3 E:TRP112 4.8 16.5 1.0 CZ2 E:TRP112 4.9 15.8 1.0 CG E:HIS119 5.0 11.6 1.0 O4 E:SO41165 5.0 15.3 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl1169 b:16.8 occ:0.89 CD F:CD1168 2.5 15.3 0.8 O F:HOH2162 2.8 17.4 1.0 O F:HOH2128 3.1 26.5 1.0 CE1 F:HIS119 3.2 11.8 1.0 CE1 F:PHE108 3.4 24.4 1.0 ND1 F:HIS119 3.5 11.1 1.0 O1 F:SO41165 3.5 18.6 1.0 NE2 C:HIS119 3.6 13.8 1.0 CE1 C:HIS119 3.6 13.3 1.0 CZ3 F:TRP112 3.7 16.2 1.0 CH2 F:TRP112 3.7 15.8 1.0 CD C:LYS137 3.8 24.3 1.0 CZ F:PHE108 3.8 26.3 1.0 O F:HIS119 3.9 13.5 1.0 O F:HOH2192 4.1 38.6 1.0 SG F:CYS139 4.1 14.5 1.0 CE C:LYS137 4.3 28.6 1.0 NE2 F:HIS119 4.5 12.5 1.0 CD1 F:PHE108 4.5 21.5 1.0 CL C:CL1169 4.6 10.8 0.8 CD2 C:HIS119 4.7 13.3 1.0 ND1 C:HIS119 4.7 11.6 1.0 S F:SO41165 4.7 17.0 0.9 CG F:HIS119 4.8 11.8 1.0 O3 F:SO41165 4.9 14.6 1.0 CE3 F:TRP112 4.9 16.8 1.0 CZ2 F:TRP112 5.0 14.5 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl1169 b:15.4 occ:0.87 CD G:CD1168 2.5 13.3 0.7 O G:HOH2133 2.6 9.6 1.0 O G:HOH2102 3.0 26.7 1.0 CE1 G:PHE108 3.4 25.0 1.0 CE1 G:HIS119 3.4 12.1 1.0 O1 G:SO41165 3.4 17.1 1.0 CZ3 G:TRP112 3.6 15.4 1.0 ND1 G:HIS119 3.6 11.2 1.0 CH2 G:TRP112 3.7 16.9 1.0 CZ G:PHE108 3.8 26.0 1.0 SG G:CYS139 4.1 13.4 1.0 O G:HIS119 4.1 9.1 1.0 O G:HOH2161 4.2 38.7 1.0 CD1 G:PHE108 4.4 20.4 1.0 NE2 G:HIS119 4.7 11.9 1.0 S G:SO41165 4.7 11.3 0.9 CE3 G:TRP112 4.8 13.1 1.0 O2 G:SO41165 4.8 7.6 0.9 NE2 G:HIS123 4.9 11.7 1.0 CZ2 G:TRP112 5.0 15.9 1.0 CG G:HIS119 5.0 11.6 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Ykud From B.Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl1169 b:9.2 occ:0.65 CD H:CD1168 2.6 15.5 0.8 O H:HOH2136 2.7 14.8 1.0 CE1 H:HIS119 3.3 8.7 1.0 CD A:LYS137 3.5 22.5 1.0 CE1 H:PHE108 3.5 25.1 1.0 O1 H:SO41165 3.5 13.6 0.7 ND1 H:HIS119 3.5 9.8 1.0 CZ3 H:TRP112 3.6 16.8 1.0 NE2 A:HIS119 3.7 12.4 1.0 CE1 A:HIS119 3.7 12.0 1.0 CH2 H:TRP112 3.7 14.9 1.0 CE A:LYS137 3.9 25.3 1.0 CZ H:PHE108 4.0 25.2 1.0 O H:HIS119 4.1 9.8 1.0 SG H:CYS139 4.2 14.9 1.0 NE2 H:HIS119 4.5 9.3 1.0 CD1 H:PHE108 4.6 24.3 1.0 CL A:CL1170 4.6 17.4 1.0 ND1 A:HIS119 4.8 11.3 1.0 CD2 A:HIS119 4.8 11.6 1.0 S H:SO41165 4.8 13.7 0.9 CE3 H:TRP112 4.9 16.4 1.0 CG A:LYS137 4.9 20.4 1.0 CG H:HIS119 4.9 10.2 1.0 O2 H:SO41165 4.9 15.7 1.0 CZ2 H:TRP112 5.0 11.6 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.