Bromine in PDB 3svd: Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex

The structure of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex, PDB code: 3svd was solved by W.Wang, J.S.Grimley, L.S.Beese, H.W.Hellinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.53 / 1.78
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	51.520, 62.660, 65.650, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19.6

The binding sites of Bromine atom in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex (pdb code 3svd). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 5 binding sites of Bromine where determined in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex, PDB code: 3svd:
Jump to Bromine binding site number: 1; 2; 3; 4; 5;

Bromine binding site 1 out of 5 in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br261 b:32.5 occ:0.37 HG1 A:THR69 2.5 26.9 1.0 HA A:THR69 2.7 22.3 1.0 HE1 A:TYR203 2.8 25.6 1.0 HH A:TYR203 2.9 29.1 1.0 HG21 A:VAL224 3.2 30.7 1.0 OG1 A:THR69 3.3 22.5 1.0 CA A:THR69 3.4 18.6 1.0 OH A:TYR203 3.4 24.4 1.0 C2 A:CR266 3.5 21.4 1.0 CA2 A:CR266 3.5 21.9 1.0 N A:THR69 3.5 17.1 1.0 N3 A:CR266 3.5 20.6 1.0 HG23 A:THR69 3.6 24.2 1.0 C1 A:CR266 3.6 19.2 1.0 N A:VAL68 3.6 20.4 1.0 N2 A:CR266 3.6 20.0 1.0 CE1 A:TYR203 3.6 21.4 1.0 HD11 A:LEU42 3.7 36.5 1.0 C A:VAL68 3.7 18.4 1.0 CB A:THR69 3.8 21.8 1.0 H A:THR69 3.9 20.4 1.0 O A:VAL68 3.9 18.6 1.0 CZ A:TYR203 3.9 22.9 1.0 OE1 A:GLU222 4.0 22.9 1.0 O2 A:CR266 4.0 19.3 1.0 CB2 A:CR266 4.1 18.8 1.0 CG2 A:VAL224 4.1 25.6 1.0 HG11 A:VAL224 4.1 30.2 1.0 CG2 A:THR69 4.2 20.3 1.0 HA12 A:CR266 4.3 22.4 1.0 HG22 A:VAL224 4.3 30.7 1.0 HG23 A:VAL68 4.3 22.3 1.0 CA3 A:CR266 4.3 17.4 1.0 C3 A:CR266 4.4 25.9 1.0 CA A:VAL68 4.4 18.2 1.0 CA1 A:CR266 4.4 18.7 1.0 H22 A:EDO260 4.4 34.0 0.8 HD12 A:LEU42 4.5 36.5 1.0 CD1 A:LEU42 4.5 30.4 1.0 HB2 A:CR266 4.5 22.5 1.0 HG23 A:VAL224 4.6 30.7 1.0 HA11 A:CR266 4.6 22.4 1.0 HG22 A:VAL68 4.7 22.3 1.0 HB A:THR69 4.7 26.0 1.0 C A:THR69 4.7 18.4 1.0 HG21 A:THR69 4.8 24.2 1.0 HG22 A:THR69 4.8 24.2 1.0 CD1 A:TYR203 4.8 21.4 1.0 CG1 A:VAL224 4.9 25.2 1.0 CG2 A:VAL68 4.9 18.6 1.0 HA32 A:CR266 4.9 20.7 1.0 HO2 A:EDO260 5.0 28.1 0.8

Bromine binding site 2 out of 5 in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br262 b:29.7 occ:0.40 HG1 A:THR108 2.5 23.1 1.0 O A:HOH356 2.6 25.6 1.0 HG2 A:GLN94 2.7 27.8 1.0 OG1 A:THR108 3.0 19.3 1.0 HE22 A:GLN94 3.1 25.5 1.0 O A:GLN94 3.2 24.3 1.0 HG3 A:ARG96 3.2 21.5 1.0 HB A:THR108 3.4 22.1 1.0 HB3 A:ALA110 3.4 25.0 1.0 HB2 A:ALA110 3.4 25.0 1.0 HB3 A:GLN94 3.5 25.5 1.0 O A:HOH271 3.5 20.2 1.0 CG A:GLN94 3.6 23.2 1.0 HA A:GLU95 3.7 24.7 1.0 C A:GLN94 3.7 25.4 1.0 CB A:THR108 3.7 18.5 1.0 NE2 A:GLN94 3.9 21.3 1.0 H A:ALA110 3.9 23.7 1.0 CB A:ALA110 3.9 20.9 1.0 HG23 A:THR63 3.9 21.1 1.0 HH11 A:ARG96 3.9 21.8 1.0 CB A:GLN94 4.0 21.3 1.0 H A:ARG96 4.0 22.0 1.0 HB2 A:ARG96 4.0 20.1 1.0 CG A:ARG96 4.1 18.0 1.0 N A:ALA110 4.2 19.8 1.0 CD A:GLN94 4.2 24.7 1.0 N A:ARG96 4.2 18.4 1.0 N A:GLU95 4.3 22.2 1.0 CA A:GLU95 4.3 20.6 1.0 HG3 A:GLN94 4.3 27.8 1.0 NH1 A:ARG96 4.3 18.2 1.0 C A:THR108 4.3 21.0 1.0 HA A:THR63 4.3 20.8 1.0 HA A:ARG109 4.3 25.7 1.0 O A:THR108 4.3 20.3 1.0 C A:GLU95 4.4 20.8 1.0 HH12 A:ARG96 4.4 21.8 1.0 HG23 A:ILE123 4.5 26.0 1.0 CB A:ARG96 4.5 16.8 1.0 HE21 A:GLN94 4.5 25.5 1.0 CA A:GLN94 4.5 20.9 1.0 O A:HOH269 4.6 26.1 1.0 HG2 A:ARG96 4.6 21.5 1.0 N A:ARG109 4.6 19.7 1.0 HB1 A:ALA110 4.6 25.0 1.0 C A:ARG109 4.7 20.0 1.0 CA A:THR108 4.7 18.2 1.0 CA A:ALA110 4.7 19.2 1.0 HG21 A:THR108 4.7 26.5 1.0 CA A:ARG109 4.8 21.5 1.0 HD2 A:ARG96 4.9 22.6 1.0 CG2 A:THR63 4.9 17.7 1.0 HB2 A:GLN94 4.9 25.5 1.0 CG2 A:THR108 4.9 22.2 1.0 H A:GLU95 4.9 26.5 1.0 CD A:ARG96 5.0 18.9 1.0

