Iodine in PDB 4n6d: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site, PDB code: 4n6d was solved by M.W.Vetting, N.F.Al Obaidi, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.98 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.703, 68.249, 108.687, 90.00, 90.00, 90.00
R / Rfree (%)	14.5 / 18.4

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Iodine atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site (pdb code 4n6d). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site, PDB code: 4n6d:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:21.0 occ:0.50 I3 A:I3C401 0.0 21.0 0.5 C6 A:I3C401 2.1 21.4 0.5 C1 A:I3C401 3.0 23.9 0.5 C5 A:I3C401 3.0 25.0 0.5 C7 A:I3C401 3.1 30.8 0.5 N13 A:I3C401 3.2 29.5 0.5 O9 A:I3C401 3.4 34.4 0.5 O8 A:I3C401 3.7 28.5 0.5 O A:HOH716 4.1 32.4 1.0 HB1 A:ALA60 4.2 28.2 1.0 C2 A:I3C401 4.3 12.3 0.5 C4 A:I3C401 4.3 22.1 0.5 C3 A:I3C401 4.8 17.1 0.5

Iodine binding site 2 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:27.3 occ:0.50 I2 A:I3C401 0.0 27.3 0.5 C4 A:I3C401 2.1 22.1 0.5 O A:HOH742 2.7 43.6 1.0 C5 A:I3C401 3.0 25.0 0.5 C3 A:I3C401 3.0 17.1 0.5 C10 A:I3C401 3.2 29.3 0.5 N13 A:I3C401 3.2 29.5 0.5 HA3 A:GLY61 3.2 21.5 1.0 O12 A:I3C401 3.3 34.9 0.5 C A:ALA60 3.7 13.0 1.0 N A:GLY61 3.7 16.5 1.0 O A:ALA60 3.8 15.0 1.0 HA A:ALA60 3.8 19.0 1.0 O11 A:I3C401 3.8 28.9 0.5 O A:HOH861 3.8 33.4 1.0 CA A:GLY61 3.9 17.9 1.0 O A:HOH860 3.9 37.9 1.0 HA2 A:GLY61 4.0 21.5 1.0 H A:GLY61 4.1 19.8 1.0 CA A:ALA60 4.3 15.8 1.0 C6 A:I3C401 4.3 21.4 0.5 C2 A:I3C401 4.3 12.3 0.5 O A:HOH836 4.6 24.2 1.0 O A:HOH719 4.8 31.2 1.0 C1 A:I3C401 4.9 23.9 0.5 O A:GLU56 4.9 14.1 1.0 HB1 A:ALA60 4.9 28.2 1.0

Iodine binding site 3 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:32.6 occ:0.50 I1 A:I3C401 0.0 32.6 0.5 C2 A:I3C401 2.1 12.3 0.5 C1 A:I3C401 3.0 23.9 0.5 C3 A:I3C401 3.1 17.1 0.5 C7 A:I3C401 3.3 30.8 0.5 C10 A:I3C401 3.3 29.3 0.5 O11 A:I3C401 3.5 28.9 0.5 O8 A:I3C401 3.6 28.5 0.5 O9 A:I3C401 3.9 34.4 0.5 O12 A:I3C401 4.0 34.9 0.5 C6 A:I3C401 4.3 21.4 0.5 C4 A:I3C401 4.3 22.1 0.5 C5 A:I3C401 4.9 25.0 0.5 O A:HOH719 4.9 31.2 1.0

Iodine binding site 4 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:23.1 occ:0.66 I3 A:I3C402 0.0 23.1 0.7 C6 A:I3C402 2.1 14.9 0.7 O A:HOH530 2.6 19.4 1.0 C1 A:I3C402 3.0 24.2 0.7 C5 A:I3C402 3.1 26.7 0.7 C7 A:I3C402 3.2 24.1 0.7 N13 A:I3C402 3.3 30.5 0.7 O8 A:I3C402 3.5 22.5 0.7 O9 A:I3C402 3.7 28.1 0.7 O A:HOH777 4.2 24.0 1.0 C2 A:I3C402 4.3 26.7 0.7 C4 A:I3C402 4.3 20.2 0.7 O A:HOH754 4.5 29.2 1.0 O A:HOH732 4.6 36.3 1.0 C3 A:I3C402 4.8 19.2 0.7

Iodine binding site 5 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:22.9 occ:0.66 I2 A:I3C402 0.0 22.9 0.7 C4 A:I3C402 2.1 20.2 0.7 C3 A:I3C402 3.0 19.2 0.7 C5 A:I3C402 3.0 26.7 0.7 C10 A:I3C402 3.2 23.2 0.7 N13 A:I3C402 3.2 30.5 0.7 HH12 A:ARG81 3.4 37.0 1.0 HE1 A:MET84 3.4 10.2 1.0 O12 A:I3C402 3.6 21.7 0.7 HE A:ARG138 3.6 26.8 1.0 NE A:ARG138 3.6 22.4 1.0 O11 A:I3C402 3.6 27.4 0.7 HD2 A:ARG138 3.8 31.2 1.0 CZ A:ARG138 3.8 25.3 1.0 HE2 A:MET84 3.9 10.2 1.0 HE3 A:MET84 3.9 10.2 1.0 CE A:MET84 3.9 8.5 1.0 HH11 A:ARG138 4.0 32.4 1.0 NH1 A:ARG138 4.0 27.0 1.0 NH1 A:ARG81 4.1 30.8 1.0 CD A:ARG138 4.2 26.0 1.0 C2 A:I3C402 4.3 26.7 0.7 C6 A:I3C402 4.3 14.9 0.7 HD3 A:ARG138 4.4 31.2 1.0 NH2 A:ARG138 4.4 29.6 1.0 HH12 A:ARG138 4.4 32.4 1.0 HH11 A:ARG81 4.5 37.0 1.0 HH22 A:ARG81 4.5 46.9 1.0 HH21 A:ARG138 4.6 35.5 1.0 HH22 A:ARG138 4.8 35.5 1.0 C1 A:I3C402 4.8 24.2 0.7

Iodine binding site 6 out of 6 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:34.8 occ:0.66 I1 A:I3C402 0.0 34.8 0.7 C2 A:I3C402 2.1 26.7 0.7 C1 A:I3C402 3.0 24.2 0.7 C3 A:I3C402 3.0 19.2 0.7 C7 A:I3C402 3.2 24.1 0.7 C10 A:I3C402 3.2 23.2 0.7 O9 A:I3C402 3.5 28.1 0.7 O11 A:I3C402 3.6 27.4 0.7 O12 A:I3C402 3.6 21.7 0.7 O8 A:I3C402 3.7 22.5 0.7 O A:HOH891 3.8 37.3 1.0 O A:HOH856 3.9 39.7 1.0 O A:HOH701 4.2 42.0 1.0 O A:HOH754 4.2 29.2 1.0 C6 A:I3C402 4.3 14.9 0.7 C4 A:I3C402 4.3 20.2 0.7 HH22 A:ARG81 4.9 46.9 1.0 C5 A:I3C402 4.9 26.7 0.7

M.W.Vetting, N.F.Al Obaidi, M.Stead, J.D.Attonito, A.Scott Glenn, S.Chowdhury, B.Evans, B.Hillerich, J.Love, R.D.Seidel, H.J.Imker, J.A.Gerlt, S.C.Almo. Crystal Structure of A Trap Periplasmic Solute Binding Protein From Desulfovibrio Salexigens DSM2638 (DESAL_3247), Target Efi-510112, Phased with I3C, Open Complex, C-Terminus of Symmetry Mate Bound in Ligand Binding Site To Be Published.