Bromine in PDB 2dgl: Crystal Structure of Escherichia Coli Gadb in Complex with Bromide

All present enzymatic activity of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide:
4.1.1.15;

The structure of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide, PDB code: 2dgl was solved by M.G.Gruetter, G.Capitani, H.Gut, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 3.15
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	297.051, 297.051, 233.731, 90.00, 90.00, 120.00
R / Rfree (%)	21.8 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide (pdb code 2dgl). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 24 binding sites of Bromine where determined in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide, PDB code: 2dgl:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br467 b:66.3 occ:0.99 OG A:SER16 3.1 31.8 1.0 CB A:SER16 3.5 27.7 1.0 CD F:ARG427 3.6 22.0 1.0 NH1 F:ARG427 3.7 26.0 1.0 CG2 F:VAL342 4.0 18.6 1.0 CZ3 F:TRP67 4.5 10.4 1.0 CG1 F:VAL342 4.5 15.6 1.0 NE F:ARG427 4.6 24.3 1.0 CG F:ARG427 4.6 19.6 1.0 CZ F:ARG427 4.6 24.7 1.0 N A:PHE18 4.6 21.7 1.0 CD1 F:LEU334 4.6 7.7 1.0 CB A:PHE18 4.6 18.3 1.0 N A:ARG17 4.7 26.5 1.0 CD2 A:PHE18 4.8 15.9 1.0 CA A:SER16 4.9 27.3 1.0 CB F:VAL342 4.9 17.5 1.0

Bromine binding site 2 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br468 b:75.0 occ:0.96 CB A:ARG17 3.6 24.3 1.0 NE A:ARG17 3.6 21.9 1.0 N A:ARG17 3.7 26.5 1.0 CB F:ASP69 4.1 28.4 1.0 NH2 A:ARG17 4.1 22.3 1.0 CA A:ARG17 4.3 24.0 1.0 CH2 F:TRP67 4.3 8.3 1.0 CZ A:ARG17 4.3 21.5 1.0 C A:SER16 4.4 26.9 1.0 OD2 F:ASP69 4.5 30.3 1.0 CA A:SER16 4.5 27.3 1.0 CD A:ARG17 4.5 22.3 1.0 CB A:SER16 4.6 27.7 1.0 CG A:ARG17 4.7 23.6 1.0 CG F:ASP69 4.8 30.8 1.0 OD2 A:ASP40 4.9 35.9 1.0 NH2 F:ARG333 4.9 25.2 1.0

Bromine binding site 3 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br469 b:67.4 occ:0.96 NE2 A:HIS73 3.4 25.7 1.0 ND2 B:ASN81 3.5 32.3 1.0 N A:ASP68 3.6 20.4 1.0 CA A:TRP67 3.8 19.5 1.0 CD1 A:TRP67 3.9 20.6 1.0 CE1 A:HIS73 4.0 26.6 1.0 O A:ASP68 4.1 23.0 1.0 C A:TRP67 4.2 19.4 1.0 CG A:TRP67 4.3 19.4 1.0 O A:THR66 4.4 20.9 1.0 NE1 A:TRP67 4.5 19.4 1.0 OD2 A:ASP68 4.5 26.1 1.0 CB A:TRP67 4.6 19.2 1.0 CA A:ASP68 4.6 22.5 1.0 CD2 A:HIS73 4.6 27.1 1.0 CG B:ASN81 4.7 28.4 1.0 CB A:ASP68 4.7 23.9 1.0 O A:HOH570 4.7 28.8 1.0 N A:TRP67 4.8 18.6 1.0 CG2 B:ILE80 4.8 26.5 1.0 C A:ASP68 4.9 23.5 1.0 C A:THR66 4.9 18.8 1.0 OD1 B:ASN81 4.9 26.0 1.0

