Sodium 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:

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) (pdb code 6y8z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5), PDB code: 6y8z:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6y8z

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Sodium binding site 1 out of 4 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:47.3
occ:1.00
O1P A:SEP121 2.3 59.2 1.0
OD2 A:ASP294 2.5 19.2 1.0
OD2 A:ASP296 2.7 17.4 1.0
HE2 A:LYS134 3.1 59.5 1.0
P A:SEP121 3.2 59.0 1.0
HG1 A:THR100 3.2 24.1 1.0
O2P A:SEP121 3.4 41.2 1.0
HG21 A:THR100 3.5 26.9 1.0
OG A:SEP121 3.5 47.5 1.0
HD2 A:LYS134 3.5 81.5 1.0
HD3 A:LYS134 3.5 81.5 1.0
NI A:NI601 3.5 22.3 1.0
CG A:ASP294 3.5 21.1 1.0
CG A:ASP296 3.6 19.5 1.0
CD A:LYS134 3.8 67.9 1.0
CE A:LYS134 3.8 49.6 1.0
HG21 A:THR119 3.9 30.3 1.0
OD1 A:ASP294 3.9 18.9 1.0
OD1 A:ASP296 4.0 18.3 1.0
OG1 A:THR100 4.0 20.1 1.0
HZ3 A:LYS393 4.1 71.7 1.0
HG23 A:THR119 4.2 30.3 1.0
CG2 A:THR100 4.3 22.4 1.0
HE3 A:LYS134 4.4 59.5 1.0
HB3 A:ASN24 4.5 78.0 1.0
HH21 A:ARG27 4.5 75.4 1.0
CG2 A:THR119 4.5 25.3 1.0
CB A:THR100 4.6 24.5 1.0
O3P A:SEP121 4.6 48.1 1.0
HB A:THR100 4.7 29.4 1.0
HB3 A:ASP296 4.7 21.6 1.0
HE2 A:LYS393 4.7 50.6 1.0
HZ3 A:LYS134 4.7 39.6 1.0
NZ A:LYS134 4.8 33.0 1.0
CB A:ASP294 4.8 16.7 1.0
CB A:ASP296 4.8 18.1 1.0
HG23 A:THR100 4.8 26.9 1.0
HB2 A:ASP294 4.8 20.1 1.0
HZ1 A:LYS134 4.8 39.6 1.0
NZ A:LYS393 4.8 59.8 1.0
CB A:SEP121 4.8 28.5 1.0
HZ1 A:LYS393 4.8 71.7 1.0
HG22 A:THR100 4.9 26.9 1.0
HH21 A:ARG297 5.0 60.3 1.0
HH22 A:ARG27 5.0 75.4 1.0

Sodium binding site 2 out of 4 in 6y8z

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Sodium binding site 2 out of 4 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:55.2
occ:1.00
O3P A:SEP121 2.3 48.1 1.0
HD3 A:ARG122 2.4 61.4 1.0
HH21 A:ARG122 2.4 64.3 1.0
HH12 A:ARG27 2.7 73.2 1.0
HB3 A:SEP121 3.0 34.1 1.0
HH22 A:ARG27 3.1 75.4 1.0
H A:ARG122 3.1 36.0 1.0
NH2 A:ARG122 3.2 53.6 1.0
HB2 A:ARG122 3.3 38.3 1.0
HB2 A:SEP121 3.3 34.1 1.0
CD A:ARG122 3.3 51.2 1.0
NH1 A:ARG27 3.5 61.0 1.0
CB A:SEP121 3.5 28.5 1.0
HD2 A:ARG122 3.6 61.4 1.0
HH21 A:ARG297 3.6 60.3 1.0
HH22 A:ARG122 3.6 64.3 1.0
HD21 A:ASN24 3.7 0.7 1.0
HE A:ARG297 3.7 59.9 1.0
P A:SEP121 3.7 59.0 1.0
NH2 A:ARG27 3.8 62.8 1.0
N A:ARG122 4.0 30.1 1.0
CZ A:ARG122 4.1 63.6 1.0
NH2 A:ARG297 4.1 50.3 1.0
NE A:ARG122 4.1 61.8 1.0
CZ A:ARG27 4.1 65.0 1.0
CB A:ARG122 4.1 31.9 1.0
HH11 A:ARG27 4.1 73.2 1.0
HD21 A:ASN123 4.1 47.7 1.0
NE A:ARG297 4.2 49.9 1.0
OG A:SEP121 4.2 47.5 1.0
O2P A:SEP121 4.3 41.2 1.0
HD22 A:ASN123 4.3 47.7 1.0
CG A:ARG122 4.3 47.1 1.0
ND2 A:ASN24 4.3 86.4 1.0
HD22 A:ASN24 4.4 0.7 1.0
CZ A:ARG297 4.4 51.2 1.0
HH21 A:ARG27 4.5 75.4 1.0
ND2 A:ASN123 4.5 39.8 1.0
HH22 A:ARG297 4.6 60.3 1.0
CA A:ARG122 4.7 29.1 1.0
HG2 A:ARG122 4.7 56.5 1.0
CA A:SEP121 4.8 26.4 1.0
HB3 A:ARG122 4.8 38.3 1.0
HD2 A:ARG297 4.8 30.1 1.0
HE A:ARG122 4.9 74.2 1.0
O A:ALA120 4.9 25.2 1.0
O1P A:SEP121 4.9 59.2 1.0
C A:SEP121 4.9 32.9 1.0

