Palladium in PDB 1ks4: The Structure of Aspergillus Niger Endoglucanase-Palladium Complex

All present enzymatic activity of The Structure of Aspergillus Niger Endoglucanase-Palladium Complex:
3.2.1.4;

The structure of The Structure of Aspergillus Niger Endoglucanase-Palladium Complex, PDB code: 1ks4 was solved by S.Khademi, D.Zhang, S.M.Swanson, A.Wartenberg, C.Witte, E.F.Meyer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	131.088, 131.088, 71.985, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 24.6

The binding sites of Palladium atom in the The Structure of Aspergillus Niger Endoglucanase-Palladium Complex (pdb code 1ks4). This binding sites where shown within 5.0 Angstroms radius around Palladium atom.
In total 3 binding sites of Palladium where determined in the The Structure of Aspergillus Niger Endoglucanase-Palladium Complex, PDB code: 1ks4:
Jump to Palladium binding site number: 1; 2; 3;

Palladium binding site 1 out of 3 in the The Structure of Aspergillus Niger Endoglucanase-Palladium Complex


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 1 of The Structure of Aspergillus Niger Endoglucanase-Palladium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd224 b:98.3 occ:1.00 SD A:MET118 2.1 44.7 1.0 OE1 A:GLU116 2.3 57.5 1.0 CG A:MET118 2.6 37.1 1.0 OE1 A:GLU204 3.4 47.4 1.0 CD A:GLU116 3.4 57.1 1.0 CE A:MET118 3.5 40.5 1.0 O A:HOH248 3.9 36.7 1.0 CB A:MET118 4.0 33.6 1.0 OE2 A:GLU116 4.1 60.5 1.0 OD2 A:ASP99 4.3 46.3 1.0 OD1 A:ASP99 4.3 47.0 1.0 CD A:GLU204 4.4 45.1 1.0 CG A:GLU116 4.5 53.5 1.0 CG A:ASP99 4.7 44.3 1.0 OE2 A:GLU204 4.7 46.3 1.0 CG2 A:THR160 4.7 31.4 1.0

Palladium binding site 2 out of 3 in the The Structure of Aspergillus Niger Endoglucanase-Palladium Complex


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 2 of The Structure of Aspergillus Niger Endoglucanase-Palladium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd225 b:53.9 occ:1.00 NE2 A:HIS46 2.4 30.5 1.0 CD2 A:TYR34 2.6 54.7 1.0 CE2 A:TYR34 2.9 56.3 1.0 CD2 A:HIS46 3.1 27.5 1.0 CE1 A:HIS46 3.5 29.3 1.0 CG A:TYR34 3.6 53.5 1.0 CZ A:TYR34 4.0 56.1 1.0 CB A:TYR34 4.2 49.6 1.0 CG A:HIS46 4.3 29.0 1.0 ND1 A:HIS46 4.4 30.7 1.0 CD1 A:TYR34 4.5 54.7 1.0 CE1 A:TYR34 4.7 56.0 1.0 OH A:TYR34 4.9 57.3 1.0

Palladium binding site 3 out of 3 in the The Structure of Aspergillus Niger Endoglucanase-Palladium Complex


Mono view


Stereo pair view

A full contact list of Palladium with other atoms in the Pd binding site number 3 of The Structure of Aspergillus Niger Endoglucanase-Palladium Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Pd226 b:59.5 occ:1.00 N A:VAL33 2.3 50.5 1.0 O A:VAL33 2.5 49.7 1.0 CB A:CYS32 2.9 57.7 1.0 C A:VAL33 3.0 47.8 1.0 C A:CYS32 3.1 49.8 1.0 O A:GLN1 3.1 98.8 1.0 CA A:CYS32 3.2 51.9 1.0 CA A:VAL33 3.2 49.2 1.0 SG A:CYS4 3.3 68.9 1.0 CE1 A:TYR34 3.5 56.0 1.0 N A:MET3 3.6 90.9 1.0 C A:THR2 3.6 93.2 1.0 CD1 A:TYR34 3.6 54.7 1.0 CA A:THR2 3.7 95.1 1.0 C A:MET3 3.8 85.7 1.0 SG A:CYS32 3.8 68.7 1.0 N A:CYS4 3.9 81.7 1.0 N A:TYR34 3.9 46.4 1.0 O A:MET3 4.0 85.6 1.0 CZ A:TYR34 4.1 56.1 1.0 C A:GLN1 4.1 98.5 1.0 CB A:VAL33 4.2 49.8 1.0 CA A:CYS4 4.2 77.3 1.0 O A:CYS32 4.2 47.5 1.0 O A:THR2 4.2 92.7 1.0 CB A:CYS4 4.3 73.7 1.0 CG A:TYR34 4.3 53.5 1.0 CG A:MET3 4.3 89.4 1.0 CA A:MET3 4.3 88.1 1.0 N A:THR2 4.4 97.1 1.0 CA A:TYR34 4.5 46.3 1.0 N A:CYS32 4.6 49.5 1.0 OH A:TYR34 4.7 57.3 1.0 CE2 A:TYR34 4.7 56.3 1.0 CD2 A:TYR34 4.8 54.7 1.0 CG2 A:THR2 4.8 95.0 1.0 CB A:MET3 4.9 89.0 1.0 CB A:THR2 4.9 95.4 1.0

S.Khademi, D.Zhang, S.M.Swanson, A.Wartenberg, K.Witte, E.F.Meyer. Determination of the Structure of An Endoglucanase From Aspergillus Niger and Its Mode of Inhibition By Palladium Chloride. Acta Crystallogr.,Sect.D V. 58 660 2002.
ISSN: ISSN 0907-4449
PubMed: 11914491
DOI: 10.1107/S0907444902003360