Nickel in PDB 9fyo: Lacto-N-Biosidase From Trueperella Pyogenes

All present enzymatic activity of Lacto-N-Biosidase From Trueperella Pyogenes:
3.2.1.140;

The structure of Lacto-N-Biosidase From Trueperella Pyogenes, PDB code: 9fyo was solved by M.Vuillemin, S.Siebenhaar, B.Zeuner, J.P.Morth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.30 / 2.77
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.759, 93.686, 94.037, 90, 90, 90
R / Rfree (%)	22.7 / 26.8

The binding sites of Nickel atom in the Lacto-N-Biosidase From Trueperella Pyogenes (pdb code 9fyo). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Lacto-N-Biosidase From Trueperella Pyogenes, PDB code: 9fyo:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in the Lacto-N-Biosidase From Trueperella Pyogenes


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Lacto-N-Biosidase From Trueperella Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1101 b:92.5 occ:1.00 NE2 A:HIS497 2.0 84.1 1.0 CD2 A:HIS497 2.9 82.7 1.0 HD2 A:HIS497 3.0 101.1 1.0 CE1 A:HIS497 3.1 86.5 1.0 HE1 A:HIS497 3.4 105.7 1.0 CG A:HIS497 4.1 83.8 1.0 ND1 A:HIS497 4.1 85.4 1.0 H2 C:GAL2 4.2 96.3 1.0 O3 C:NAG1 4.3 76.5 1.0 HG2 A:MET558 4.7 149.7 1.0 HD1 A:HIS497 4.9 104.4 1.0 H4 C:NAG1 5.0 90.5 1.0

Nickel binding site 2 out of 3 in the Lacto-N-Biosidase From Trueperella Pyogenes


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Lacto-N-Biosidase From Trueperella Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1102 b:131.4 occ:1.00 O A:HOH1209 1.6 113.7 1.0 NE2 A:HIS807 2.0 79.1 1.0 O A:HOH1217 2.2 79.8 1.0 O A:HOH1221 2.4 90.6 1.0 CE1 A:HIS807 3.0 76.5 1.0 CD2 A:HIS807 3.0 76.1 1.0 HE1 A:HIS807 3.1 93.7 1.0 HD2 A:HIS807 3.3 93.3 1.0 ND1 A:HIS807 4.1 74.9 1.0 CG A:HIS807 4.2 74.8 1.0 O A:PRO805 4.5 73.4 1.0 HA A:ASP806 4.6 86.8 1.0 HD1 A:HIS807 4.9 91.8 1.0 O A:HOH1220 4.9 57.3 1.0

Nickel binding site 3 out of 3 in the Lacto-N-Biosidase From Trueperella Pyogenes


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Lacto-N-Biosidase From Trueperella Pyogenes within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni1103 b:128.5 occ:1.00 NE2 A:HIS292 2.0 91.7 1.0 O A:HOH1203 2.3 111.7 1.0 O A:HOH1214 2.4 102.5 1.0 O A:HOH1223 2.4 104.2 1.0 CD2 A:HIS292 2.8 87.4 1.0 HD2 A:HIS292 2.8 106.8 1.0 CE1 A:HIS292 3.1 86.9 1.0 HE1 A:HIS292 3.5 106.2 1.0 O A:VAL287 3.9 124.5 1.0 CG A:HIS292 3.9 83.3 1.0 ND1 A:HIS292 4.1 83.3 1.0 HG A:SER291 4.8 127.7 1.0 HD1 A:HIS292 4.9 101.9 1.0 HD2 A:PRO288 5.0 140.1 1.0 C A:VAL287 5.0 123.1 1.0 OG A:SER291 5.0 104.8 1.0

M.Vuillemin, J.Muschiol, Y.Zhang, J.Holck, K.Barrett, J.P.Morth, A.S.Meyer, B.Zeuner. Discovery of Lacto-N-Biosidases and A Novel N-Acetyllactosaminidase Activity in the Cazy Family GH20: Functional Diversity and Structural Insights. Chembiochem 00710 2024.
ISSN: ESSN 1439-7633
PubMed: 39239753
DOI: 10.1002/CBIC.202400710