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

Protein crystallography data

The structure of Engineered Low-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex, PDB code: 3sve 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) 34.78 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.296, 62.212, 69.549, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 17.9

Bromine Binding Sites:

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

Bromine binding site 1 out of 3 in 3sve

Go back to Bromine Binding Sites List in 3sve
Bromine binding site 1 out of 3 in the Engineered Low-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 Low-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br260

b:19.8
occ:0.66
HE22 A:GLN94 2.7 17.7 1.0
HG1 A:THR108 2.7 19.7 1.0
HG2 A:GLN94 2.9 16.2 1.0
HG3 A:ARG96 3.1 15.0 1.0
OG1 A:THR108 3.1 16.5 1.0
HB2 A:ALA110 3.3 16.3 1.0
HB A:THR108 3.3 19.1 1.0
O A:HOH296 3.3 18.3 1.0
HB3 A:GLN94 3.4 13.9 1.0
NE2 A:GLN94 3.5 14.8 1.0
HB3 A:ALA110 3.5 16.3 1.0
O A:HOH281 3.5 14.7 1.0
CG A:GLN94 3.7 13.5 1.0
CB A:THR108 3.7 16.0 1.0
CB A:ALA110 3.8 13.6 1.0
O A:GLN94 3.9 16.2 1.0
H A:ALA110 4.0 17.8 1.0
CB A:GLN94 4.0 11.6 1.0
HG23 A:THR63 4.0 16.1 1.0
HE21 A:GLN94 4.0 17.7 1.0
CG A:ARG96 4.1 12.6 1.0
CD A:GLN94 4.1 15.0 1.0
HA A:GLU95 4.1 17.1 1.0
H A:ARG96 4.1 14.7 1.0
HH11 A:ARG96 4.1 16.4 1.0
C A:GLN94 4.2 14.3 1.0
HB2 A:ARG96 4.2 16.6 1.0
N A:ALA110 4.2 14.9 1.0
HG23 A:ILE123 4.3 19.5 1.0
HA A:THR63 4.3 12.7 1.0
N A:ARG96 4.4 12.3 1.0
HA A:ARG109 4.4 16.8 1.0
HG21 A:THR108 4.4 16.4 1.0
C A:THR108 4.5 15.2 1.0
NH1 A:ARG96 4.5 13.7 1.0
HG3 A:GLN94 4.5 16.2 1.0
O A:THR108 4.5 15.9 1.0
N A:GLU95 4.5 13.1 1.0
HG2 A:ARG96 4.6 15.0 1.0
HB1 A:ALA110 4.6 16.3 1.0
HD2 A:ARG96 4.6 16.7 1.0
CA A:GLU95 4.6 14.3 1.0
C A:GLU95 4.6 13.7 1.0
CB A:ARG96 4.6 13.8 1.0
N A:ARG109 4.7 14.1 1.0
CA A:ALA110 4.7 13.8 1.0
C A:ARG109 4.7 14.5 1.0
CG2 A:THR108 4.7 13.7 1.0
HH12 A:ARG96 4.7 16.4 1.0
CA A:GLN94 4.8 14.4 1.0
CA A:THR108 4.8 13.2 1.0
HB2 A:GLN94 4.8 13.9 1.0
CD A:ARG96 4.8 14.0 1.0
CA A:ARG109 4.8 14.0 1.0
HG12 A:ILE123 4.8 17.6 1.0
CZ A:ARG96 5.0 13.4 1.0
HG21 A:ILE123 5.0 19.5 1.0
CG2 A:THR63 5.0 13.5 1.0

Bromine binding site 2 out of 3 in 3sve

Go back to Bromine Binding Sites List in 3sve
Bromine binding site 2 out of 3 in the Engineered Low-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 Low-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br261

