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Nickel in PDB 3k6l: The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827

Enzymatic activity of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827

All present enzymatic activity of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827:
3.5.1.88;

Protein crystallography data

The structure of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827, PDB code: 3k6l was solved by R.K.Y.Cheng, L.Crawley, M.Wood, J.Barker, B.Felicetti, M.Whittaker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 241.50 / 2.15
Space group P 43 2 2
Cell size a, b, c (Å), α, β, γ (°) 73.960, 73.960, 241.500, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 31.9

Nickel Binding Sites:

The binding sites of Nickel atom in the The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827 (pdb code 3k6l). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827, PDB code: 3k6l:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 3k6l

Go back to Nickel Binding Sites List in 3k6l
Nickel binding site 1 out of 3 in the The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni169

b:21.4
occ:1.00
NE2 A:HIS136 2.1 9.6 1.0
NE2 A:HIS132 2.1 20.1 1.0
O2 A:2BB170 2.2 23.5 1.0
SG A:CYS90 2.2 22.5 1.0
O3 A:2BB170 2.3 25.7 1.0
C7 A:2BB170 2.9 25.0 1.0
N1 A:2BB170 3.0 25.9 1.0
CE1 A:HIS132 3.1 19.5 1.0
CE1 A:HIS136 3.1 13.6 1.0
CD2 A:HIS136 3.1 11.0 1.0
CD2 A:HIS132 3.1 18.9 1.0
NE2 A:GLN50 3.3 20.9 1.0
CB A:CYS90 3.4 24.5 1.0
O A:HOH174 3.8 23.0 1.0
CD A:GLN50 3.9 21.8 1.0
CA A:CYS90 3.9 25.0 1.0
OE1 A:GLN50 4.1 22.0 1.0
ND1 A:HIS132 4.2 19.1 1.0
ND1 A:HIS136 4.2 11.3 1.0
CG A:HIS132 4.2 18.2 1.0
CG A:HIS136 4.2 12.0 1.0
N A:LEU91 4.2 25.9 1.0
OE1 A:GLU133 4.3 21.7 1.0
C6 A:2BB170 4.3 25.1 1.0
C A:CYS90 4.5 25.5 1.0
O A:HOH173 4.7 17.4 1.0
C5 A:2BB170 4.7 23.6 1.0
OE2 A:GLU133 4.8 23.9 1.0
N A:SER92 4.9 26.8 1.0
C4 A:2BB170 4.9 21.1 1.0
CD A:GLU133 4.9 21.7 1.0
CG A:GLN50 5.0 19.5 1.0

Nickel binding site 2 out of 3 in 3k6l

Go back to Nickel Binding Sites List in 3k6l
Nickel binding site 2 out of 3 in the The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni169

b:26.9
occ:1.00
NE2 B:HIS132 2.0 17.9 1.0
NE2 B:HIS136 2.1 16.1 1.0
SG B:CYS90 2.3 26.7 1.0
O3 B:2BB170 2.3 41.8 1.0
O2 B:2BB170 2.8 46.8 1.0
CE1 B:HIS132 2.9 18.4 1.0
CD2 B:HIS136 3.0 15.8 1.0
CD2 B:HIS132 3.1 19.8 1.0
CE1 B:HIS136 3.1 16.8 1.0
N1 B:2BB170 3.2 43.8 1.0
C7 B:2BB170 3.3 45.6 1.0
CB B:CYS90 3.4 29.8 1.0
NE2 B:GLN50 3.5 23.7 1.0
O B:HOH174 3.5 22.7 1.0
OE1 B:GLN50 3.9 22.3 1.0
CD B:GLN50 3.9 23.8 1.0
CA B:CYS90 4.0 30.1 1.0
ND1 B:HIS132 4.1 17.9 1.0
CG B:HIS132 4.2 18.1 1.0
ND1 B:HIS136 4.2 15.2 1.0
CG B:HIS136 4.2 17.2 1.0
OE2 B:GLU133 4.5 30.2 1.0
O B:HOH188 4.5 19.4 1.0
N B:LEU91 4.6 30.8 1.0
OE1 B:GLU133 4.6 27.5 1.0
C6 B:2BB170 4.7 46.4 1.0
C B:CYS90 4.7 30.4 1.0
O B:GLY89 4.8 31.1 1.0
CD B:GLU133 4.9 25.9 1.0
CG B:GLN50 5.0 25.0 1.0

Nickel binding site 3 out of 3 in 3k6l

Go back to Nickel Binding Sites List in 3k6l
Nickel binding site 3 out of 3 in the The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni169

b:58.5
occ:1.00
O C:HOH208 2.4 48.0 1.0
NE2 C:HIS136 2.5 56.4 1.0
SG C:CYS90 2.6 78.0 1.0
NE2 C:HIS132 2.6 60.2 1.0
NE2 C:GLN50 2.9 68.4 1.0
CD2 C:HIS132 3.2 60.9 1.0
CE1 C:HIS136 3.2 56.0 1.0
CD2 C:HIS136 3.2 56.2 1.0
CB C:CYS90 3.6 79.1 1.0
CD C:GLN50 3.7 68.3 1.0
CE1 C:HIS132 3.7 60.5 1.0
OE1 C:GLN50 3.8 68.5 1.0
CA C:CYS90 4.0 79.2 1.0
N C:LEU91 4.1 79.1 1.0
ND1 C:HIS136 4.1 55.4 1.0
CG C:HIS136 4.2 55.5 1.0
CG C:HIS132 4.4 60.9 1.0
C C:CYS90 4.6 79.2 1.0
OE1 C:GLU133 4.6 58.9 1.0
ND1 C:HIS132 4.6 61.2 1.0
OE2 C:GLU133 4.8 58.2 1.0
CG C:GLN50 4.9 68.1 1.0

Reference:

R.K.Y.Cheng, L.Crawley, M.Wood, J.Barker, B.Felicetti, M.Whittaker. The Structure of E.Coli Peptide Deformylase (Pdf) in Complex with Peptidomimetic Ligand BB2827 To Be Published.
Page generated: Fri Sep 25 08:25:58 2020
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