Atomistry » Bromine » PDB 1e7b-1ih6 » 1em0
Atomistry »
  Bromine »
    PDB 1e7b-1ih6 »
      1em0 »

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

Protein crystallography data

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

Other elements in 1em0:

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

Bromine Binding Sites:

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 1em0

Go back to Bromine Binding Sites List in 1em0
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 1em0

Go back to Bromine Binding Sites List in 1em0
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 1em0

Go back to Bromine Binding Sites List in 1em0
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 1em0

Go back to Bromine Binding Sites List in 1em0
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

Reference:

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
Page generated: Sat Dec 12 02:00:32 2020

Last articles

Zn in 7L0B
Zn in 7KZZ
Zn in 7KZL
Zn in 7L3O
Zn in 7L52
Zn in 7L6T
Zn in 7KZ7
Zn in 7L6R
Zn in 7KKM
Zn in 7KKQ
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy