Sodium in PDB 2wqt: Dodecahedral Assembly of Mhpd

All present enzymatic activity of Dodecahedral Assembly of Mhpd:
4.2.1.80;

The structure of Dodecahedral Assembly of Mhpd, PDB code: 2wqt was solved by M.G.Montgomery, S.P.Wood, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.26 / 2.80
Space group	H 3 1
Cell size a, b, c (Å), α, β, γ (°)	207.350, 207.350, 545.471, 90.00, 90.00, 120.00
R / Rfree (%)	22.194 / 23.382

The structure of Dodecahedral Assembly of Mhpd also contains other interesting chemical elements:

Potassium

(K)

20 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Sodium atom in the Dodecahedral Assembly of Mhpd (pdb code 2wqt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 20 binding sites of Sodium where determined in the Dodecahedral Assembly of Mhpd, PDB code: 2wqt:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1265 b:22.9 occ:1.00 OD2 A:ASP49 3.1 40.8 1.0 OD1 A:ASP49 3.8 42.9 1.0 CG A:ASP49 3.9 38.2 1.0 CG A:ARG14 4.3 30.5 1.0 NH1 A:ARG54 4.6 21.8 1.0 CB A:ASN45 4.6 29.7 1.0 CD A:ARG14 4.7 32.8 1.0 O A:ASN45 4.7 30.2 1.0 CG A:ASN45 4.9 28.6 1.0 CA A:ARG14 5.0 29.7 1.0

Sodium binding site 2 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1310 b:24.3 occ:1.00 OD2 C:ASP49 3.5 40.8 1.0 O M:HOH2002 3.7 16.4 1.0 CE1 M:HIS4 4.3 33.6 1.0 OD1 C:ASP49 4.3 42.9 1.0 CG C:ASP49 4.3 38.2 1.0 NE2 M:HIS4 4.5 32.9 1.0 CG C:ARG14 4.5 30.5 1.0 NH1 C:ARG54 4.6 21.9 1.0 CB C:ALA17 4.8 34.4 1.0 CA C:ARG14 4.9 29.8 1.0

Sodium binding site 3 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1304 b:18.3 occ:1.00 OD2 D:ASP49 3.5 40.8 1.0 OD1 D:ASP49 4.2 42.9 1.0 CG D:ASP49 4.3 38.2 1.0 CG D:ARG14 4.4 30.6 1.0 CB D:ALA17 4.7 34.4 1.0 CA D:ARG14 4.7 29.8 1.0 NH1 D:ARG54 4.8 21.7 1.0 CD D:ARG14 5.0 32.8 1.0

Sodium binding site 4 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1311 b:17.9 occ:1.00 OD2 E:ASP49 3.3 40.9 1.0 CG E:ASP49 4.2 38.3 1.0 OD1 E:ASP49 4.2 42.9 1.0 CE1 F:HIS4 4.3 33.6 1.0 NE2 F:HIS4 4.4 32.9 1.0 NH1 E:ARG54 4.4 21.8 1.0 CG E:ARG14 4.6 30.6 1.0 CB E:ALA17 5.0 34.4 1.0

Sodium binding site 5 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ F:Na1312 b:26.2 occ:1.00 O N:HOH2001 3.5 19.2 1.0 OD2 F:ASP49 3.5 40.8 1.0 CE1 N:HIS4 4.1 33.6 1.0 OD1 F:ASP49 4.1 42.9 1.0 CG F:ASP49 4.2 38.3 1.0 CG F:ARG14 4.4 30.5 1.0 NE2 N:HIS4 4.4 33.0 1.0 NH1 F:ARG54 4.7 21.9 1.0 CA F:ARG14 4.8 29.8 1.0 CB F:ALA17 4.9 34.4 1.0 CD F:ARG14 4.9 32.8 1.0

Sodium binding site 6 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1313 b:18.6 occ:1.00 OD2 G:ASP49 3.5 40.9 1.0 OD1 G:ASP49 4.2 42.9 1.0 CG G:ARG14 4.3 30.5 1.0 CG G:ASP49 4.3 38.3 1.0 CE1 B:HIS4 4.4 33.6 1.0 O B:HOH2001 4.5 13.4 1.0 NE2 B:HIS4 4.7 33.0 1.0 CA G:ARG14 4.8 29.8 1.0 NH1 G:ARG54 4.8 21.8 1.0 CD G:ARG14 4.9 32.8 1.0 CB G:ALA17 4.9 34.4 1.0 CB G:ASN45 4.9 29.6 1.0 CB G:ARG14 5.0 29.6 1.0

Sodium binding site 7 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ I:Na1306 b:32.6 occ:1.00 OD2 I:ASP49 3.3 40.9 1.0 OD1 I:ASP49 4.1 42.8 1.0 CG I:ASP49 4.1 38.3 1.0 O R:HOH2001 4.4 18.6 1.0 CE1 R:HIS4 4.5 33.6 1.0 CG I:ARG14 4.5 30.5 1.0 NH1 I:ARG54 4.5 21.8 1.0 NE2 R:HIS4 4.7 33.0 1.0 CA I:ARG14 5.0 29.8 1.0 CB I:ALA17 5.0 34.4 1.0

Sodium binding site 8 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ K:Na1305 b:21.5 occ:1.00 OD2 K:ASP49 3.4 40.8 1.0 O I:HOH2001 3.6 22.0 1.0 OD1 K:ASP49 4.1 43.0 1.0 CE1 I:HIS4 4.1 33.5 1.0 CG K:ASP49 4.2 38.3 1.0 CG K:ARG14 4.4 30.5 1.0 NE2 I:HIS4 4.4 33.0 1.0 NH1 K:ARG54 4.7 21.9 1.0 CA K:ARG14 4.8 29.8 1.0 CB K:ALA17 4.9 34.5 1.0 CD K:ARG14 4.9 32.8 1.0 CB K:ASN45 5.0 29.7 1.0

Sodium binding site 9 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ L:Na1314 b:21.6 occ:1.00 O T:HOH2001 3.3 12.0 1.0 OD2 L:ASP49 3.4 40.8 1.0 CE1 T:HIS4 4.1 33.5 1.0 OD1 L:ASP49 4.2 42.9 1.0 CG L:ASP49 4.2 38.2 1.0 NE2 T:HIS4 4.4 32.9 1.0 CG L:ARG14 4.4 30.5 1.0 NH1 L:ARG54 4.6 21.8 1.0 CB L:ALA17 4.8 34.4 1.0 CA L:ARG14 4.9 29.8 1.0 CD L:ARG14 5.0 32.8 1.0

Sodium binding site 10 out of 20 in the Dodecahedral Assembly of Mhpd


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Dodecahedral Assembly of Mhpd within 5.0Å range: probe atom residue distance (Å) B Occ L:Na1319 b:18.4 occ:1.00 O L:HOH2002 3.5 13.9 1.0 CE1 L:HIS4 4.5 33.5 1.0 NE2 L:HIS4 4.7 33.0 1.0

M.G.Montgomery, A.R.Coker, I.A.Taylor, S.P.Wood. Assembly of A 20NM Protein Cage By Escherichia Coli 2-Hydroxypentadienoic Acid Hydratase (Mhpd). J.Mol.Biol. V. 396 1379 2010.
ISSN: ISSN 0022-2836
PubMed: 20053352
DOI: 10.1016/J.JMB.2009.12.056