Iodine in PDB 4p1e: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide, PDB code: 4p1e 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, K.L.Whalen, 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)	38.98 / 1.90
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	67.820, 67.820, 156.351, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 23.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 37;

Binding sites:

The binding sites of Iodine atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide (pdb code 4p1e). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 37 binding sites of Iodine where determined in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide, PDB code: 4p1e:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I401 b:26.2 occ:0.60 HA A:ARG95 3.1 26.0 1.0 HD3 A:ARG95 3.4 31.0 1.0 HH21 A:ARG95 3.4 43.4 1.0 NH2 A:ARG95 3.5 36.2 1.0 O A:HOH608 3.5 19.4 1.0 HH22 A:ARG95 3.7 43.4 1.0 HB1 A:ALA94 3.8 15.7 1.0 CZ A:ARG95 3.8 34.6 1.0 CA A:ARG95 3.8 21.7 1.0 HB2 A:ARG95 3.8 26.9 1.0 N A:ARG95 3.9 19.2 1.0 C A:ALA94 4.0 15.8 1.0 HB3 A:ALA94 4.0 15.7 1.0 O A:ALA94 4.0 13.7 1.0 NE A:ARG95 4.1 31.5 1.0 CD A:ARG95 4.2 25.9 1.0 H A:ARG95 4.2 23.1 1.0 CB A:ALA94 4.3 13.1 1.0 O A:HOH707 4.3 30.0 1.0 CB A:ARG95 4.3 22.4 1.0 NH1 A:ARG95 4.5 36.9 1.0 HH12 A:ARG95 4.7 44.3 1.0 HE A:ARG95 4.7 37.8 1.0 CA A:ALA94 4.8 12.0 1.0 O A:HOH661 4.8 32.9 1.0 O A:HOH617 4.8 18.5 1.0 HD2 A:ARG95 4.9 31.0 1.0 CG A:ARG95 4.9 25.5 1.0 HH11 A:ARG95 5.0 44.3 1.0

Iodine binding site 2 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I402 b:21.1 occ:0.52 HB A:THR34 2.8 39.4 1.0 H A:SER35 2.8 41.0 1.0 H A:LEU36 3.1 41.2 1.0 HA A:THR34 3.3 39.0 1.0 O A:HOH627 3.3 42.0 1.0 O A:HOH702 3.5 30.0 1.0 CB A:LEU36 3.5 34.8 1.0 N A:SER35 3.6 34.1 1.0 CB A:THR34 3.6 32.8 1.0 HG22 A:ILE42 3.6 15.6 1.0 HG21 A:ILE42 3.7 15.6 1.0 N A:LEU36 3.8 34.4 1.0 HB A:VAL90 3.8 16.7 1.0 CA A:THR34 3.8 32.5 1.0 HG A:SER35 3.9 44.4 1.0 HD12 A:LEU46 4.0 15.1 1.0 HD11 A:LEU46 4.0 15.1 1.0 CG2 A:ILE42 4.1 13.0 1.0 C A:THR34 4.2 30.4 1.0 HG21 A:VAL90 4.2 13.8 1.0 HG22 A:THR34 4.3 38.0 1.0 CA A:LEU36 4.3 33.0 1.0 CD1 A:LEU46 4.5 12.6 1.0 HB A:ILE42 4.5 14.8 1.0 CG2 A:THR34 4.5 31.7 1.0 HD2 A:TYR43 4.6 21.9 1.0 OG A:SER35 4.6 37.0 1.0 OG1 A:THR34 4.6 36.9 1.0 CB A:VAL90 4.6 13.9 1.0 C A:SER35 4.6 37.7 1.0 HG11 A:VAL90 4.7 18.9 1.0 CA A:SER35 4.7 36.6 1.0 CG2 A:VAL90 4.8 11.5 1.0 HG21 A:THR34 4.8 38.0 1.0 HG23 A:VAL90 4.8 13.8 1.0 HG1 A:THR34 4.8 44.3 1.0 HG23 A:ILE42 4.9 15.6 1.0 HB2 A:TYR43 4.9 15.5 1.0 HA A:TYR43 4.9 15.1 1.0 CB A:ILE42 4.9 12.3 1.0 HD13 A:LEU46 5.0 15.1 1.0 HA A:LEU36 5.0 39.5 1.0

