Bromine in PDB 3wcr: Crystal Structure of Plant Lectin (Ligand-Free Form)

The structure of Crystal Structure of Plant Lectin (Ligand-Free Form), PDB code: 3wcr was solved by M.Nagae, Y.Yamaguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.24 / 2.45
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.856, 68.856, 242.539, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Bromine atom in the Crystal Structure of Plant Lectin (Ligand-Free Form) (pdb code 3wcr). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 19 binding sites of Bromine where determined in the Crystal Structure of Plant Lectin (Ligand-Free Form), PDB code: 3wcr:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Bromine binding site 1 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1002 b:55.4 occ:1.00 OG A:SER248 3.1 16.5 1.0 O A:HOH1124 3.2 15.8 1.0 OG A:SER92 3.3 16.0 1.0 O A:SER92 3.6 14.9 1.0 N A:TRP249 3.7 15.1 1.0 OG A:SER250 3.8 18.5 1.0 CB A:SER248 3.8 15.9 1.0 C A:SER248 3.8 15.5 1.0 CA A:TRP249 3.9 15.2 1.0 CA A:PHE93 3.9 15.2 1.0 C A:SER92 3.9 15.1 1.0 N A:SER250 3.9 15.9 1.0 O A:SER248 4.0 15.4 1.0 C A:TRP249 4.0 15.4 1.0 N A:PHE93 4.1 15.2 1.0 CB A:SER92 4.3 14.9 1.0 CB A:SER250 4.3 17.1 1.0 C A:PHE93 4.4 15.7 1.0 CA A:SER248 4.5 16.3 1.0 N A:THR94 4.5 15.8 1.0 NE2 A:GLN30 4.7 44.4 1.0 O A:TRP249 4.7 15.8 1.0 CA A:SER92 4.8 14.8 1.0 CA A:SER250 4.8 16.6 1.0 OG1 A:THR94 5.0 15.9 1.0

Bromine binding site 2 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1003 b:41.1 occ:1.00 CD A:LYS180 3.7 28.4 1.0 CE2 A:PHE178 3.9 20.0 1.0 CD A:PRO105 3.9 22.7 1.0 CB A:LYS180 4.1 25.0 1.0 CB A:VAL99 4.1 20.7 1.0 CG1 A:VAL99 4.3 19.9 1.0 CG A:LYS180 4.3 25.6 1.0 CG2 A:VAL99 4.3 20.1 1.0 O A:SER103 4.4 30.2 1.0 CG A:PRO105 4.6 23.1 1.0 N A:PRO105 4.7 23.1 1.0 CD2 A:PHE178 4.7 20.1 1.0 CZ A:PHE178 4.8 19.6 1.0 CE A:LYS180 4.8 29.4 1.0 CA A:GLY104 4.8 25.2 1.0 N A:LYS180 5.0 23.7 1.0

Bromine binding site 3 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1004 b:76.2 occ:1.00 CD A:PRO62 3.6 28.4 1.0 CD A:PRO100 3.7 22.9 1.0 N A:PRO100 3.8 22.9 1.0 CG A:PRO62 3.8 27.4 1.0 CB A:ASP98 3.9 20.4 1.0 O A:ASP98 3.9 21.5 1.0 C A:ASP98 3.9 21.1 1.0 C A:VAL99 4.0 21.9 1.0 N A:VAL99 4.1 21.1 1.0 CG A:ASP98 4.1 21.6 1.0 CG2 A:THR243 4.2 17.1 1.0 CA A:PRO100 4.3 23.8 1.0 CA A:VAL99 4.3 21.1 1.0 OD2 A:ASP98 4.4 22.1 1.0 CB A:PRO100 4.4 23.4 1.0 CG A:PRO100 4.5 22.9 1.0 OD1 A:ASP98 4.5 20.9 1.0 O A:VAL99 4.5 24.1 1.0 CA A:ASP98 4.5 20.5 1.0 O A:GLY60 4.7 39.8 1.0 CB A:PRO62 4.9 27.1 1.0 N A:PRO62 4.9 28.7 1.0 OG1 A:THR243 4.9 17.4 1.0

