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Nickel in PDB 2ai9: S.Aureus Polypeptide Deformylase

Enzymatic activity of S.Aureus Polypeptide Deformylase

All present enzymatic activity of S.Aureus Polypeptide Deformylase:
3.5.1.88;

Protein crystallography data

The structure of S.Aureus Polypeptide Deformylase, PDB code: 2ai9 was solved by K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group I 4
Cell size a, b, c (Å), α, β, γ (°) 167.300, 167.300, 42.250, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.2

Nickel Binding Sites:

The binding sites of Nickel atom in the S.Aureus Polypeptide Deformylase (pdb code 2ai9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the S.Aureus Polypeptide Deformylase, PDB code: 2ai9:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 2ai9

Go back to Nickel Binding Sites List in 2ai9
Nickel binding site 1 out of 2 in the S.Aureus Polypeptide Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of S.Aureus Polypeptide Deformylase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:59.6
occ:0.85
SG A:CYS110 2.2 29.1 1.0
NE2 A:HIS153 2.4 23.9 1.0
NE2 A:HIS157 2.5 19.2 1.0
O A:HOH322 3.0 24.2 1.0
CB A:CYS110 3.0 39.4 1.0
CE1 A:HIS157 3.2 20.1 1.0
CE1 A:HIS153 3.2 21.4 1.0
O A:HOH327 3.2 36.3 1.0
CD2 A:HIS153 3.4 20.9 1.0
CA A:CYS110 3.6 40.2 1.0
O A:HOH412 3.7 29.3 1.0
NE2 A:GLN64 3.7 22.6 1.0
CD2 A:HIS157 3.7 18.3 1.0
O A:GLY109 4.2 46.3 1.0
ND1 A:HIS153 4.4 25.6 1.0
ND1 A:HIS157 4.4 18.7 1.0
CD A:GLN64 4.4 25.3 1.0
CG A:HIS153 4.5 20.6 1.0
C A:CYS110 4.5 41.6 1.0
N A:LEU111 4.6 41.9 1.0
CG A:HIS157 4.7 16.3 1.0
OE2 A:GLU154 4.7 17.1 1.0
N A:CYS110 4.8 44.0 1.0
OE1 A:GLN64 4.8 24.1 1.0
C A:GLY109 4.9 44.2 1.0
O A:HOH392 4.9 30.6 1.0

Nickel binding site 2 out of 2 in 2ai9

Go back to Nickel Binding Sites List in 2ai9
Nickel binding site 2 out of 2 in the S.Aureus Polypeptide Deformylase


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of S.Aureus Polypeptide Deformylase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni301

b:57.7
occ:0.86
SG B:CYS110 2.2 20.3 1.0
NE2 B:HIS157 2.4 14.7 1.0
O B:HOH3010 2.5 25.2 1.0
NE2 B:HIS153 2.5 25.8 1.0
CE1 B:HIS157 3.1 10.6 1.0
CB B:CYS110 3.2 22.5 1.0
CE1 B:HIS153 3.2 25.7 1.0
O B:HOH3035 3.2 11.9 1.0
CD2 B:HIS153 3.5 27.5 1.0
CD2 B:HIS157 3.6 8.7 1.0
NE2 B:GLN64 3.8 8.1 1.0
CA B:CYS110 3.8 24.8 1.0
O B:HOH3050 4.0 35.5 1.0
ND1 B:HIS157 4.3 8.1 1.0
ND1 B:HIS153 4.3 28.4 1.0
CD B:GLN64 4.4 14.5 1.0
O B:GLY109 4.5 31.0 1.0
CG B:HIS153 4.5 23.6 1.0
OE1 B:GLN64 4.5 16.7 1.0
N B:LEU111 4.5 24.9 1.0
O B:HOH3013 4.6 12.6 1.0
CG B:HIS157 4.6 11.3 1.0
C B:CYS110 4.6 26.0 1.0
OE2 B:GLU154 4.7 18.7 1.0
N B:CYS110 4.9 26.0 1.0

Reference:

K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen. Structural Variation and Inhibitor Binding in Polypeptide Deformylase From Four Different Bacterial Species. Protein Sci. V. 12 349 2003.
ISSN: ISSN 0961-8368
PubMed: 12538898
DOI: 10.1110/PS.0229303
Page generated: Fri Sep 25 08:05:50 2020
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