b:22.3
occ:0.50
H A:TRP57 2.5 14.2 1.0
O A:HOH358 3.0 23.2 1.0
O A:HOH313 3.0 21.0 1.0
HA A:PRO56 3.1 14.1 1.0
HD1 A:TYR143 3.1 14.1 1.0
HD3 A:PRO58 3.2 11.9 1.0
HB2 A:TRP57 3.2 13.4 1.0
N A:TRP57 3.3 11.9 1.0
HD2 A:PRO58 3.4 11.9 1.0
O A:HOH396 3.5 28.6 1.0
HB3 A:PRO56 3.6 16.3 1.0
CD A:PRO58 3.8 10.0 1.0
CA A:PRO56 3.8 11.8 1.0
CD1 A:TRP57 3.8 12.2 1.0
CB A:TRP57 4.0 11.2 1.0
CD1 A:TYR143 4.0 11.8 1.0
C A:PRO56 4.0 11.7 1.0
CB A:PRO56 4.2 13.6 1.0
CA A:TRP57 4.2 10.6 1.0
HE1 A:TYR143 4.3 17.0 1.0
CG A:TRP57 4.3 11.2 1.0
O A:HOH371 4.3 33.5 1.0
O A:HOH269 4.3 17.1 1.0
HB2 A:TYR143 4.3 15.3 1.0
HD1 A:HIS139 4.4 27.6 1.0
CE1 A:TYR143 4.5 14.2 1.0
HZ2 A:LYS209 4.6 18.8 1.0
HB2 A:PRO56 4.7 16.3 1.0
HG2 A:PRO58 4.7 14.3 1.0
HB3 A:TRP57 4.8 13.4 1.0
CG A:PRO58 4.8 12.0 1.0
N A:PRO58 4.8 11.2 1.0
HA A:TYR143 4.9 14.3 1.0
CG A:TYR143 5.0 12.6 1.0
O A:HOH459 5.0 32.8 1.0
HA A:TRP57 5.0 12.7 1.0

Bromine binding site 3 out of 3 in 3sve

Go back to Bromine Binding Sites List in 3sve
Bromine binding site 3 out of 3 in the Engineered Low-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 Low-Affinity Halide-Binding Protein Derived From Yfp: Bromide Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br262

b:24.6
occ:0.31
H A:LEU207 2.2 14.8 1.0
HA A:ASN144 2.7 14.7 1.0
O A:HOH449 2.7 36.1 1.0
HA A:ALA206 2.8 14.4 1.0
O A:HOH363 2.9 28.1 1.0
N A:LEU207 3.0 12.3 1.0
O A:HOH65 3.2 27.4 1.0
H A:TYR145 3.2 15.8 1.0
HG A:LEU207 3.3 17.3 1.0
HB2 A:LEU207 3.4 14.7 1.0
CA A:ASN144 3.6 12.2 1.0
HB2 A:ASN144 3.6 16.0 1.0
CA A:ALA206 3.7 12.1 1.0
N A:TYR145 3.7 13.2 1.0
O A:LEU207 3.8 15.8 1.0
C A:ALA206 3.8 12.2 1.0
CB A:LEU207 3.9 12.3 1.0
CB A:ASN144 3.9 13.4 1.0
CA A:LEU207 3.9 12.6 1.0
HB3 A:ASN144 4.0 16.0 1.0
C A:ASN144 4.0 11.7 1.0
CG A:LEU207 4.1 14.5 1.0
O A:HOH337 4.1 31.4 1.0
HB1 A:ALA206 4.1 16.4 1.0
HB2 A:TYR145 4.2 13.8 1.0
O A:SER205 4.2 17.1 1.0
O A:HOH391 4.2 35.3 1.0
O A:HOH381 4.3 42.5 1.0
C A:LEU207 4.3 13.9 1.0
CB A:ALA206 4.4 13.7 1.0
O A:TYR143 4.4 14.7 1.0
HB3 A:TYR145 4.5 13.8 1.0
HD12 A:LEU207 4.6 16.6 1.0
N A:ASN144 4.7 12.8 1.0
CB A:TYR145 4.7 11.6 1.0
CA A:TYR145 4.7 10.6 1.0
HB2 A:ALA206 4.7 16.4 1.0
O A:TYR145 4.7 17.2 1.0
N A:ALA206 4.7 13.0 1.0
HD23 A:LEU207 4.7 18.9 1.0
HA A:LEU207 4.8 15.0 1.0
HB3 A:LEU207 4.8 14.7 1.0
C A:SER205 4.9 14.7 1.0
CD1 A:LEU207 5.0 13.9 1.0
C A:TYR143 5.0 12.9 1.0

Reference:

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.
Page generated: Sat Dec 12 02:15:42 2020

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