Atomistry » Nickel » PDB 7z5r-8cja » 8bdd
Atomistry »
  Nickel »
    PDB 7z5r-8cja »
      8bdd »

Nickel in PDB 8bdd: Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase

Protein crystallography data

The structure of Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase, PDB code: 8bdd was solved by M.E.Roenne, T.Tandrup, C.Wilkens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.21 / 1.61
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 89.59, 120.95, 90.24, 90, 117.76, 90
R / Rfree (%) 19 / 21.2

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase (pdb code 8bdd). 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 Bacteroides Ovatus CP926 PL17 Alginate Lyase, PDB code: 8bdd:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 8bdd

Go back to Nickel Binding Sites List in 8bdd
Nickel binding site 1 out of 2 in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase


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 Bacteroides Ovatus CP926 PL17 Alginate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni801

b:19.0
occ:0.55
NE2 A:HIS467 2.1 22.9 1.0
O A:HOH920 2.1 27.4 1.0
O A:HOH923 2.2 30.5 1.0
ND1 A:HIS418 2.2 22.7 1.0
OD1 A:ASP436 2.3 28.8 1.0
O A:HOH1220 2.4 26.6 1.0
CE1 A:HIS418 2.9 23.5 1.0
CD2 A:HIS467 2.9 22.0 1.0
CE1 A:HIS467 3.2 20.6 1.0
CG A:ASP436 3.2 31.3 1.0
CG A:HIS418 3.4 24.1 1.0
OD2 A:ASP436 3.4 28.9 1.0
O A:HOH970 3.8 32.1 1.0
CB A:HIS418 3.9 22.9 1.0
N A:ASN312 4.1 31.0 1.0
CG A:HIS467 4.1 18.8 1.0
NE2 A:HIS418 4.1 24.0 1.0
ND1 A:HIS467 4.2 20.0 1.0
O A:ALA461 4.2 21.8 1.0
O A:ASN312 4.2 31.9 1.0
O A:HIS310 4.3 32.0 1.0
CD2 A:HIS418 4.3 23.6 1.0
N A:GLY438 4.3 30.7 1.0
OD2 A:ASP420 4.4 25.9 1.0
CA A:ASN312 4.5 31.4 1.0
CB A:ASP436 4.6 26.8 1.0
N A:TYR437 4.7 27.6 1.0
O A:GLY438 4.7 28.1 1.0
C A:ASN312 4.7 33.9 1.0
CA A:GLY438 4.9 28.9 1.0
C A:ILE311 4.9 30.2 1.0

Nickel binding site 2 out of 2 in 8bdd

Go back to Nickel Binding Sites List in 8bdd
Nickel binding site 2 out of 2 in the Crystal Structure of Bacteroides Ovatus CP926 PL17 Alginate Lyase


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 Bacteroides Ovatus CP926 PL17 Alginate Lyase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni801

b:25.7
occ:0.44
NE2 B:HIS467 2.1 23.3 1.0
ND1 B:HIS418 2.2 24.7 1.0
O B:HOH909 2.3 36.5 1.0
O B:HOH904 2.4 37.6 1.0
O B:HOH1046 2.5 32.4 1.0
OD1 B:ASP436 2.5 49.6 1.0
CD2 B:HIS467 2.8 24.7 1.0
CE1 B:HIS418 2.8 26.1 1.0
OD2 B:ASP436 3.2 41.2 1.0
CG B:ASP436 3.2 45.2 1.0
CE1 B:HIS467 3.3 21.2 1.0
CG B:HIS418 3.4 24.9 1.0
CG B:HIS467 4.0 19.3 1.0
NE2 B:HIS418 4.0 24.7 1.0
CB B:HIS418 4.1 23.4 1.0
N B:ASN312 4.1 42.1 1.0
O B:ALA461 4.1 22.8 1.0
O B:ASN312 4.2 42.0 1.0
ND1 B:HIS467 4.2 21.1 1.0
N B:GLY438 4.2 42.1 1.0
CD2 B:HIS418 4.3 27.9 1.0
O B:HIS310 4.4 64.2 1.0
CA B:ASN312 4.4 40.3 1.0
OD2 B:ASP420 4.5 30.0 1.0
N B:TYR437 4.6 43.1 1.0
C B:ASN312 4.6 44.2 1.0
CB B:ASP436 4.6 42.4 1.0
O B:GLY438 4.6 39.1 1.0
CA B:GLY438 4.7 41.7 1.0

Reference:

M.E.Roenne, T.Tandrup, C.Wilkens. Three Alginate Lyases Providing A New Gut Bacteroides Ovatus Isolate with the Ability to Grow on Alginate Appl.Environ.Microbiol. 2023.
ISSN: ESSN 1098-5336
Page generated: Thu Oct 10 09:35:55 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy