Bromine in PDB 1em0: Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin

The structure of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin, PDB code: 1em0 was solved by S.Neidle, M.Sanderson, M.Bennett, A.Krah, F.Wien, E.Garman, R.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 0.90
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	32.210, 32.210, 62.257, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 17.2

The structure of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin also contains other interesting chemical elements:

Nickel	(Ni)	2 atoms
Magnesium	(Mg)	2 atoms

The binding sites of Bromine atom in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin (pdb code 1em0). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 4 binding sites of Bromine where determined in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin, PDB code: 1em0:
Jump to Bromine binding site number: 1; 2; 3; 4;

Bromine binding site 1 out of 4 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Br1 b:9.4 occ:1.00 BR A:CBR1 0.0 9.4 1.0 C5 A:CBR1 1.9 8.7 1.0 H42 A:CBR1 2.7 11.5 1.0 C6 A:CBR1 2.8 8.6 1.0 H6 A:CBR1 2.9 11.2 1.0 C4 A:CBR1 2.9 7.6 1.0 N4 A:CBR1 3.2 8.8 1.0 N9 D:DG24 3.6 7.7 1.0 C8 D:DG24 3.6 8.2 1.0 H2'' D:DG24 3.7 10.3 1.0 O A:HOH506 3.8 10.7 1.0 H2' D:DG24 3.8 10.3 1.0 C4 D:DG24 3.8 7.5 1.0 H42 A:DC2 3.9 11.1 1.0 N7 D:DG24 3.9 8.2 1.0 H8 D:DG24 4.0 10.6 1.0 H41 A:CBR1 4.0 11.5 1.0 C5 D:DG24 4.0 7.5 1.0 O A:HOH518 4.0 10.8 1.0 O A:HOH530 4.1 13.0 1.0 C2' D:DG24 4.1 8.0 1.0 N1 A:CBR1 4.1 8.3 1.0 N3 A:CBR1 4.1 8.0 1.0 N4 A:DC2 4.3 8.5 1.0 C1' D:DG24 4.3 7.4 1.0 O D:HOH512 4.3 9.8 1.0 H41 A:DC2 4.3 11.1 1.0 N3 D:DG24 4.4 7.1 1.0 H1' D:DG24 4.4 9.6 1.0 C2 A:CBR1 4.7 9.0 1.0 O D:HOH516 4.8 11.7 1.0 H2' A:CBR1 4.9 12.4 1.0 C6 D:DG24 4.9 7.5 1.0 O6 B:DG11 4.9 8.2 1.0 H5'' A:CBR1 4.9 10.9 1.0

Bromine binding site 2 out of 4 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Br7 b:9.8 occ:1.00 BR B:CBR7 0.0 9.8 1.0 C5 B:CBR7 1.9 9.8 1.0 H42 B:CBR7 2.7 11.6 1.0 C6 B:CBR7 2.8 9.4 1.0 C4 B:CBR7 2.9 9.0 1.0 H6 B:CBR7 2.9 12.2 1.0 N4 B:CBR7 3.1 8.9 1.0 C3B B:PNI25 3.3 9.7 1.0 H7B B:PNI25 3.4 12.7 1.0 C4B B:PNI25 3.4 8.8 1.0 H3B B:PNI25 3.5 12.6 1.0 C2B B:PNI25 3.7 9.1 1.0 C5B B:PNI25 3.7 8.2 1.0 C7B B:PNI25 3.8 9.8 1.0 NB B:PNI25 3.9 8.2 1.0 C6B B:PNI25 3.9 8.5 1.0 H41 B:CBR7 4.0 11.6 1.0 C1B B:PNI25 4.0 8.7 1.0 H2B B:PNI25 4.1 11.8 1.0 N1 B:CBR7 4.1 8.6 1.0 N3 B:CBR7 4.2 9.5 1.0 C1C B:PNI25 4.3 8.9 1.0 O5' B:CBR7 4.4 14.0 1.0 HO5' B:CBR7 4.6 18.1 1.0 C8B B:PNI25 4.6 10.1 1.0 C2 B:CBR7 4.6 9.1 1.0 NC B:PNI25 4.8 8.7 1.0 C0B B:PNI25 4.8 8.8 1.0 H2' B:CBR7 4.9 16.6 1.0 H8B B:PNI25 5.0 13.2 1.0 C5A B:PNI25 5.0 8.4 1.0

