Sodium in PDB 2iwk: Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution

All present enzymatic activity of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution:
1.7.99.6;

The structure of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution, PDB code: 2iwk was solved by K.Paraskevopoulos, S.V.Antonyuk, R.G.Sawers, R.R.Eady, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.7
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.114, 120.913, 137.343, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / 20.7

The structure of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution also contains other interesting chemical elements:

Iodine	(I)	15 atoms
Copper	(Cu)	12 atoms
Chlorine	(Cl)	8 atoms
Calcium	(Ca)	28 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30;

Binding sites:

The binding sites of Sodium atom in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution (pdb code 2iwk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 30 binding sites of Sodium where determined in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution, PDB code: 2iwk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1625 b:34.2 occ:1.00 OD1 A:ASN167 2.7 21.6 1.0 NA A:NA1627 2.7 32.7 1.0 N A:GLY169 2.9 27.2 1.0 CB A:MET172 3.3 26.4 1.0 CA A:GLY169 3.4 26.9 1.0 N A:ASP168 3.5 26.2 1.0 CA A:ASN167 3.5 25.4 1.0 C A:ASN167 3.6 25.9 1.0 CA A:MET172 3.6 26.0 1.0 N A:MET172 3.7 26.9 1.0 CG A:ASN167 3.8 24.9 1.0 CA B:GLY572 3.8 22.1 1.0 C A:GLY169 3.8 27.0 1.0 N A:SER170 4.0 26.8 1.0 CG A:PRO164 4.1 26.6 1.0 C A:ASP168 4.1 27.6 1.0 N B:VAL573 4.2 21.1 1.0 O A:VAL166 4.2 27.7 1.0 CB A:ASN167 4.2 25.2 1.0 O A:ASN167 4.3 25.3 1.0 CG A:MET172 4.3 25.4 1.0 N A:THR171 4.4 26.0 1.0 CA A:ASP168 4.4 27.6 1.0 C B:GLY572 4.4 21.9 1.0 C A:THR171 4.5 26.8 1.0 CD A:PRO164 4.5 26.0 1.0 OD1 A:ASP168 4.5 30.4 1.0 CB A:PRO164 4.5 25.9 1.0 O A:GLY169 4.6 27.9 1.0 N A:ASN167 4.7 26.2 1.0 CG1 B:VAL573 4.7 22.1 1.0 N B:GLY572 4.8 21.8 1.0 SD A:MET172 4.8 25.6 1.0 C A:VAL166 4.9 28.2 1.0 ND2 A:ASN167 4.9 26.0 1.0 OG1 A:THR171 5.0 24.7 1.0

Sodium binding site 2 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1626 b:35.4 occ:1.00 N A:LEU441 3.1 21.5 1.0 CB A:LEU441 3.7 22.5 1.0 CD1 A:LEU383 3.8 26.2 1.0 CA A:VAL440 3.9 23.0 1.0 CA A:LEU441 4.0 22.6 1.0 C A:VAL440 4.0 22.0 1.0 CG1 A:VAL440 4.3 24.3 1.0 O A:LEU441 4.3 24.5 1.0 O A:MET439 4.6 24.7 1.0 CB A:VAL440 4.7 23.3 1.0 C A:LEU441 4.7 22.7 1.0

Sodium binding site 3 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1627 b:32.7 occ:1.00 NA A:NA1625 2.7 34.2 1.0 O A:VAL166 2.8 27.7 1.0 OG1 A:THR171 2.9 24.7 1.0 N A:THR171 3.1 26.0 1.0 OG A:SER170 3.5 26.5 1.0 OD1 A:ASP168 3.6 30.4 1.0 CB A:PRO164 3.6 25.9 1.0 O A:HOH2131 3.7 38.7 1.0 N A:SER170 3.7 26.8 1.0 CA A:THR171 3.7 26.3 1.0 CB A:THR171 3.7 27.2 1.0 CG A:PRO164 3.8 26.6 1.0 C A:THR171 3.9 26.8 1.0 N A:MET172 3.9 26.9 1.0 C A:VAL166 3.9 28.2 1.0 N A:ASP168 4.0 26.2 1.0 C A:SER170 4.1 26.7 1.0 CA A:ASN167 4.1 25.4 1.0 CG2 A:THR171 4.2 27.7 1.0 N A:GLY169 4.2 27.2 1.0 CA A:SER170 4.3 26.8 1.0 C A:GLY169 4.4 27.0 1.0 CB A:SER170 4.4 27.3 1.0 N A:ASN167 4.5 26.2 1.0 C A:ASN167 4.5 25.9 1.0 CA A:MET172 4.6 26.0 1.0 O A:THR171 4.6 26.0 1.0 CA A:GLY169 4.7 26.9 1.0 CG A:ASP168 4.8 30.3 1.0 OD1 A:ASN167 4.8 21.6 1.0 CD A:PRO164 4.9 26.0 1.0 O A:HOH2128 5.0 28.2 1.0 C A:ASP168 5.0 27.6 1.0

