Bromine in PDB 4ilz: Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata

The structure of Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata, PDB code: 4ilz was solved by V.S.De Serrano, J.Zhao, J.Zhao, S.Franzen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.00 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.589, 67.184, 68.910, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 28.5

The structure of Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Bromine atom in the Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata (pdb code 4ilz). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 3 binding sites of Bromine where determined in the Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata, PDB code: 4ilz:
Jump to Bromine binding site number: 1; 2; 3;

Bromine binding site 1 out of 3 in the Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Br211 b:6.3 occ:0.06 BR2 A:TBP211 0.0 6.3 0.1 C2 A:TBP211 1.9 6.2 0.1 CE A:MET63 2.7 2.0 1.0 CG1 A:VAL59 2.8 5.0 1.0 C3 A:TBP211 2.8 6.2 0.1 C1 A:TBP211 2.8 6.3 0.1 O1 A:TBP211 3.1 6.3 0.1 C3B A:HEM201 3.4 8.3 1.0 CD2 A:LEU100 3.5 5.5 0.7 CAB A:HEM201 3.6 8.2 1.0 C2B A:HEM201 3.6 8.3 1.0 O A:VAL59 3.8 4.4 1.0 CMB A:HEM201 4.0 8.1 1.0 CD1 A:LEU100 4.0 5.6 0.3 CB A:MET63 4.0 2.0 1.0 C4B A:HEM201 4.0 8.4 1.0 C A:VAL59 4.0 4.3 1.0 CBB A:HEM201 4.1 8.2 1.0 C6 A:TBP211 4.1 6.3 0.1 C4 A:TBP211 4.1 6.3 0.1 CE1 A:PHE60 4.2 4.0 1.0 CB A:VAL59 4.2 4.9 1.0 CD1 A:PHE60 4.2 3.8 1.0 SD A:MET63 4.3 2.0 1.0 C1B A:HEM201 4.3 8.5 1.0 CZ A:PHE60 4.4 3.9 1.0 N A:PHE60 4.5 3.9 1.0 NB A:HEM201 4.5 8.4 1.0 CG A:PHE60 4.5 3.7 1.0 CG A:MET63 4.5 2.0 1.0 CA A:PHE60 4.6 3.5 1.0 CE2 A:PHE60 4.6 3.9 1.0 CA A:VAL59 4.6 4.8 1.0 CG A:LEU100 4.7 5.5 0.7 CHC A:HEM201 4.7 8.3 1.0 C5 A:TBP211 4.7 6.3 0.1 CD2 A:PHE60 4.7 3.9 1.0 O2 A:OXY212 5.0 12.3 0.7 CD1 A:LEU100 5.0 5.4 0.7

Bromine binding site 2 out of 3 in the Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Br211 b:6.3 occ:0.10 BR4 A:TBP211 0.0 6.3 0.1 C4 A:TBP211 1.9 6.3 0.1 CD1 A:LEU100 2.0 5.4 0.7 C3 A:TBP211 2.8 6.2 0.1 C5 A:TBP211 2.9 6.3 0.1 O A:ILE20 3.3 5.2 1.0 CG2 A:ILE20 3.3 5.7 1.0 CG A:LEU100 3.4 5.5 0.7 CB A:PHE24 3.5 5.3 1.0 CG A:LEU100 3.6 5.5 0.3 CZ A:PHE60 3.6 3.9 1.0 CD2 A:LEU100 3.6 5.5 0.3 C A:ILE20 3.6 5.4 1.0 N A:PHE21 3.9 5.2 1.0 CA A:PHE21 4.0 5.1 1.0 O A:LEU100 4.0 5.4 0.7 CG A:PHE24 4.1 5.3 1.0 C2 A:TBP211 4.1 6.2 0.1 O A:LEU100 4.1 5.4 0.3 C6 A:TBP211 4.2 6.3 0.1 CB A:ILE20 4.2 5.5 1.0 CD2 A:LEU100 4.2 5.5 0.7 CE1 A:PHE60 4.3 4.0 1.0 CD1 A:LEU100 4.4 5.6 0.3 CB A:LEU100 4.4 5.5 0.7 CA A:LEU100 4.5 5.5 0.7 CD2 A:PHE24 4.5 5.2 1.0 CA A:ILE20 4.5 5.5 1.0 CE2 A:PHE60 4.6 3.9 1.0 C A:LEU100 4.6 5.5 0.7 C1 A:TBP211 4.6 6.3 0.1 CB A:LEU100 4.6 5.5 0.3 CA A:PHE24 4.7 5.4 1.0 CA A:LEU100 4.7 5.5 0.3 C A:LEU100 4.8 5.5 0.3 CB A:LEU104 4.8 3.9 1.0 N A:PHE24 4.8 5.2 1.0 CD1 A:PHE24 4.8 5.2 1.0 C A:PHE21 4.9 5.2 1.0 O A:PHE21 4.9 5.2 1.0 CB A:PHE21 5.0 5.2 1.0

Bromine binding site 3 out of 3 in the Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Structural and Kinetic Study of An Internal Substrate Binding Site of Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata within 5.0Å range: probe atom residue distance (Å) B Occ A:Br211 b:6.3 occ:0.10 BR6 A:TBP211 0.0 6.3 0.1 C6 A:TBP211 1.9 6.3 0.1 C1 A:TBP211 2.8 6.3 0.1 O2 A:OXY212 2.8 12.3 0.7 C5 A:TBP211 2.9 6.3 0.1 O1 A:TBP211 2.9 6.3 0.1 C2C A:HEM201 3.3 8.3 1.0 CE2 A:PHE24 3.4 5.2 1.0 C3C A:HEM201 3.4 8.5 1.0 CZ A:PHE35 3.5 7.8 1.0 C1C A:HEM201 3.6 8.3 1.0 CE1 A:PHE21 3.7 5.3 1.0 O1 A:OXY212 3.7 11.5 0.7 C4C A:HEM201 3.7 8.6 1.0 CBC A:HEM201 3.7 8.6 1.0 NC A:HEM201 3.8 8.5 1.0 CMC A:HEM201 3.9 8.2 1.0 CD2 A:PHE24 4.0 5.2 1.0 CAC A:HEM201 4.1 8.5 1.0 C2 A:TBP211 4.1 6.2 0.1 CD1 A:PHE21 4.1 5.2 1.0 CZ A:PHE24 4.2 5.2 1.0 C4 A:TBP211 4.2 6.3 0.1 CD2 A:LEU100 4.2 5.5 0.7 CE1 A:PHE35 4.2 8.0 1.0 CHC A:HEM201 4.2 8.3 1.0 CD1 A:LEU100 4.2 5.6 0.3 CHD A:HEM201 4.5 8.9 1.0 CE2 A:PHE35 4.5 7.9 1.0 CD1 A:LEU100 4.6 5.4 0.7 C3 A:TBP211 4.6 6.2 0.1 CZ A:PHE21 4.8 5.2 1.0 CG A:LEU100 4.9 5.5 0.7 CG A:LEU100 4.9 5.5 0.3 C4B A:HEM201 5.0 8.4 1.0

J.Zhao, V.De Serrano, J.Zhao, P.Le, S.Franzen. Structural and Kinetic Study of An Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A From Amphitrite Ornata. Biochemistry V. 52 2427 2013.
ISSN: ISSN 0006-2960
PubMed: 23480178
DOI: 10.1021/BI301307F