Bromine binding site 4 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1005 b:78.5 occ:1.00 OG1 A:THR173 3.1 19.5 1.0 N A:THR175 3.5 19.8 1.0 C A:THR174 3.6 20.1 1.0 CB A:THR173 3.8 19.8 1.0 OG1 A:THR175 3.8 20.6 1.0 CA A:THR174 3.9 20.1 1.0 N A:THR174 3.9 19.9 1.0 C A:THR173 4.0 20.1 1.0 CB A:HIS160 4.1 24.1 1.0 CA A:THR175 4.1 19.7 1.0 O A:THR174 4.2 20.8 1.0 CE A:LYS157 4.2 51.6 1.0 O A:THR173 4.3 20.5 1.0 CA A:THR173 4.6 19.9 1.0 CB A:THR175 4.6 20.1 1.0 NZ A:LYS157 4.7 50.1 1.0 CG A:HIS160 4.7 24.4 1.0 CG A:LYS157 4.8 49.2 1.0 CD A:PRO158 4.8 34.2 1.0 CG2 A:THR173 5.0 19.1 1.0

Bromine binding site 5 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1006 b:57.8 occ:1.00 N A:GLY125 3.3 21.9 1.0 CA A:GLY124 3.7 23.0 1.0 CG1 A:ILE236 3.7 37.5 1.0 C A:GLY124 4.0 22.7 1.0 CA A:GLY125 4.2 21.7 1.0 CB A:ILE236 4.5 35.3 1.0 OH A:TYR133 4.7 25.3 1.0 O A:LYS123 4.8 25.5 1.0 OD1 A:ASP107 4.8 27.9 1.0 N A:GLY124 4.8 24.6 1.0 CD1 A:ILE236 4.9 37.2 1.0 OD2 A:ASP107 5.0 27.9 1.0

Bromine binding site 6 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1007 b:58.6 occ:1.00 N A:ILE236 3.4 31.0 1.0 OG1 A:THR237 3.4 43.6 1.0 N A:THR237 3.6 38.2 1.0 CB A:ASN240 3.8 28.9 1.0 CA A:GLY235 3.9 25.6 1.0 C A:GLY235 4.1 27.5 1.0 CG A:ASN240 4.1 29.1 1.0 CA A:ILE236 4.2 34.3 1.0 ND2 A:ASN240 4.3 30.5 1.0 CB A:ILE236 4.3 35.3 1.0 CB A:THR237 4.3 42.6 1.0 CG2 A:THR237 4.4 41.8 1.0 C A:ILE236 4.4 35.9 1.0 CD1 A:LEU149 4.5 38.5 1.0 CB A:ALA106 4.5 21.5 1.0 CA A:THR237 4.5 41.3 1.0 O A:THR237 4.7 41.4 1.0 OD1 A:ASP107 4.7 27.9 1.0 OD1 A:ASN240 4.8 28.3 1.0 O A:ASN240 4.9 26.6 1.0 CG1 A:ILE236 5.0 37.5 1.0

Bromine binding site 7 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1008 b:54.8 occ:1.00 N A:TRP225 3.4 19.6 1.0 CD1 A:TRP225 3.6 17.6 1.0 N A:GLU224 3.8 22.3 1.0 CB A:GLU224 3.9 25.6 1.0 CB A:TRP225 3.9 17.6 1.0 CA A:GLU224 4.1 22.9 1.0 CG A:TRP225 4.1 17.6 1.0 C A:GLU224 4.2 21.1 1.0 CB A:PRO223 4.2 20.9 1.0 CA A:TRP225 4.2 18.6 1.0 O A:TRP225 4.4 18.6 1.0 C A:PRO223 4.5 22.0 1.0 CG A:GLU224 4.8 30.4 1.0 C A:TRP225 4.8 18.4 1.0 NE1 A:TRP225 4.8 17.9 1.0 CA A:PRO223 4.8 21.6 1.0 OE2 A:GLU224 5.0 33.6 1.0