Sodium binding site 4 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1628 b:48.3 occ:1.00 O A:HOH2348 2.4 29.8 1.0 O A:HOH2037 3.2 25.4 1.0 O A:ASN61 3.8 17.4 1.0 CB A:GLU478 3.9 25.5 1.0 CD A:ARG65 4.1 22.0 0.5 CG A:GLU478 4.1 29.1 1.0 CB A:ASN61 4.2 18.4 1.0 CB A:ARG65 4.2 20.0 1.0 C A:ASN61 4.3 19.0 1.0 O A:HOH2042 4.4 24.9 1.0 O A:HOH2047 4.4 46.7 1.0 CG A:ARG65 4.6 21.9 1.0 CA A:ASN61 4.7 18.3 1.0 O A:HOH2414 4.8 23.5 1.0 N A:GLU62 5.0 18.9 1.0

Sodium binding site 5 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1629 b:33.1 occ:1.00 O A:HOH2257 2.5 27.3 1.0 O A:GLY397 3.1 21.3 1.0 C A:GLY397 3.1 19.8 1.0 N A:PHE343 3.2 18.8 1.0 CA A:GLY397 3.4 20.3 1.0 CA A:ALA342 3.5 18.5 1.0 CD1 A:PHE343 3.6 22.4 1.0 OG1 A:THR394 3.6 21.9 1.0 CB A:ALA342 3.8 18.2 1.0 N A:GLU398 3.8 20.6 1.0 CD A:LYS393 3.8 26.0 1.0 C A:ALA342 3.8 18.1 1.0 CG A:GLU398 4.0 25.8 1.0 CB A:PHE343 4.2 19.4 1.0 O A:PHE343 4.2 19.2 1.0 CA A:PHE343 4.2 19.5 1.0 CG A:PHE343 4.3 19.5 1.0 CA A:GLU398 4.4 21.3 1.0 CE1 A:PHE343 4.5 20.9 1.0 N A:GLY397 4.5 19.5 1.0 O A:THR341 4.6 18.4 1.0 C A:PHE343 4.7 19.1 1.0 N A:THR394 4.7 20.2 1.0 CE A:LYS393 4.7 27.9 1.0 CG A:LYS393 4.8 22.6 1.0 N A:ALA342 4.8 18.9 1.0 CB A:GLU398 4.9 22.9 1.0 CB A:THR394 5.0 20.0 1.0 CD A:GLU398 5.0 30.2 1.0

Sodium binding site 6 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1630 b:21.4 occ:1.00 O A:ILE66 2.6 19.1 1.0 O A:HOH2112 2.7 16.5 1.0 NE A:ARG69 2.8 18.4 1.0 N A:ILE132 3.0 18.7 1.0 O A:ILE132 3.2 16.9 1.0 C A:ILE66 3.5 19.5 1.0 CB A:ARG69 3.5 20.4 1.0 CD A:ARG69 3.5 21.8 1.0 CA A:ALA131 3.5 19.1 1.0 CA A:ILE66 3.7 19.0 1.0 CZ A:ARG69 3.7 20.0 1.0 NH2 A:ARG69 3.7 20.5 1.0 CG2 A:ILE66 3.8 20.7 1.0 C A:ALA131 3.8 18.9 1.0 CA A:ILE132 3.9 17.5 1.0 C A:ILE132 4.0 17.6 1.0 CA A:CA1619 4.0 37.2 1.0 CG A:ARG69 4.1 21.4 1.0 CB A:ALA131 4.1 19.7 1.0 CB A:ILE66 4.2 18.8 1.0 CB A:ILE132 4.3 18.2 1.0 O A:HOH2040 4.4 23.4 1.0 O A:ASP130 4.5 19.7 1.0 CG1 A:ILE66 4.7 20.0 1.0 N A:ALA131 4.7 19.6 1.0 O A:ARG65 4.7 19.7 1.0 N A:HIS67 4.7 18.9 1.0 CA A:ARG69 4.8 20.8 1.0 N A:ARG69 4.8 20.2 1.0 O A:HOH2033 4.8 29.5 1.0 N A:ILE66 4.9 19.3 1.0 NH1 A:ARG69 5.0 22.6 1.0