Sodium binding site 3 out of 4 in 6y8z

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Sodium binding site 3 out of 4 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:40.6
occ:1.00
HH A:TYR522 2.1 37.9 1.0
OE2 A:GLU381 2.3 24.6 1.0
OH A:TYR522 2.8 31.6 1.0
HD3 A:ARG520 3.0 40.1 1.0
HE1 A:TYR522 3.2 21.9 1.0
HD2 A:ARG431 3.2 36.9 1.0
HD2 A:ARG520 3.3 40.1 1.0
HB3 A:SER382 3.4 30.7 1.0
HH11 A:ARG431 3.4 35.0 1.0
CD A:GLU381 3.4 22.2 1.0
HH12 A:ARG507 3.4 53.1 1.0
CD A:ARG520 3.5 33.4 1.0
HH11 A:ARG507 3.6 53.1 1.0
NH1 A:ARG431 3.7 29.2 1.0
CZ A:TYR522 3.7 19.8 1.0
NH1 A:ARG507 3.8 44.3 1.0
CE1 A:TYR522 3.8 18.3 1.0
OE1 A:GLU381 3.8 21.8 1.0
HD3 A:ARG431 3.9 36.9 1.0
CD A:ARG431 3.9 30.8 1.0
C1 A:GOL608 4.0 56.9 1.0
NE A:ARG520 4.0 38.4 1.0
HH12 A:ARG431 4.1 35.0 1.0
O A:HOH824 4.2 25.4 1.0
CZ A:ARG431 4.2 30.4 1.0
NE A:ARG431 4.2 28.2 1.0
HE A:ARG520 4.3 46.0 1.0
CB A:SER382 4.3 25.6 1.0
HH11 A:ARG520 4.4 51.4 1.0
O A:HOH711 4.5 50.7 1.0
CZ A:ARG520 4.6 46.9 1.0
HG A:SER382 4.6 29.0 1.0
CG A:GLU381 4.7 22.3 1.0
O2 A:GOL608 4.7 53.7 1.0
NH1 A:ARG520 4.7 42.9 1.0
HG3 A:GLU381 4.7 26.8 1.0
HB2 A:SER382 4.8 30.7 1.0
OG A:SER382 4.8 24.2 1.0
HB3 A:ARG520 4.8 24.3 1.0
O1 A:GOL608 4.9 69.5 1.0
HE A:ARG431 4.9 33.9 1.0
CG A:ARG520 4.9 23.8 1.0
HD3 A:ARG507 4.9 47.4 1.0
HG2 A:GLU381 4.9 26.8 1.0
HG2 A:PRO340 4.9 34.7 1.0
C2 A:GOL608 4.9 52.4 1.0
CZ A:ARG507 4.9 43.6 1.0
HB2 A:PRO340 4.9 23.8 1.0
O A:HOH810 5.0 31.0 1.0

Sodium binding site 4 out of 4 in 6y8z

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Sodium binding site 4 out of 4 in the Structure of Baltic Herring (Clupea Harengus) Phosphoglucomutase 5 (PGM5)


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) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:46.8
occ:1.00
OE2 A:GLU191 2.3 56.5 1.0
HH11 A:ARG89 2.3 52.2 1.0
HH21 A:ARG176 2.8 60.2 1.0
NH1 A:ARG89 3.0 43.5 1.0
HD3 A:ARG189 3.1 49.1 1.0
HD3 A:ARG89 3.1 30.9 1.0
HH12 A:ARG89 3.2 52.2 1.0
HD2 A:ARG89 3.3 30.9 1.0
HH11 A:ARG189 3.4 64.3 1.0
HG3 A:GLU191 3.4 57.9 1.0
HD2 A:ARG189 3.4 49.1 1.0
CD A:GLU191 3.4 55.7 1.0
NH2 A:ARG176 3.5 50.2 1.0
CD A:ARG89 3.6 25.7 1.0
CD A:ARG189 3.7 40.9 1.0
CG A:GLU191 3.8 48.2 1.0
HH22 A:ARG176 3.8 60.2 1.0
CZ A:ARG89 3.9 38.2 1.0
HE A:ARG176 3.9 66.7 1.0
HG2 A:GLU191 4.0 57.9 1.0
NE A:ARG89 4.1 36.0 1.0
HG2 A:ARG189 4.2 37.0 1.0
NH1 A:ARG189 4.2 53.6 1.0
CZ A:ARG176 4.3 56.7 1.0
NE A:ARG176 4.4 55.6 1.0
OE1 A:GLU191 4.5 57.1 1.0
CG A:ARG189 4.5 30.9 1.0
HH12 A:ARG189 4.7 64.3 1.0
NE A:ARG189 4.7 52.6 1.0
HE A:ARG89 4.9 43.2 1.0
CZ A:ARG189 4.9 59.8 1.0
CG A:ARG89 5.0 30.6 1.0
HG3 A:ARG89 5.0 36.6 1.0
NH2 A:ARG89 5.0 31.5 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 13:13:50 2020

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