Bromine binding site 4 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ A:Br470 b:98.4 occ:1.00 CD1 A:ILE418 3.5 52.1 1.0 N A:GLY185 3.8 48.0 1.0 NZ A:LYS381 4.0 51.9 1.0 CA A:PRO184 4.1 47.6 1.0 OE2 A:GLU364 4.3 57.5 1.0 CD1 A:LEU187 4.3 47.7 1.0 CE A:LYS381 4.4 51.1 1.0 CD2 A:LEU187 4.5 47.6 1.0 C A:PRO184 4.5 47.8 1.0 CG A:LEU187 4.5 47.4 1.0 CA A:GLY185 4.8 49.1 1.0 CB A:PRO184 4.8 47.9 1.0 CG1 A:ILE418 5.0 51.5 1.0 CD A:LYS381 5.0 50.5 1.0 CD1 A:ILE366 5.0 35.7 1.0

Bromine binding site 5 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br467 b:69.5 occ:1.00 OG B:SER16 3.1 44.2 1.0 CB B:SER16 3.4 41.2 1.0 NH1 C:ARG427 3.5 27.2 1.0 CD C:ARG427 3.6 27.6 1.0 CZ3 C:TRP67 4.3 28.7 1.0 CZ C:ARG427 4.4 26.7 1.0 NE C:ARG427 4.4 27.4 1.0 CG2 C:VAL342 4.6 24.4 1.0 CG C:ARG427 4.6 25.7 1.0 CG1 C:VAL342 4.7 23.2 1.0 N B:PHE18 4.8 39.2 1.0 CA B:SER16 4.8 40.7 1.0 CD1 C:LEU334 4.8 23.7 1.0 CD2 C:LEU334 4.8 23.6 1.0 N B:ARG17 4.8 42.0 1.0 CD2 B:PHE18 4.9 40.2 1.0 CB B:PHE18 4.9 39.5 1.0 OE1 C:GLU330 4.9 35.5 1.0 CH2 C:TRP67 5.0 27.2 1.0

Bromine binding site 6 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br468 b:78.0 occ:0.94 N B:ARG17 3.3 42.0 1.0 CB B:ARG17 3.3 39.3 1.0 NE B:ARG17 3.7 38.6 1.0 CA B:ARG17 3.9 39.5 1.0 CB C:ASP69 4.3 31.5 1.0 C B:SER16 4.3 42.0 1.0 CA B:SER16 4.3 40.7 1.0 NH2 B:ARG17 4.4 44.8 1.0 CB B:SER16 4.4 41.2 1.0 CH2 C:TRP67 4.4 27.2 1.0 CZ B:ARG17 4.4 41.9 1.0 CG B:ARG17 4.5 37.8 1.0 CD B:ARG17 4.5 38.5 1.0 OD2 C:ASP69 5.0 35.2 1.0

Bromine binding site 7 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br469 b:56.1 occ:1.00 OG C:SER16 2.5 21.3 1.0 CD B:ARG427 3.3 16.7 1.0 NH1 B:ARG427 3.4 11.9 1.0 CB C:SER16 3.6 23.4 1.0 CZ3 B:TRP67 4.2 16.6 1.0 NE B:ARG427 4.2 14.3 1.0 CZ B:ARG427 4.3 12.0 1.0 CG2 B:VAL342 4.3 17.7 1.0 CG B:ARG427 4.4 18.4 1.0 CG1 B:VAL342 4.6 16.0 1.0 CD2 C:PHE18 4.8 23.1 1.0 CD1 B:LEU334 4.8 5.4 1.0 N C:ARG17 4.8 23.8 1.0 N C:PHE18 4.8 22.2 1.0 CA C:SER16 4.9 23.4 1.0 CH2 B:TRP67 4.9 13.9 1.0 OE1 B:GLU330 5.0 30.3 1.0 CB C:PHE18 5.0 22.2 1.0 CE3 B:TRP67 5.0 17.1 1.0

