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Nickel in PDB 5j7m: Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836

Protein crystallography data

The structure of Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836, PDB code: 5j7m was solved by C.Chang, M.Cuff, G.Chhor, M.Endres, A.Joachimiak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.85 / 2.07
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 61.162, 61.162, 120.973, 90.00, 90.00, 120.00
R / Rfree (%) 18 / 22.4

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836 (pdb code 5j7m). 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 Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836, PDB code: 5j7m:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 5j7m

Go back to Nickel Binding Sites List in 5j7m
Nickel binding site 1 out of 2 in the Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836


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 Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni202

b:66.5
occ:1.00
OD2 A:ASP49 2.2 32.4 1.0
NE2 A:HIS51 2.3 27.8 1.0
O4 A:PEG203 2.4 27.4 1.0
OE1 A:GLU55 2.4 22.7 1.0
NE2 A:HIS89 2.6 22.3 1.0
O A:EOH201 2.8 32.5 1.0
CD2 A:HIS51 3.1 15.8 1.0
CG A:ASP49 3.3 39.7 1.0
CE1 A:HIS51 3.4 20.4 1.0
CD A:GLU55 3.4 24.9 1.0
CE1 A:HIS89 3.5 27.7 1.0
C4 A:PEG203 3.5 36.9 1.0
CD2 A:HIS89 3.6 24.7 1.0
OE2 A:GLU55 3.8 29.4 1.0
C1 A:EOH201 3.8 33.5 1.0
O A:HOH334 3.9 38.2 1.0
CB A:ASP49 4.0 34.5 1.0
OD1 A:ASP49 4.3 40.5 1.0
C3 A:PEG203 4.3 38.2 1.0
CG A:HIS51 4.3 25.2 1.0
ND1 A:HIS51 4.4 22.2 1.0
O2 A:PEG203 4.5 42.7 1.0
ND1 A:HIS89 4.6 23.7 1.0
C2 A:EOH201 4.6 27.7 1.0
CG A:HIS89 4.7 24.6 1.0
CG A:GLU55 4.7 20.3 1.0
CB A:GLU55 4.9 13.0 1.0
CE A:MSE36 4.9 27.1 1.0

Nickel binding site 2 out of 2 in 5j7m

Go back to Nickel Binding Sites List in 5j7m
Nickel binding site 2 out of 2 in the Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836


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 Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni202

b:60.2
occ:1.00
OD2 B:ASP49 2.2 38.3 1.0
NE2 B:HIS51 2.3 22.7 1.0
OE1 B:GLU55 2.3 24.5 1.0
NE2 B:HIS89 2.4 27.7 1.0
O1 B:PEG203 2.4 32.9 1.0
O B:EOH201 2.6 24.1 1.0
CE1 B:HIS89 3.1 23.9 1.0
CD2 B:HIS51 3.2 14.5 1.0
CG B:ASP49 3.3 40.1 1.0
CD B:GLU55 3.3 29.2 1.0
CE1 B:HIS51 3.3 20.3 1.0
OE2 B:GLU55 3.5 26.9 1.0
CD2 B:HIS89 3.6 25.0 1.0
C1 B:PEG203 3.6 38.6 1.0
C1 B:EOH201 3.7 27.6 1.0
CB B:ASP49 3.9 33.6 1.0
O4 B:PEG203 4.1 47.6 1.0
OD1 B:ASP49 4.2 44.9 1.0
ND1 B:HIS89 4.4 27.0 1.0
CG B:HIS51 4.4 19.5 1.0
ND1 B:HIS51 4.4 20.0 1.0
C2 B:PEG203 4.5 43.0 1.0
CG B:HIS89 4.6 26.7 1.0
C2 B:EOH201 4.6 20.9 1.0
CG B:GLU55 4.7 25.2 1.0
O2 B:PEG203 4.7 47.6 1.0
CB B:GLU55 4.8 16.7 1.0
CE B:MSE36 4.9 27.6 1.0
CD1 B:LEU83 4.9 33.4 1.0

Reference:

C.Chang, M.Cuff, G.Chhor, M.Endres, A.Joachimiak. Crystal Structure of Cupin 2 Conserved Barrel Domain Protein From Kribbella Flavida Dsm 17836 To Be Published.
Page generated: Wed Dec 16 01:41:13 2020

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