Nickel in PDB 7jw4: Crystal Structure of PDGH110B in Complex with D-Galactose

The structure of Crystal Structure of PDGH110B in Complex with D-Galactose, PDB code: 7jw4 was solved by A.G.Hettle, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.98 / 2.34
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	169.786, 128.093, 100.014, 90.00, 123.16, 90.00
R / Rfree (%)	18.5 / 23.1

The structure of Crystal Structure of PDGH110B in Complex with D-Galactose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of PDGH110B in Complex with D-Galactose (pdb code 7jw4). 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 PDGH110B in Complex with D-Galactose, PDB code: 7jw4:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Crystal Structure of PDGH110B in Complex with D-Galactose


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 PDGH110B in Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni702 b:32.6 occ:0.70 O A:HOH838 3.1 30.3 1.0 O A:HOH972 3.1 27.4 1.0 O A:HOH1052 3.2 28.0 1.0 NH1 A:ARG435 3.2 27.0 1.0 NH2 A:ARG435 3.3 26.9 1.0 N A:ALA438 3.7 28.7 1.0 CZ A:ARG435 3.7 28.7 1.0 O A:CYS328 3.8 25.0 1.0 CG2 A:ILE349 4.1 27.4 1.0 CB A:ALA438 4.2 29.5 1.0 CB A:TYR437 4.2 33.5 1.0 CA A:TYR437 4.3 29.2 1.0 CD1 A:TYR437 4.4 21.9 1.0 C A:TYR437 4.4 30.9 1.0 O A:HIS350 4.5 23.6 1.0 N A:HIS350 4.5 26.5 1.0 CA A:ALA438 4.5 30.7 1.0 CA A:SER459 4.6 26.9 1.0 C A:HIS350 4.6 27.3 1.0 CA A:HIS350 4.7 27.6 1.0 C A:ILE349 4.8 27.4 1.0 CG A:TYR437 4.8 33.0 1.0 N A:ARG460 4.8 29.3 1.0 N A:CYS328 4.9 25.1 1.0 C A:CYS328 4.9 29.2 1.0 O A:ALA438 4.9 30.9 1.0 CB A:SER459 4.9 31.9 1.0 O A:ASN458 4.9 25.9 1.0 O A:ILE349 5.0 29.3 1.0

Nickel binding site 2 out of 2 in the Crystal Structure of PDGH110B in Complex with D-Galactose


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 PDGH110B in Complex with D-Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni702 b:33.2 occ:0.65 O B:HOH956 3.1 27.1 1.0 O B:HOH1026 3.1 25.9 1.0 O B:HOH838 3.2 27.4 1.0 NH1 B:ARG435 3.2 26.4 1.0 NH2 B:ARG435 3.3 27.6 1.0 CZ B:ARG435 3.7 28.5 1.0 N B:ALA438 3.8 33.1 1.0 O B:CYS328 3.8 24.4 1.0 CG2 B:ILE349 4.0 31.6 1.0 CB B:ALA438 4.2 30.8 1.0 CB B:TYR437 4.2 29.6 1.0 CD1 B:TYR437 4.3 26.7 1.0 CA B:TYR437 4.3 30.6 1.0 O B:HIS350 4.4 24.6 1.0 C B:HIS350 4.5 27.3 1.0 CA B:SER459 4.5 28.2 1.0 C B:TYR437 4.6 35.9 1.0 CA B:ALA438 4.6 32.5 1.0 N B:HIS350 4.7 27.8 1.0 CA B:HIS350 4.8 26.6 1.0 CG B:TYR437 4.8 33.1 1.0 N B:CYS328 4.8 26.1 1.0 N B:ARG460 4.8 29.4 1.0 C B:ILE349 4.8 31.6 1.0 C B:CYS328 4.9 27.7 1.0 CB B:SER459 4.9 31.9 1.0 O B:ILE349 4.9 29.2 1.0 O B:ASN458 5.0 26.4 1.0

B.E.Mcguire, A.Hettle, C.Vickers, D.T.King, D.J.Vocadlo, A.B.Boraston. The Structure of A Family 110 Glycoside Hydrolase Provides Insight Into the Hydrolysis of Alpha-(1,3)-Galactosidic Linkages in Lambda-Carrageenan and Blood Group Antigens. J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
PubMed: 33127644
DOI: 10.1074/JBC.RA120.015776