Iodine binding site 3 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I403 b:86.2 occ:1.00 HA A:LYS310 3.5 29.4 1.0 HD2 A:TYR306 3.6 25.0 1.0 HB2 A:TYR306 3.7 24.6 1.0 HG2 A:GLU309 3.8 40.2 1.0 CB A:LYS310 3.9 28.4 1.0 CA A:LYS310 4.0 24.5 1.0 H A:LYS310 4.0 26.9 1.0 N A:LYS310 4.0 22.4 1.0 HB3 A:GLU309 4.1 35.7 1.0 OE2 A:GLU309 4.3 36.5 1.0 O A:TYR306 4.4 17.3 1.0 CD2 A:TYR306 4.5 20.8 1.0 CG A:GLU309 4.5 33.5 1.0 CD A:GLU309 4.6 36.7 1.0 CB A:TYR306 4.7 20.5 1.0 C A:GLU309 4.7 23.0 1.0 CB A:GLU309 4.7 29.8 1.0

Iodine binding site 4 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I404 b:34.0 occ:0.49 HA3 A:GLY139 3.4 21.8 1.0 O A:SER138 3.6 16.7 1.0 C A:SER138 3.7 12.3 1.0 HB3 A:GLN82 3.7 26.0 1.0 HA A:SER138 3.8 17.3 1.0 N A:GLY139 4.0 16.8 1.0 HE21 A:GLN82 4.0 28.9 1.0 CA A:GLY139 4.1 18.2 1.0 HG2 A:GLN82 4.3 25.1 1.0 CA A:SER138 4.3 14.4 1.0 NE2 A:GLN82 4.4 24.1 1.0 H A:GLY139 4.4 20.2 1.0 O A:LYS137 4.5 17.5 1.0 CB A:GLN82 4.6 21.7 1.0 HA2 A:GLY139 4.6 21.8 1.0 I A:IOD405 4.7 46.9 0.4 O A:GLN82 4.7 17.8 1.0 CG A:GLN82 4.7 20.9 1.0 HE22 A:GLN82 4.7 28.9 1.0 HA A:GLN82 4.7 25.0 1.0 CD A:GLN82 4.8 23.9 1.0

Iodine binding site 5 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I405 b:46.9 occ:0.44 HA A:ALA83 3.1 18.9 1.0 O A:HOH704 3.2 30.0 1.0 HB3 A:GLN82 3.7 26.0 1.0 HB2 A:ALA83 3.8 17.6 1.0 CA A:ALA83 3.9 15.7 1.0 N A:ALA83 4.0 17.8 1.0 C A:GLN82 4.1 20.2 1.0 O A:GLN82 4.1 17.8 1.0 CB A:ALA83 4.3 14.7 1.0 HB2 A:GLN82 4.4 26.0 1.0 CB A:GLN82 4.4 21.7 1.0 H A:ALA83 4.4 21.4 1.0 HB1 A:ALA83 4.6 17.6 1.0 I A:IOD404 4.7 34.0 0.5 CA A:GLN82 4.9 20.8 1.0

Iodine binding site 6 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


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 Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I406 b:37.7 occ:0.44 HE1 A:HIS80 3.2 29.1 1.0 HE2 A:HIS80 3.5 31.3 1.0 HB2 A:GLU76 3.5 31.4 1.0 CE1 A:HIS80 3.7 24.2 1.0 OE1 A:GLU76 3.9 34.9 1.0 NE2 A:HIS80 3.9 26.1 1.0 O A:HOH683 4.0 30.2 1.0 O A:HOH516 4.1 39.8 1.0 HB3 A:GLU76 4.4 31.4 1.0 CB A:GLU76 4.4 26.2 1.0 CD A:GLU76 4.9 33.0 1.0 ND1 A:HIS80 4.9 21.2 1.0

