Atomistry » Nickel » PDB 6wgq-9ant » 7jw4
Atomistry »
  Nickel »
    PDB 6wgq-9ant »
      7jw4 »

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

Protein crystallography data

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

Other elements in 7jw4:

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

Chlorine (Cl) 2 atoms

Nickel Binding Sites:

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 7jw4

Go back to Nickel Binding Sites List in 7jw4
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 7jw4

Go back to Nickel Binding Sites List in 7jw4
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

Reference:

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
Page generated: Wed Dec 16 02:00:39 2020

Last articles

Tb in 6TVY
Si in 6Y7O
Rh in 6WRM
Rh in 6WRL
Ni in 6Y8Z
Ni in 6Y8Y
Na in 6ZXZ
Na in 7ACG
Na in 6YLS
Na in 6Y8Z
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy