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Nickel in PDB 5q9m: Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268)

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268), PDB code: 5q9m was solved by J.A.Newman, H.Aitkenhead, S.Y.Lee, K.Kupinska, N.Burgess-Brown, R.Tallon, T.Krojer, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.94 / 1.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.962, 56.915, 115.005, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23

Nickel Binding Sites:

The binding sites of Nickel atom in the Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268) (pdb code 5q9m). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268), PDB code: 5q9m:

Nickel binding site 1 out of 1 in 5q9m

Go back to Nickel Binding Sites List in 5q9m
Nickel binding site 1 out of 1 in the Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of DCLRE1A After Initial Refinement with No Ligand Modelled (Structure 268) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni1102

b:14.0
occ:1.00
O8 A:MLI1101 2.1 17.1 1.0
O7 A:MLI1101 2.2 16.6 1.0
OD2 A:ASP815 2.2 13.6 1.0
NE2 A:HIS732 2.3 12.2 1.0
ND1 A:HIS734 2.3 14.0 1.0
NE2 A:HIS793 2.3 11.3 1.0
C3 A:MLI1101 3.0 25.8 1.0
CE1 A:HIS734 3.1 12.8 1.0
C2 A:MLI1101 3.1 20.1 1.0
CD2 A:HIS732 3.2 10.7 1.0
CE1 A:HIS793 3.2 10.7 1.0
CE1 A:HIS732 3.2 13.2 1.0
CG A:ASP815 3.3 12.7 1.0
CD2 A:HIS793 3.3 10.1 1.0
CG A:HIS734 3.3 13.1 1.0
C1 A:MLI1101 3.4 23.8 1.0
CB A:ASP815 3.7 11.2 1.0
CB A:HIS734 3.7 13.8 1.0
O9 A:MLI1101 4.2 32.9 1.0
NE2 A:HIS737 4.2 17.4 1.0
O6 A:MLI1101 4.3 22.6 1.0
NE2 A:HIS734 4.3 14.4 1.0
CG A:HIS732 4.3 10.8 1.0
ND1 A:HIS793 4.3 10.6 1.0
ND1 A:HIS732 4.3 12.7 1.0
CD2 A:HIS737 4.4 17.5 1.0
OD1 A:ASP815 4.4 14.3 1.0
CD2 A:HIS734 4.4 13.4 1.0
CG A:HIS793 4.4 9.6 1.0
CE1 A:HIS994 4.6 11.9 1.0
NE2 A:HIS994 4.7 13.1 1.0
O A:HOH1233 4.9 25.0 1.0
O A:HOH1418 5.0 18.1 1.0

Reference:

J.A.Newman, H.Aitkenhead, S.Y.Lee, K.Kupinska, N.Burgess-Brown, R.Tallon, T.Krojer, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Pandda Analysis Group Deposition To Be Published.
Page generated: Wed Dec 16 01:49:03 2020

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