Bromine binding site 3 out of 5 in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br263 b:24.9 occ:0.66 H A:TRP57 2.7 20.4 1.0 O A:HOH318 3.1 36.1 1.0 HD1 A:TYR143 3.1 24.4 1.0 HD3 A:PRO58 3.2 22.1 1.0 HA A:PRO56 3.2 24.1 1.0 HB2 A:TRP57 3.2 20.8 1.0 O A:HOH296 3.2 26.2 1.0 O A:HOH391 3.3 33.0 1.0 N A:TRP57 3.4 17.1 1.0 HB3 A:PRO56 3.4 25.6 1.0 HD2 A:PRO58 3.5 22.1 1.0 O A:HOH334 3.7 30.6 1.0 CD A:PRO58 3.8 18.5 1.0 CA A:PRO56 3.8 20.2 1.0 CD1 A:TRP57 3.9 19.6 1.0 CD1 A:TYR143 4.0 20.4 1.0 CB A:TRP57 4.0 17.4 1.0 CB A:PRO56 4.1 21.4 1.0 C A:PRO56 4.1 21.0 1.0 O A:HOH307 4.2 37.9 1.0 O A:HOH322 4.3 26.8 1.0 HE1 A:TYR143 4.3 25.1 1.0 CA A:TRP57 4.3 17.7 1.0 HD1 A:HIS139 4.3 36.1 1.0 CG A:TRP57 4.3 19.5 1.0 HB2 A:TYR143 4.4 26.1 1.0 HB2 A:PRO56 4.5 25.6 1.0 CE1 A:TYR143 4.6 21.0 1.0 HZ1 A:LYS209 4.6 24.9 1.0 HB3 A:TRP57 4.8 20.8 1.0 HG2 A:PRO58 4.8 24.4 1.0 HA A:TYR143 4.8 26.4 1.0 CG A:PRO58 4.8 20.4 1.0 N A:PRO58 4.9 17.1 1.0 CG A:TYR143 4.9 20.8 1.0

Bromine binding site 4 out of 5 in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br264 b:36.7 occ:0.62 HA A:ASN23 3.0 31.8 1.0 HG22 A:ILE128 3.3 36.5 1.0 HZ1 A:LYS126 3.5 56.6 1.0 HZ2 A:LYS126 3.5 56.6 1.0 HA A:ILE128 3.6 34.2 1.0 HE3 A:LYS126 3.8 55.7 1.0 NZ A:LYS126 3.9 47.2 1.0 CA A:ASN23 3.9 26.6 1.0 H A:GLY24 4.0 35.5 1.0 H A:ASN23 4.0 31.6 1.0 HB A:ILE128 4.2 33.8 1.0 N A:GLY24 4.2 29.7 1.0 O A:GLY127 4.2 25.1 1.0 CG2 A:ILE128 4.2 30.5 1.0 C A:ASN23 4.2 26.5 1.0 CE A:LYS126 4.4 46.5 1.0 N A:ASN23 4.4 26.4 1.0 H A:ASP129 4.5 34.9 0.6 CA A:ILE128 4.5 28.6 1.0 H A:ASP129 4.5 34.9 0.5 CB A:ILE128 4.5 28.2 1.0 HG21 A:ILE128 4.6 36.5 1.0 HZ3 A:LYS126 4.7 56.6 1.0 OD1 A:ASN23 4.7 27.8 1.0 HG23 A:ILE128 4.8 36.5 1.0 HE2 A:LYS126 5.0 55.7 1.0

Bromine binding site 5 out of 5 in the Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Engineered Medium-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br265 b:53.8 occ:0.48 HH11 A:ARG215 2.3 26.4 1.0 HD2 A:ARG215 3.1 29.2 1.0 NH1 A:ARG215 3.2 22.0 1.0 HD3 A:ARG215 3.2 29.2 1.0 HH12 A:ARG215 3.5 26.4 1.0 CD A:ARG215 3.6 24.4 1.0 HA A:THR49 3.7 26.6 1.0 HG22 A:THR49 3.7 32.4 1.0 HG21 A:ILE47 3.8 25.0 1.0 CZ A:ARG215 4.2 27.0 1.0 HG22 A:ILE47 4.3 25.0 1.0 NE A:ARG215 4.4 23.6 1.0 HB A:THR49 4.4 30.0 1.0 CG2 A:ILE47 4.5 20.9 1.0 CA A:THR49 4.6 22.3 1.0 CG2 A:THR49 4.6 27.1 1.0 HG2 A:ARG215 4.7 30.4 1.0 CB A:THR49 4.8 25.1 1.0 CG A:ARG215 4.8 25.4 1.0 O A:THR49 4.8 29.7 1.0 HG23 A:ILE47 4.8 25.0 1.0

W.Wang, J.S.Grimley, G.J.Augustine, L.S.Beese, H.W.Hellinga. Determination of Engineered Chloride-Binding Site Structures in Fluorescent Proteins Reveals Principles of Halide Recognition To Be Published.