Sodium binding site 7 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1631 b:23.9 occ:1.00 O A:HOH2144 2.7 25.9 1.0 O A:SER152 2.8 18.8 1.0 NH2 A:ARG107 2.9 27.1 1.0 NH1 A:ARG107 3.4 27.1 1.0 CB A:SER152 3.5 18.0 1.0 CZ A:ARG107 3.6 28.0 1.0 C A:SER152 3.7 17.8 1.0 CB A:ALA187 3.8 19.2 1.0 NH2 A:ARG151 3.9 28.3 1.0 CB A:SER98 3.9 18.6 1.0 CZ A:PHE110 4.0 16.5 1.0 CA A:SER152 4.0 17.9 1.0 OD1 A:ASP188 4.3 27.2 1.0 CZ A:ARG151 4.3 24.9 1.0 NH1 A:ARG151 4.5 25.3 1.0 N A:SER152 4.5 17.0 1.0 CD1 A:TYR108 4.5 21.5 1.0 OG A:SER152 4.6 19.7 1.0 CE1 A:PHE110 4.8 15.8 1.0 O A:ALA187 4.8 24.1 1.0 N A:ASN153 4.8 17.9 1.0 OG A:SER98 4.9 19.8 1.0 CA A:SER98 4.9 17.5 1.0 C A:ALA187 4.9 21.2 1.0 CE2 A:PHE110 4.9 17.4 1.0 NE A:ARG107 4.9 24.5 1.0 CA A:ALA187 4.9 19.3 1.0

Sodium binding site 8 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1632 b:25.7 occ:1.00 O A:HOH2036 2.8 17.1 1.0 O A:HOH2413 2.8 19.1 1.0 OE1 A:GLU62 2.9 20.3 1.0 O A:HOH2409 3.0 26.3 1.0 OG A:SER562 3.4 26.8 1.0 CB A:SER562 3.4 21.2 1.0 CD A:GLU62 3.6 20.4 1.0 CB A:GLU62 3.7 19.3 1.0 CB A:THR60 3.8 19.7 1.0 CA A:SER562 3.8 20.1 1.0 CG A:GLU62 3.8 22.5 1.0 OG1 A:THR60 3.8 20.2 1.0 CG2 A:THR60 3.9 20.9 1.0 NE2 A:GLN560 4.0 21.0 1.0 O A:HOH2034 4.4 25.6 1.0 N A:SER563 4.4 20.9 1.0 O A:THR561 4.5 19.2 1.0 O A:HOH2410 4.6 28.2 1.0 OE2 A:GLU62 4.7 24.2 1.0 C A:SER562 4.7 19.7 1.0 CD2 A:LEU475 4.8 29.9 1.0 N A:GLU62 4.9 18.9 1.0 CA A:GLU62 4.9 19.4 1.0 N A:SER562 4.9 19.4 1.0 CD A:GLN560 5.0 19.0 1.0

Sodium binding site 9 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1633 b:39.0 occ:1.00 OD1 A:ASN570 2.6 27.9 1.0 CG A:ASN570 3.5 24.3 1.0 CD A:PRO571 3.9 22.3 1.0 CB A:ASN570 3.9 22.7 1.0 CD B:LYS77 4.1 31.4 1.0 CG B:LYS74 4.2 33.3 1.0 CE B:LYS77 4.2 34.1 1.0 CA A:ASN570 4.2 22.4 1.0 NZ B:LYS77 4.3 36.5 1.0 ND2 A:ASN570 4.6 26.4 1.0 CD B:LYS74 4.8 36.0 1.0 N A:PRO571 4.8 22.9 1.0 O A:ALA569 4.9 22.3 1.0 CG A:PRO571 4.9 24.3 1.0

Sodium binding site 10 out of 30 in the Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Inhibitor-Bound Form of Nitrous Oxide Reductase From Achromobacter Cycloclastes at 1.7 Angstrom Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1634 b:24.2 occ:1.00 O A:VAL488 3.5 26.0 1.0 C A:VAL488 3.8 24.9 1.0 O A:HOH2356 4.1 25.4 1.0 CA A:ASP489 4.1 25.2 1.0 N A:ASP489 4.1 24.9 1.0 CG A:GLU484 4.1 28.2 1.0 CA A:GLU484 4.2 25.5 1.0 CB A:ASP489 4.3 25.4 1.0 O A:HOH2353 4.4 28.3 1.0 N A:VAL488 4.4 24.0 1.0 C A:GLU487 4.6 24.7 1.0 CB A:GLU484 4.7 25.9 1.0 CA A:VAL488 4.7 24.7 1.0 O A:GLU484 4.9 24.9 1.0 CG A:ASP489 4.9 29.1 1.0 N A:GLU484 4.9 24.7 1.0 O A:ALA483 4.9 23.3 1.0 CA A:GLU487 5.0 25.2 1.0

K.Paraskevopoulos, S.V.Antonyuk, R.G.Sawers, R.R.Eady, S.S.Hasnain. Insight Into Catalysis of Nitrous Oxide Reductase From High-Resolution Structures of Resting and Inhibitor-Bound Enzyme From Achromobacter Cycloclastes. J.Mol.Biol. V. 362 55 2006.
ISSN: ISSN 0022-2836
PubMed: 16904686
DOI: 10.1016/J.JMB.2006.06.064