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Nickel in PDB 6y8z: Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)

Protein crystallography data

The structure of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5), PDB code: 6y8z was solved by R.Gustafsson, U.Eckhard, M.Selmer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.93 / 2.05
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.200, 94.210, 146.690, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 23.6

Other elements in 6y8z:

The structure of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Sodium (Na) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) (pdb code 6y8z). 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 Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5), PDB code: 6y8z:

Nickel binding site 1 out of 1 in 6y8z

Go back to Nickel Binding Sites List in 6y8z
Nickel binding site 1 out of 1 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:22.3
occ:1.00
O2P A:SEP121 1.9 41.2 1.0
OD1 A:ASP296 1.9 18.3 1.0
OD2 A:ASP292 2.0 21.4 1.0
OD1 A:ASP294 2.0 18.9 1.0
CG A:ASP296 2.8 19.5 1.0
CG A:ASP294 2.9 21.1 1.0
P A:SEP121 3.0 59.0 1.0
CG A:ASP292 3.0 20.9 1.0
OD2 A:ASP294 3.1 19.2 1.0
OG A:SEP121 3.1 47.5 1.0
OD2 A:ASP296 3.1 17.4 1.0
HG3 A:ARG297 3.1 36.6 1.0
HB2 A:SEP121 3.1 34.1 1.0
HE A:ARG297 3.2 59.9 1.0
OD1 A:ASP292 3.4 17.4 1.0
H A:ASP296 3.4 15.8 1.0
NA A:NA603 3.5 47.3 1.0
CB A:SEP121 3.6 28.5 1.0
HA A:SEP121 3.6 31.7 1.0
H A:ASP294 3.8 19.5 1.0
O1P A:SEP121 3.8 59.2 1.0
NE A:ARG297 3.8 49.9 1.0
CG A:ARG297 3.9 30.5 1.0
HD2 A:ARG297 4.0 30.1 1.0
H A:ARG297 4.0 13.4 1.0
CD A:ARG297 4.1 25.1 1.0
CA A:SEP121 4.2 26.4 1.0
CB A:ASP296 4.2 18.1 1.0
HD2 A:ARG122 4.2 61.4 1.0
N A:ASP296 4.2 13.2 1.0
O3P A:SEP121 4.3 48.1 1.0
CB A:ASP294 4.3 16.7 1.0
CB A:ASP292 4.3 21.5 1.0
HB2 A:ASP292 4.3 25.8 1.0
HE2 A:LYS393 4.3 50.6 1.0
HB2 A:ARG297 4.4 25.1 1.0
HB3 A:SEP121 4.4 34.1 1.0
H A:GLY295 4.4 20.3 1.0
N A:ARG297 4.5 11.2 1.0
N A:ASP294 4.5 16.3 1.0
HB3 A:ASP296 4.6 21.6 1.0
HG2 A:ARG297 4.6 36.6 1.0
CA A:ASP296 4.6 15.7 1.0
HB3 A:ASP294 4.6 20.1 1.0
HH21 A:ARG297 4.7 60.3 1.0
HB3 A:ASP292 4.7 25.8 1.0
CB A:ARG297 4.7 20.9 1.0
N A:GLY295 4.7 16.9 1.0
CA A:ASP294 4.8 19.9 1.0
C A:ASP296 4.8 17.4 1.0
HG1 A:THR100 4.8 24.1 1.0
HB2 A:ASP296 4.8 21.6 1.0
C A:ASP294 4.8 13.3 1.0
HB2 A:ASP294 4.9 20.1 1.0
CZ A:ARG297 4.9 51.2 1.0

Reference:

R.Gustafsson, U.Eckhard, W.Ye, E.D.Enbody, M.Pettersson, P.Jemth, L.Andersson, M.Selmer. Structure and Characterization of Phosphoglucomutase 5 From Atlantic and Baltic Herring-An Inactive Enzyme with Intact Substrate Binding Biomolecules 2020.
ISSN: ESSN 2218-273X
DOI: 10.3390/BIOM10121631
Page generated: Thu Dec 17 13:19:45 2020

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