Bromine binding site 8 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1009 b:44.7 occ:1.00 N2 A:NAG1001 3.1 33.2 1.0 N A:GLU34 3.3 26.9 1.0 CG A:GLU34 3.6 36.4 1.0 ND2 A:ASN33 3.6 27.7 1.0 CG A:ASN33 3.7 25.5 1.0 C8 A:NAG1001 3.7 31.6 1.0 CA A:ASN33 3.7 24.8 1.0 C1 A:NAG1001 3.8 32.4 1.0 C7 A:NAG1001 3.8 32.4 1.0 OD1 A:ASN33 3.8 23.8 1.0 CB A:GLU34 3.9 30.9 1.0 CG1 A:VAL45 4.0 19.8 1.0 C2 A:NAG1001 4.0 34.7 1.0 C A:ASN33 4.0 25.6 1.0 CB A:VAL45 4.0 20.0 1.0 CD A:GLU34 4.1 41.4 1.0 CA A:GLU34 4.2 27.1 1.0 OE2 A:GLU34 4.3 44.4 1.0 CB A:ASN33 4.3 24.6 1.0 O A:PHE32 4.7 25.2 1.0 C3 A:NAG1001 4.7 36.0 1.0 OE1 A:GLU34 4.7 41.7 1.0 O A:VAL45 4.7 20.9 1.0 CG2 A:VAL45 4.7 20.0 1.0 O A:HOH1116 4.8 15.4 1.0 N A:ASN33 4.9 23.9 1.0 O7 A:NAG1001 4.9 33.8 1.0

Bromine binding site 9 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1010 b:74.4 occ:1.00 N A:GLN77 3.2 18.9 1.0 O A:HOH1107 3.3 20.5 1.0 OG1 A:THR25 3.6 25.7 1.0 CB A:GLN77 3.8 19.9 1.0 CZ3 A:TRP225 3.9 17.6 1.0 CA A:ILE76 4.0 17.3 1.0 CA A:GLN77 4.1 20.2 1.0 C A:ILE76 4.1 17.8 1.0 CB A:SER23 4.1 28.6 1.0 CH2 A:TRP225 4.2 17.9 1.0 O A:PRO75 4.4 17.0 1.0 OG A:SER23 4.5 31.8 1.0 CG2 A:ILE76 4.6 18.0 1.0 O A:GLN77 4.6 22.5 1.0 CB A:THR25 4.7 25.6 1.0 CE3 A:TRP225 4.7 17.5 1.0 C A:GLN77 4.9 21.4 1.0 CB A:ILE76 4.9 17.5 1.0 O A:GLN24 4.9 24.3 1.0

Bromine binding site 10 out of 19 in the Crystal Structure of Plant Lectin (Ligand-Free Form)


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 Plant Lectin (Ligand-Free Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Br1002 b:25.8 occ:1.00 CA B:ARG41 3.7 17.3 1.0 CD B:ARG41 3.8 18.2 1.0 N B:ARG41 3.9 17.0 1.0 NE B:ARG41 4.5 18.1 1.0 CB B:ARG41 4.5 17.5 1.0 C B:ARG41 4.5 17.7 1.0 O B:ARG41 4.6 17.7 1.0 CG B:ARG41 4.6 18.7 1.0

M.Nagae, K.Soga, K.Morita-Matsumoto, S.Hanashima, A.Ikeda, K.Yamamoto, Y.Yamaguchi. Phytohemagglutinin From Phaseolus Vulgaris (Pha-E) Displays A Novel Glycan Recognition Mode Using A Common Legume Lectin Fold Glycobiology V. 24 368 2014.
ISSN: ISSN 0959-6658
PubMed: 24436051
DOI: 10.1093/GLYCOB/CWU004