Iodine binding site 7 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I407 b:33.5 occ:0.49 HD3 A:LYS50 2.9 16.9 1.0 O A:HOH569 3.3 15.6 1.0 O A:HOH642 3.5 2.5 1.0 HE21 A:GLN47 3.6 24.6 1.0 HB3 A:GLN47 3.6 16.8 1.0 HG2 A:GLN47 3.6 18.8 1.0 HE3 A:LYS50 3.7 18.3 1.0 CD A:LYS50 3.7 14.1 1.0 HE2 A:LYS50 3.9 18.3 1.0 HD2 A:LYS50 4.0 16.9 1.0 CE A:LYS50 4.0 15.2 1.0 NE2 A:GLN47 4.1 20.5 1.0 HA A:GLN47 4.3 14.2 1.0 CG A:GLN47 4.3 15.7 1.0 CB A:GLN47 4.3 14.0 1.0 CD A:GLN47 4.6 18.6 1.0 HB3 A:LYS50 4.6 14.1 1.0 O A:GLN47 4.6 11.3 1.0 HE22 A:GLN47 4.6 24.6 1.0 CA A:GLN47 4.7 11.8 1.0 CG A:LYS50 4.9 12.5 1.0 HG2 A:LYS50 4.9 15.0 1.0

Iodine binding site 8 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I408 b:25.6 occ:0.68 H A:LEU65 2.8 19.6 1.0 HE2 A:LYS50 2.9 18.3 1.0 O A:HOH642 3.1 2.5 1.0 HA A:LYS64 3.2 17.6 1.0 HZ2 A:LYS50 3.6 21.5 1.0 N A:LEU65 3.7 16.3 1.0 HG A:LEU65 3.7 18.2 1.0 HD2 A:LYS50 3.7 16.9 1.0 CE A:LYS50 3.7 15.2 1.0 HB2 A:LEU65 3.9 22.3 1.0 NZ A:LYS50 4.0 17.9 1.0 HZ3 A:LYS50 4.0 21.5 1.0 O A:ILE63 4.1 12.2 1.0 CA A:LYS64 4.1 14.7 1.0 CD A:LYS50 4.3 14.1 1.0 O A:LEU65 4.4 21.8 1.0 HG2 A:LYS64 4.4 23.0 1.0 CB A:LEU65 4.4 18.6 1.0 C A:LYS64 4.5 17.2 1.0 HE3 A:LYS50 4.5 18.3 1.0 CG A:LEU65 4.5 15.2 1.0 CA A:LEU65 4.6 17.2 1.0 HB3 A:LYS64 4.7 20.9 1.0 HD12 A:LEU65 4.8 19.0 1.0 HD3 A:LYS50 4.8 16.9 1.0 CB A:LYS64 4.8 17.4 1.0 HZ1 A:LYS50 4.8 21.5 1.0 HG3 A:LYS64 4.9 23.0 1.0 CG A:LYS64 4.9 19.2 1.0 C A:LEU65 5.0 20.7 1.0

