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Sodium in PDB 6y8y: Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate

Protein crystallography data

The structure of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate, PDB code: 6y8y 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) 47.34 / 1.95
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.230, 94.680, 146.970, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21

Other elements in 6y8y:

The structure of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate also contains other interesting chemical elements:

Nickel (Ni) 1 atom
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate (pdb code 6y8y). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate, PDB code: 6y8y:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6y8y

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Sodium binding site 1 out of 5 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na611

b:54.5
occ:1.00
OD2 A:ASP260 2.5 35.9 1.0
CG A:ASP260 3.4 31.4 1.0
CA A:GLY263 3.6 25.5 1.0
CB A:ASP260 3.6 27.9 1.0
N A:GLY263 4.0 22.2 1.0
O A:HOH1057 4.5 48.0 1.0
OD1 A:ASP260 4.5 26.1 1.0
O A:ASP260 4.8 22.7 1.0
C A:GLY263 4.9 29.6 1.0
C A:GLY262 4.9 23.0 1.0

Sodium binding site 2 out of 5 in 6y8y

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Sodium binding site 2 out of 5 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na612

b:59.2
occ:1.00
O3P A:SEP121 2.4 50.7 1.0
O A:HOH933 2.5 53.3 1.0
NH1 A:ARG27 2.7 51.2 1.0
OG1 A:THR511 3.3 39.4 1.0
CZ A:ARG27 3.5 52.6 1.0
NH2 A:ARG27 3.5 46.7 1.0
O5 A:G1P603 3.5 33.4 1.0
CB A:THR511 3.7 37.9 1.0
P A:SEP121 3.9 48.3 1.0
NH2 A:ARG297 3.9 30.6 1.0
CG2 A:THR511 4.0 34.4 1.0
O6 A:G1P603 4.1 35.0 1.0
C6 A:G1P603 4.3 34.2 1.0
CG A:ARG122 4.3 41.8 1.0
O1P A:SEP121 4.3 43.3 1.0
C1 A:G1P603 4.4 29.1 1.0
CD A:ARG122 4.4 38.0 1.0
C5 A:G1P603 4.5 32.6 1.0
OD1 A:ASN123 4.5 41.9 1.0
CB A:SEP121 4.6 26.3 1.0
C3 A:GOL608 4.7 49.8 1.0
NE A:ARG27 4.7 50.0 1.0
C2 A:GOL608 4.7 50.1 1.0
O A:THR511 4.8 45.0 1.0
OG A:SEP121 4.9 39.6 1.0
O2P A:SEP121 4.9 43.1 1.0
CZ A:ARG297 4.9 36.7 1.0
O3P A:G1P603 5.0 27.2 1.0

Sodium binding site 3 out of 5 in 6y8y

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Sodium binding site 3 out of 5 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na613

b:50.1
occ:1.00
OD2 A:ASP415 2.5 50.7 1.0
N A:GLY412 3.0 30.8 1.0
CG A:ASP415 3.5 43.1 1.0
O A:HOH900 3.7 34.4 1.0
CA A:GLN411 3.7 32.4 1.0
CB A:ASP415 3.7 33.6 1.0
O A:HOH993 3.8 51.2 1.0
C A:GLN411 3.8 28.0 1.0
CA A:GLY412 3.8 32.3 1.0
CB A:GLN411 4.1 35.5 1.0
OD1 A:ASP415 4.6 36.5 1.0
CG A:GLN411 4.6 36.5 1.0
C A:GLY412 4.7 30.8 1.0
O A:LYS410 4.8 42.1 1.0
O A:GLY412 4.8 25.7 1.0
N A:GLN411 5.0 32.3 1.0
O A:GLN411 5.0 26.6 1.0

Sodium binding site 4 out of 5 in 6y8y

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Sodium binding site 4 out of 5 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na614

b:45.8
occ:1.00
O A:LEU181 2.4 33.1 1.0
OE1 A:GLU2 2.6 37.9 1.0
C A:LEU181 3.3 37.0 1.0
O A:HOH827 3.3 31.2 1.0
N A:LEU181 3.4 30.8 1.0
CB A:ASP180 3.6 35.7 1.0
O A:LYS184 3.6 33.0 1.0
O A:HOH732 3.6 50.8 1.0
CB A:GLU2 3.7 41.4 1.0
C A:ASP180 3.7 27.6 1.0
CD A:GLU2 3.8 43.2 1.0
CA A:ASP180 3.9 32.4 1.0
CB A:PRO5 3.9 40.8 1.0
CA A:LEU181 3.9 33.4 1.0
N A:GLU182 4.2 36.5 1.0
CG A:ASP180 4.3 39.2 1.0
CG A:GLU2 4.3 40.9 1.0
O A:ASP180 4.5 34.1 1.0
CA A:GLU182 4.5 41.1 1.0
OD1 A:ASP180 4.6 39.2 1.0
CA A:PRO5 4.7 41.1 1.0
C A:LYS184 4.7 33.0 1.0
OE2 A:GLU2 4.8 40.3 1.0
N A:LYS184 4.9 38.4 1.0
CA A:GLU2 4.9 40.2 1.0
N A:ASN183 5.0 41.6 1.0
CG A:PRO5 5.0 42.3 1.0
OD2 A:ASP180 5.0 42.9 1.0

Sodium binding site 5 out of 5 in 6y8y

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Sodium binding site 5 out of 5 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5) with Bound Glucose-1-Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na615

b:48.4
occ:1.00
O A:ARG333 2.5 40.3 1.0
N A:ALA355 3.0 25.9 1.0
C A:ARG333 3.5 36.7 1.0
CB A:ALA355 3.6 31.3 1.0
CG1 A:VAL354 3.8 31.7 1.0
CA A:VAL354 3.9 30.9 1.0
CA A:ALA355 3.9 34.3 1.0
C A:VAL354 3.9 27.1 1.0
CA A:GLY334 4.1 29.6 1.0
N A:GLY334 4.2 32.2 1.0
CB A:VAL354 4.4 32.2 1.0
CA A:ARG333 4.5 35.2 1.0
O A:HOH763 4.6 35.6 1.0
O A:ALA355 4.7 28.2 1.0
O A:LYS353 4.8 36.8 1.0
C A:ALA355 4.8 31.8 1.0
O A:VAL332 4.9 40.4 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 13:13:49 2020

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