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Nickel in PDB 1lqy: Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin

Enzymatic activity of Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin

All present enzymatic activity of Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin, PDB code: 1lqy was solved by M.Mathieu, V.Mikol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.00 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 42.013, 43.075, 92.225, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 24.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin (pdb code 1lqy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin, PDB code: 1lqy:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 1lqy

Go back to Nickel Binding Sites List in 1lqy
Nickel binding site 1 out of 2 in the Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin


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 Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni301

b:13.6
occ:1.00
NE2 A:HIS153 2.1 3.2 1.0
O2 A:BB2401 2.2 13.1 1.0
NE2 A:HIS157 2.2 2.0 1.0
O4 A:BB2401 2.2 5.5 1.0
SG A:CYS110 2.7 13.0 1.0
N1 A:BB2401 2.8 9.0 1.0
C3 A:BB2401 2.9 4.4 1.0
CD2 A:HIS153 3.0 6.0 1.0
NE2 A:GLN65 3.1 9.0 1.0
CE1 A:HIS157 3.1 6.6 1.0
CD2 A:HIS157 3.2 6.7 1.0
CE1 A:HIS153 3.2 6.6 1.0
CD A:GLN65 3.8 7.4 1.0
O A:HOH402 3.9 3.6 1.0
CB A:CYS110 3.9 7.8 1.0
OE1 A:GLN65 4.1 8.4 1.0
CA A:CYS110 4.2 7.5 1.0
CG A:HIS153 4.2 5.1 1.0
ND1 A:HIS157 4.2 2.7 1.0
ND1 A:HIS153 4.3 3.9 1.0
CG A:HIS157 4.3 3.9 1.0
C5 A:BB2401 4.3 6.8 1.0
OE1 A:GLU154 4.4 4.3 1.0
N A:LEU111 4.4 8.0 1.0
C6 A:BB2401 4.6 4.8 1.0
O A:HOH418 4.8 10.9 1.0
C A:CYS110 4.8 7.1 1.0
OE2 A:GLU154 4.8 5.3 1.0
CG A:GLN65 4.9 8.3 1.0
C7 A:BB2401 4.9 5.6 1.0
CD A:GLU154 5.0 6.6 1.0

Nickel binding site 2 out of 2 in 1lqy

Go back to Nickel Binding Sites List in 1lqy
Nickel binding site 2 out of 2 in the Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Bacillus Stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni302

b:30.8
occ:1.00
NE2 A:HIS97 2.1 8.3 1.0
O A:HOH485 2.3 19.2 1.0
O A:HOH549 2.3 28.3 1.0
O A:HOH617 2.4 39.7 1.0
O A:HOH555 2.5 28.8 1.0
CD2 A:HIS97 3.0 10.3 1.0
CE1 A:HIS97 3.2 9.8 1.0
CG A:HIS97 4.2 10.6 1.0
ND1 A:HIS97 4.2 6.3 1.0
O A:HOH426 4.4 11.8 1.0
OH A:TYR124 4.4 15.0 1.0
O A:HOH560 4.9 29.4 1.0
CZ A:TYR124 4.9 10.8 1.0

Reference:

J.P.Guilloteau, M.Mathieu, C.Giglione, V.Blanc, A.Dupuy, M.Chevrier, P.Gil, A.Famechon, T.Meinnel, V.Mikol. The Crystal Structures of Four Peptide Deformylases Bound to the Antibiotic Actinonin Reveal Two Distinct Types: A Platform For the Structure-Based Design of Antibacterial Agents. J.Mol.Biol. V. 320 951 2002.
ISSN: ISSN 0022-2836
PubMed: 12126617
DOI: 10.1016/S0022-2836(02)00549-1
Page generated: Fri Sep 25 07:56:40 2020
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