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Nickel in PDB 3nf3: Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide

Protein crystallography data

The structure of Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide, PDB code: 3nf3 was solved by J.E.Zuniga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.02 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 56.100, 189.600, 41.510, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 23.1

Other elements in 3nf3:

The structure of Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide (pdb code 3nf3). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide, PDB code: 3nf3:

Nickel binding site 1 out of 1 in 3nf3

Go back to Nickel Binding Sites List in 3nf3
Nickel binding site 1 out of 1 in the Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Bont/A Lc with Jth-Nb-7239 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni700

b:40.9
occ:1.00
NE2 A:HIS269 2.3 30.3 1.0
O A:HOH505 2.4 47.4 1.0
O A:HOH502 2.4 40.9 1.0
NZ A:LYS272 2.4 37.2 1.0
O A:HOH459 2.4 46.7 1.0
O A:HOH503 2.6 38.8 1.0
O A:HOH504 2.7 66.5 1.0
CD2 A:HIS269 3.2 31.7 1.0
CE1 A:HIS269 3.3 29.0 1.0
O A:HOH506 3.7 53.0 1.0
CE A:LYS272 3.8 46.6 1.0
CD A:LYS272 4.2 52.7 1.0
CG A:HIS269 4.4 37.9 1.0
ND1 A:HIS269 4.4 37.7 1.0

Reference:

J.E.Zuniga, J.T.Hammill, O.Drory, J.E.Nuss, J.C.Burnett, R.Gussio, P.Wipf, S.Bavari, A.T.Brunger. Iterative Structure-Based Peptide-Like Inhibitor Design Against the Botulinum Neurotoxin Serotype A. Plos One V. 5 E1137 2010.
ISSN: ESSN 1932-6203
PubMed: 20614028
DOI: 10.1371/JOURNAL.PONE.0011378
Page generated: Thu Oct 29 06:21:16 2020
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