Bromine binding site 8 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br470 b:65.3 occ:0.90 NE2 B:HIS73 3.3 21.4 1.0 N B:ASP68 3.5 19.8 1.0 ND2 A:ASN81 3.5 34.6 1.0 CA B:TRP67 3.8 18.5 1.0 CE1 B:HIS73 4.0 21.8 1.0 O B:ASP68 4.0 20.0 1.0 CD1 B:TRP67 4.1 19.1 1.0 C B:TRP67 4.1 18.7 1.0 OD2 B:ASP68 4.1 26.4 1.0 CG B:TRP67 4.3 17.1 1.0 CD2 B:HIS73 4.4 21.3 1.0 CA B:ASP68 4.4 20.9 1.0 O B:THR66 4.4 19.9 1.0 CB B:ASP68 4.5 22.0 1.0 CG2 A:ILE80 4.6 26.7 1.0 CB B:TRP67 4.6 16.4 1.0 CG A:ASN81 4.6 33.0 1.0 NE1 B:TRP67 4.6 18.8 1.0 C B:ASP68 4.7 21.4 1.0 N B:TRP67 4.7 19.1 1.0 CG B:ASP68 4.8 24.8 1.0 OD1 A:ASN81 4.9 31.8 1.0 C B:THR66 4.9 19.7 1.0

Bromine binding site 9 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ B:Br471 b:83.5 occ:0.92 NZ B:LYS381 3.3 36.8 1.0 CD1 B:ILE418 3.6 54.8 1.0 N B:GLY185 4.2 48.3 1.0 CE B:LYS381 4.2 36.1 1.0 CD1 B:LEU187 4.3 42.4 1.0 OE2 B:GLU364 4.4 52.8 1.0 CD B:LYS381 4.5 34.7 1.0 CA B:PRO184 4.5 46.7 1.0 CG B:LEU187 4.6 42.8 1.0 CD1 B:ILE366 4.6 28.1 1.0 CD2 B:LEU187 4.7 41.3 1.0 C B:PRO184 4.9 47.5 1.0 CG1 B:ILE366 4.9 25.8 1.0

Bromine binding site 10 out of 24 in the Crystal Structure of Escherichia Coli Gadb in Complex with Bromide


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 10 of Crystal Structure of Escherichia Coli Gadb in Complex with Bromide within 5.0Å range: probe atom residue distance (Å) B Occ C:Br467 b:76.3 occ:0.93 N C:ASP68 3.4 24.5 1.0 NE2 C:HIS73 3.4 25.2 1.0 CA C:TRP67 3.7 22.9 1.0 ND2 D:ASN81 3.7 28.9 1.0 CD1 C:TRP67 3.7 25.3 1.0 O C:ASP68 3.9 27.3 1.0 C C:TRP67 4.0 24.0 1.0 CG C:TRP67 4.0 24.9 1.0 CE1 C:HIS73 4.1 24.7 1.0 OD1 C:ASP68 4.2 29.4 1.0 NE1 C:TRP67 4.3 26.1 1.0 CB C:TRP67 4.4 22.3 1.0 O C:THR66 4.4 23.6 1.0 CA C:ASP68 4.4 25.8 1.0 CD2 C:HIS73 4.5 25.0 1.0 C C:ASP68 4.6 27.2 1.0 CB C:ASP68 4.7 27.3 1.0 N C:TRP67 4.7 22.4 1.0 CD2 C:TRP67 4.7 27.7 1.0 CE2 C:TRP67 4.8 27.6 1.0 CG D:ASN81 4.9 30.3 1.0 CG2 D:ILE80 4.9 24.1 1.0 C C:THR66 4.9 23.1 1.0 CG C:ASP68 5.0 29.2 1.0

H.Gut, E.Pennacchietti, R.A.John, F.Bossa, G.Capitani, D.De Biase, M.G.Gruetter. Escherichia Coli Acid Resistance: pH-Sensing, Activation By Chloride and Autoinhibition in Gadb Embo J. V. 25 2643 2006.
ISSN: ISSN 0261-4189
PubMed: 16675957
DOI: 10.1038/SJ.EMBOJ.7601107