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Nickel 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:

Bromine (Br) 4 atoms
Magnesium (Mg) 2 atoms

Nickel Binding Sites:

The binding sites of Nickel 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 Nickel atom.
In total 2 binding sites of Nickel where determined in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin, PDB code: 1em0:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1em0

Go back to Nickel Binding Sites List in 1em0
Nickel binding site 1 out of 2 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
B:Ni25

b:8.2
occ:1.00
NI B:PNI25 0.0 8.2 1.0
NA B:PNI25 1.9 8.6 1.0
NB B:PNI25 1.9 8.2 1.0
NC B:PNI25 1.9 8.7 1.0
ND B:PNI25 2.0 9.2 1.0
C1D B:PNI25 2.9 9.7 1.0
C1A B:PNI25 3.0 8.6 1.0
C4A B:PNI25 3.0 8.4 1.0
C4D B:PNI25 3.0 9.1 1.0
C4B B:PNI25 3.0 8.8 1.0
C1C B:PNI25 3.0 8.9 1.0
C1B B:PNI25 3.0 8.7 1.0
C4C B:PNI25 3.0 9.7 1.0
C5A B:PNI25 3.3 8.4 1.0
C5D B:PNI25 3.3 9.5 1.0
C5B B:PNI25 3.4 8.2 1.0
C5C B:PNI25 3.4 9.3 1.0
N3 B:CBR7 3.6 9.5 1.0
C4 B:CBR7 3.8 9.0 1.0
C2 B:CBR7 4.0 9.1 1.0
H1 A:DG6 4.1 12.1 1.0
N4 B:CBR7 4.1 8.9 1.0
C5 B:CBR7 4.1 9.8 1.0
C2A B:PNI25 4.1 9.2 1.0
C2C B:PNI25 4.2 9.9 1.0
H41 B:CBR7 4.2 11.6 1.0
C3A B:PNI25 4.2 9.9 1.0
C2D B:PNI25 4.2 10.7 1.0
C3D B:PNI25 4.2 9.8 1.0
C2B B:PNI25 4.2 9.1 1.0
C3C B:PNI25 4.3 10.8 1.0
C3B B:PNI25 4.3 9.7 1.0
N1 A:DG6 4.3 9.3 1.0
H22 A:DG6 4.4 12.3 1.0
H42 B:CBR7 4.5 11.6 1.0
C6 B:CBR7 4.5 9.4 1.0
O2 B:CBR7 4.6 9.5 1.0
N1 B:CBR7 4.6 8.6 1.0
C2 A:DG6 4.7 8.8 1.0
N2 A:DG6 4.7 9.5 1.0
C6D B:PNI25 4.8 10.7 1.0
C6 A:DG6 4.8 9.4 1.0
C6B B:PNI25 4.8 8.5 1.0
C6A B:PNI25 4.9 8.0 1.0
C6C B:PNI25 4.9 10.0 1.0
O6 A:DG6 5.0 10.0 1.0
H2A B:PNI25 5.0 12.0 1.0
H2C B:PNI25 5.0 12.9 1.0

Nickel binding site 2 out of 2 in 1em0

Go back to Nickel Binding Sites List in 1em0
Nickel binding site 2 out of 2 in the Complex of D(Cctagg) with Tetra-[N-Methyl-Pyridyl] Porphyrin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni 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
D:Ni26

b:8.2
occ:1.00
NI D:PNI26 0.0 8.2 1.0
ND D:PNI26 1.9 8.9 1.0
NB D:PNI26 1.9 8.3 1.0
NA D:PNI26 1.9 7.8 1.0
NC D:PNI26 2.0 9.6 1.0
C4D D:PNI26 2.9 8.9 1.0
C4B D:PNI26 2.9 8.7 1.0
C4C D:PNI26 3.0 9.4 1.0
C1C D:PNI26 3.0 9.7 1.0
C1A D:PNI26 3.0 9.1 1.0
C1B D:PNI26 3.0 9.1 1.0
C4A D:PNI26 3.0 8.8 1.0
C1D D:PNI26 3.0 9.5 1.0
C5B D:PNI26 3.3 9.2 1.0
C5A D:PNI26 3.4 8.8 1.0
C5D D:PNI26 3.4 8.1 1.0
C5C D:PNI26 3.4 9.3 1.0
N3 D:CBR19 3.6 9.5 1.0
C4 D:CBR19 3.7 9.2 1.0
C2 D:CBR19 4.0 8.9 1.0
H1 C:DG18 4.1 12.2 1.0
N4 D:CBR19 4.1 9.0 1.0
C3B D:PNI26 4.1 9.1 1.0
H41 D:CBR19 4.1 11.8 1.0
C2B D:PNI26 4.2 9.3 1.0
C3D D:PNI26 4.2 9.5 1.0
C5 D:CBR19 4.2 9.7 1.0
C3A D:PNI26 4.2 9.2 1.0
C2C D:PNI26 4.2 10.1 1.0
C2D D:PNI26 4.2 10.4 1.0
C2A D:PNI26 4.2 9.5 1.0
C3C D:PNI26 4.3 10.7 1.0
N1 C:DG18 4.3 9.4 1.0
H22 C:DG18 4.4 12.0 1.0
H42 D:CBR19 4.5 11.8 1.0
C6 D:CBR19 4.5 8.4 1.0
O2 D:CBR19 4.5 9.2 1.0
N1 D:CBR19 4.6 9.2 1.0
C2 C:DG18 4.6 9.4 1.0
N2 C:DG18 4.7 9.2 1.0
C6B D:PNI26 4.8 10.1 1.0
C6 C:DG18 4.8 9.7 1.0
C6A D:PNI26 4.9 7.8 1.0
C6D D:PNI26 4.9 8.5 1.0
C6C D:PNI26 4.9 9.8 1.0
H3B D:PNI26 5.0 11.8 1.0
O6 C:DG18 5.0 10.7 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: Wed Dec 16 01:11:47 2020

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