Iodine binding site 9 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I409 b:20.1 occ:0.79 HE21 A:GLN255 3.1 21.3 1.0 HB A:THR57 3.2 13.0 1.0 O A:HOH614 3.2 26.4 1.0 HG22 A:THR57 3.3 13.3 1.0 HA A:THR57 3.3 11.8 1.0 HG3 A:GLN255 3.3 16.6 1.0 HB2 A:GLU60 3.5 25.5 1.0 HG2 A:GLN255 3.6 16.6 1.0 CB A:THR57 3.8 10.9 1.0 NE2 A:GLN255 3.9 17.7 1.0 CG A:GLN255 3.9 13.9 1.0 HG3 A:GLU60 3.9 31.8 1.0 CG2 A:THR57 4.0 11.1 1.0 CA A:THR57 4.0 9.8 1.0 HB3 A:GLU60 4.2 25.5 1.0 CB A:GLU60 4.2 21.2 1.0 HG21 A:THR57 4.3 13.3 1.0 O A:THR57 4.3 14.7 1.0 CD A:GLN255 4.4 17.2 1.0 HD12 A:ILE258 4.5 14.6 1.0 HE22 A:GLN255 4.5 21.3 1.0 CG A:GLU60 4.6 26.5 1.0 C A:THR57 4.6 13.0 1.0 HG1 A:THR252 4.7 21.8 1.0 HG23 A:VAL61 4.7 18.7 1.0 HG23 A:THR57 4.8 13.3 1.0 O A:HOH715 4.8 30.0 1.0 HA A:GLN255 4.9 17.9 1.0 HD13 A:ILE258 4.9 14.6 1.0

Iodine binding site 10 out of 37 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide within 5.0Å range: probe atom residue distance (Å) B Occ A:I410 b:24.6 occ:0.39 HG A:LEU77 2.5 31.8 1.0 HD1 A:HIS80 2.7 25.5 1.0 O A:HOH546 2.9 16.9 1.0 HD11 A:LEU77 3.1 38.0 1.0 O A:LEU71 3.2 34.2 1.0 HD13 A:LEU77 3.2 38.0 1.0 HA A:LEU77 3.2 22.8 1.0 CG A:LEU77 3.3 26.4 1.0 CD1 A:LEU77 3.4 31.7 1.0 ND1 A:HIS80 3.5 21.2 1.0 HB3 A:LEU71 3.6 26.3 1.0 HG13 A:VAL87 3.8 29.1 1.0 HB2 A:HIS80 4.0 23.0 1.0 HG12 A:VAL87 4.0 29.1 1.0 CA A:LEU77 4.0 19.0 1.0 C A:LEU71 4.2 31.2 1.0 HD23 A:LEU77 4.2 29.5 1.0 O A:HOH516 4.2 39.8 1.0 HG22 A:VAL87 4.2 26.3 1.0 HG23 A:VAL87 4.2 26.3 1.0 CB A:LEU77 4.2 22.4 1.0 CG1 A:VAL87 4.3 24.2 1.0 HD12 A:LEU77 4.3 38.0 1.0 CD2 A:LEU77 4.3 24.6 1.0 HA3 A:GLY72 4.4 33.3 1.0 CE1 A:HIS80 4.4 24.2 1.0 HB A:VAL87 4.4 25.1 1.0 HE1 A:HIS80 4.4 29.1 1.0 CG A:HIS80 4.4 21.4 1.0 CB A:LEU71 4.5 21.9 1.0 CG2 A:VAL87 4.5 21.9 1.0 CB A:HIS80 4.5 19.2 1.0 HB3 A:HIS80 4.6 23.0 1.0 HB3 A:LEU77 4.6 26.9 1.0 HD22 A:LEU77 4.6 29.5 1.0 CB A:VAL87 4.6 21.0 1.0 N A:LEU77 4.7 18.9 1.0 HG3 A:GLU76 4.8 36.4 1.0 HD23 A:LEU71 4.8 31.4 1.0 CA A:LEU71 4.8 27.0 1.0 HA A:LEU71 4.8 32.4 1.0 HD12 A:LEU71 4.9 28.4 1.0 HB2 A:LEU71 4.9 26.3 1.0 HB2 A:LEU77 5.0 26.9 1.0

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, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of A Trap Periplasmic Solute Binding Protein From Escherichia Fergusonii (EFER_1530), Target Efi-510119, Apo Open Structure, Phased with Iodide To Be Published.