Nickel in PDB 9fyn: 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: 9fyn 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)	41.88 / 1.79
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.788, 93.628, 93.729, 90, 90, 90
R / Rfree (%)	20.6 / 24.4

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

Nickel binding site 1 out of 2 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:66.4 occ:1.00 NE2 A:HIS497 2.0 70.0 1.0 O A:HOH1465 2.3 60.6 1.0 O A:HOH1484 2.4 59.0 1.0 O A:HOH1489 2.5 64.1 1.0 CE1 A:HIS497 3.0 70.3 1.0 CD2 A:HIS497 3.0 70.7 1.0 O A:HOH1499 3.1 69.6 1.0 HD2 A:HIS497 3.2 85.4 1.0 HE1 A:HIS497 3.2 84.9 1.0 ND1 A:HIS497 4.1 66.2 1.0 CG A:HIS497 4.1 69.6 1.0 HE3 A:MET558 4.2 83.5 1.0 O A:HOH1366 4.4 61.4 1.0 HG2 A:MET558 4.5 98.6 1.0 O A:HOH1491 4.5 60.3 1.0 HE2 A:MET558 4.8 83.5 1.0 HD1 A:HIS497 4.9 80.0 1.0 HB3 A:ASP554 4.9 74.6 1.0 CE A:MET558 5.0 69.1 1.0

Nickel binding site 2 out of 2 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:75.5 occ:1.00 NE2 A:HIS807 2.0 48.7 1.0 O A:HOH1311 2.1 60.6 1.0 O A:HOH1501 2.2 70.6 1.0 O A:HOH1470 2.4 65.6 1.0 CE1 A:HIS807 2.7 57.8 1.0 HE1 A:HIS807 2.7 69.9 1.0 O A:HOH1498 3.0 52.3 1.0 CD2 A:HIS807 3.2 59.3 1.0 HD2 A:HIS807 3.6 71.7 1.0 ND1 A:HIS807 4.0 56.6 1.0 O A:PRO805 4.2 58.9 1.0 CG A:HIS807 4.2 49.5 1.0 O A:HOH1463 4.2 65.0 1.0 HD1 A:HIS807 4.7 68.5 1.0 HA A:ASP806 4.8 67.7 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