Sodium in PDB 1nvj: Deletion Mutant (Delta 141) of Molybdopterin Synthase

The structure of Deletion Mutant (Delta 141) of Molybdopterin Synthase, PDB code: 1nvj was solved by M.J.Rudolph, M.M.Wuebbens, O.Turque, K.V.Rajagopalan, H.Schindelin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.14 / 2.15
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	104.128, 127.832, 138.118, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 22.7

The binding sites of Sodium atom in the Deletion Mutant (Delta 141) of Molybdopterin Synthase (pdb code 1nvj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Deletion Mutant (Delta 141) of Molybdopterin Synthase, PDB code: 1nvj:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Deletion Mutant (Delta 141) of Molybdopterin Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Deletion Mutant (Delta 141) of Molybdopterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na141 b:44.2 occ:1.00 O B:GLY91 2.4 29.9 1.0 O B:HOH169 2.4 39.1 1.0 O A:HOH176 2.4 44.5 1.0 O A:HOH161 2.4 36.1 1.0 O A:HOH175 2.6 46.6 1.0 C B:GLY91 3.4 29.3 1.0 CE B:LYS37 3.8 35.2 1.0 CA B:GLY91 4.0 30.5 1.0 NZ B:LYS37 4.1 37.2 1.0 O A:ALA23 4.2 35.8 1.0 OD1 A:ASP26 4.3 39.2 1.0 O B:HOH188 4.4 50.9 1.0 N B:ASP92 4.5 29.4 1.0 O A:GLU24 4.5 39.9 1.0 O A:HOH166 4.7 43.7 1.0 CG B:GLU93 4.7 33.8 1.0 CD B:LYS37 4.7 34.3 1.0 CA B:ASP92 4.8 28.2 1.0 O A:HOH169 4.8 47.4 1.0 CG B:LYS37 4.9 30.3 1.0 OE2 B:GLU93 5.0 43.8 1.0

Sodium binding site 2 out of 4 in the Deletion Mutant (Delta 141) of Molybdopterin Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Deletion Mutant (Delta 141) of Molybdopterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na141 b:32.3 occ:1.00 O C:HOH143 2.4 24.4 1.0 O D:GLY91 2.4 28.1 1.0 O C:HOH144 2.5 28.3 1.0 O D:HOH158 2.5 36.1 1.0 O D:HOH156 2.5 29.0 1.0 O C:HOH158 2.7 28.3 1.0 NA D:NA142 3.3 39.7 1.0 C D:GLY91 3.4 27.5 1.0 CE D:LYS37 3.7 25.9 1.0 CA D:GLY91 3.9 28.5 1.0 O C:ALA23 3.9 28.6 1.0 NZ D:LYS37 4.2 25.8 1.0 O C:HOH166 4.2 26.6 1.0 O C:HOH160 4.4 35.1 1.0 OE2 D:GLU93 4.4 34.1 1.0 CG D:GLU93 4.5 29.2 1.0 O C:GLU24 4.5 29.1 1.0 N D:ASP92 4.5 27.0 1.0 OD1 C:ASP26 4.5 30.0 1.0 O C:HOH167 4.6 29.1 1.0 O D:HOH171 4.7 28.9 1.0 CD D:LYS37 4.7 24.8 1.0 O D:HOH154 4.8 27.2 1.0 O D:HOH217 4.8 41.0 1.0 CD D:GLU93 4.8 30.8 1.0 CA D:ASP92 4.8 26.5 1.0

Sodium binding site 3 out of 4 in the Deletion Mutant (Delta 141) of Molybdopterin Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Deletion Mutant (Delta 141) of Molybdopterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na142 b:39.7 occ:1.00 O C:HOH177 2.4 33.9 1.0 O D:HOH199 2.4 24.4 0.5 O D:HOH156 2.5 29.0 1.0 O D:HOH158 2.6 36.1 1.0 O C:HOH158 2.6 28.3 1.0 NA D:NA141 3.3 32.3 1.0 O D:HOH211 3.8 44.6 1.0 O C:HOH166 4.1 26.6 1.0 O D:HOH177 4.2 36.5 1.0 O D:HOH154 4.4 27.2 1.0 O C:HOH186 4.4 49.0 1.0 O C:HOH160 4.5 35.1 1.0 O C:HOH167 4.7 29.1 1.0 O D:HOH217 4.7 41.0 1.0 O D:HOH171 4.8 28.9 1.0 O D:GLY91 4.8 28.1 1.0 O C:HOH143 4.9 24.4 1.0

Sodium binding site 4 out of 4 in the Deletion Mutant (Delta 141) of Molybdopterin Synthase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Deletion Mutant (Delta 141) of Molybdopterin Synthase within 5.0Å range: probe atom residue distance (Å) B Occ F:Na141 b:50.0 occ:1.00 O E:HOH154 2.3 34.7 1.0 O F:HOH168 2.4 46.0 1.0 O F:HOH183 2.5 49.1 1.0 O F:GLY91 2.5 42.1 1.0 O A:HOH193 2.7 54.4 1.0 C F:GLY91 3.3 42.6 1.0 CA F:GLY91 3.6 44.1 1.0 CE F:LYS37 3.8 45.0 1.0 OD1 E:ASP26 4.2 51.9 1.0 O E:ALA23 4.2 45.4 1.0 O E:GLU24 4.3 48.4 1.0 O F:HOH173 4.3 55.6 1.0 O E:HOH161 4.4 43.6 1.0 N F:ASP92 4.5 42.2 1.0 NZ F:LYS37 4.5 46.5 1.0 CA F:ASP92 4.9 42.2 1.0 CD F:LYS37 4.9 43.9 1.0 O E:HOH155 5.0 43.9 1.0

M.J.Rudolph, M.M.Wuebbens, O.Turque, K.V.Rajagopalan, H.Schindelin. Structural Studies of Molybdopterin Synthase Provide Insights Into Its Catalytic Mechanism J.Biol.Chem. V. 278 14514 2003.
ISSN: ISSN 0021-9258
PubMed: 12571227
DOI: 10.1074/JBC.M300449200