Bromine binding site 3 out of 4 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ C:Br13 b:9.3 occ:1.00 BR C:CBR13 0.0 9.3 1.0 C5 C:CBR13 1.9 8.7 1.0 H42 C:CBR13 2.7 11.4 1.0 C6 C:CBR13 2.8 8.7 1.0 H6 C:CBR13 2.8 11.3 1.0 C4 C:CBR13 2.9 7.5 1.0 N4 C:CBR13 3.1 8.8 1.0 N9 B:DG12 3.6 7.3 1.0 C8 B:DG12 3.6 8.1 1.0 H2'' B:DG12 3.7 10.4 1.0 O C:HOH509 3.8 10.4 1.0 C4 B:DG12 3.8 7.5 1.0 H2' B:DG12 3.8 10.4 1.0 N7 B:DG12 3.9 8.1 1.0 H42 C:DC14 3.9 10.9 1.0 H8 B:DG12 3.9 10.5 1.0 H41 C:CBR13 4.0 11.4 1.0 C5 B:DG12 4.0 7.5 1.0 O C:HOH531 4.0 12.9 1.0 O C:HOH542 4.0 10.5 1.0 C2' B:DG12 4.1 8.0 1.0 N3 C:CBR13 4.1 7.8 1.0 N1 C:CBR13 4.1 8.5 1.0 N4 C:DC14 4.3 8.4 1.0 C1' B:DG12 4.3 7.7 1.0 O B:HOH508 4.3 9.4 1.0 H41 C:DC14 4.3 10.9 1.0 N3 B:DG12 4.4 7.3 1.0 H1' B:DG12 4.5 10.1 1.0 C2 C:CBR13 4.6 8.7 1.0 C6 B:DG12 4.9 7.7 1.0 H5'' C:CBR13 4.9 10.8 1.0 O B:HOH515 4.9 11.6 1.0 H2' C:CBR13 4.9 12.6 1.0 O6 D:DG23 4.9 8.0 1.0

Bromine binding site 4 out of 4 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin within 5.0Å range: probe atom residue distance (Å) B Occ D:Br19 b:9.7 occ:1.00 BR D:CBR19 0.0 9.7 1.0 C5 D:CBR19 1.9 9.7 1.0 H42 D:CBR19 2.7 11.8 1.0 C6 D:CBR19 2.8 8.4 1.0 C4 D:CBR19 2.8 9.2 1.0 H6 D:CBR19 2.9 11.0 1.0 N4 D:CBR19 3.1 9.0 1.0 C2A D:PNI26 3.3 9.5 1.0 H7D D:PNI26 3.4 12.6 1.0 C1A D:PNI26 3.5 9.1 1.0 H2A D:PNI26 3.5 12.4 1.0 O D:HOH503 3.7 8.4 1.0 C3A D:PNI26 3.7 9.2 1.0 C5D D:PNI26 3.7 8.1 1.0 C7D D:PNI26 3.8 9.7 1.0 NA D:PNI26 3.9 7.8 1.0 C6D D:PNI26 4.0 8.5 1.0 H41 D:CBR19 4.0 11.8 1.0 C4A D:PNI26 4.0 8.8 1.0 H3A D:PNI26 4.1 11.9 1.0 N1 D:CBR19 4.1 9.2 1.0 N3 D:CBR19 4.1 9.5 1.0 C4D D:PNI26 4.3 8.9 1.0 O5' D:CBR19 4.5 14.7 1.0 HO5' D:CBR19 4.6 19.1 1.0 C8D D:PNI26 4.6 10.3 1.0 C2 D:CBR19 4.7 8.9 1.0 ND D:PNI26 4.7 8.9 1.0 H2' D:CBR19 4.8 15.9 1.0 C0D D:PNI26 4.8 9.6 1.0 H8D D:PNI26 4.9 13.4 1.0 C5A D:PNI26 5.0 8.8 1.0

M.Bennett, A.Krah, F.Wien, E.Garman, R.Mckenna, M.Sanderson, S.Neidle. A Dna-Porphyrin Minor-Groove Complex at Atomic Resolution: the Structural Consequences of Porphyrin Ruffling. Proc.Natl.Acad.Sci.Usa V. 97 9476 2000.
ISSN: ISSN 0027-8424
PubMed: 10920199
DOI: 10.1073/PNAS.160271897