Sodium in PDB 3m1a: The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A

The structure of The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A, PDB code: 3m1a was solved by A.J.Stein, E.Evdokimova, O.Egorova, A.Savchenko, A.Joachimiak, Midwestcenter For Structural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.55 / 2.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	136.638, 202.779, 106.339, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The binding sites of Sodium atom in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A (pdb code 3m1a). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A, PDB code: 3m1a:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na282 b:28.9 occ:1.00 NE2 A:GLN215 2.9 58.7 1.0 O C:HOH913 3.1 42.9 1.0 CG C:GLN215 3.8 61.1 1.0 CD A:ARG211 3.9 34.6 1.0 CZ C:PHE196 3.9 26.9 1.0 CD A:GLN215 4.0 55.3 1.0 CB C:ALA194 4.0 23.9 1.0 CE2 C:PHE196 4.0 21.8 1.0 OE1 A:GLN215 4.2 57.4 1.0 CA C:GLN215 4.4 62.3 1.0 CB C:GLN215 4.4 62.6 1.0 NE2 C:GLN215 4.5 65.0 1.0 CD C:GLN215 4.6 62.1 1.0 CD2 A:PHE196 4.6 23.8 1.0 O C:VAL214 4.7 63.5 1.0 CG A:ARG211 4.7 30.0 1.0 CG A:PHE196 4.8 23.6 1.0 NE A:ARG211 5.0 37.0 1.0

Sodium binding site 2 out of 4 in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A within 5.0Å range: probe atom residue distance (Å) B Occ B:Na282 b:20.2 occ:1.00 O B:HOH586 3.0 31.8 1.0 N B:VAL60 3.1 21.7 1.0 NE B:ARG37 3.3 38.7 1.0 O B:HOH546 3.5 28.7 1.0 CB B:VAL60 3.7 24.4 1.0 NH1 B:ARG37 3.7 38.5 1.0 CD2 B:LEU109 3.8 24.6 1.0 CA B:ASP59 3.8 23.3 1.0 OD1 B:ASP59 3.9 27.4 1.0 CZ B:ARG37 3.9 39.9 1.0 C B:ASP59 3.9 22.5 1.0 CA B:VAL60 4.0 22.9 1.0 O B:LEU58 4.0 23.1 1.0 CG B:ARG37 4.1 33.7 1.0 O B:HOH422 4.2 29.4 1.0 O B:HOH383 4.2 26.1 1.0 CB B:ALA87 4.2 22.7 1.0 CD B:ARG37 4.3 37.4 1.0 CG2 B:VAL60 4.5 24.2 1.0 CG B:ASP59 4.5 26.2 1.0 CG1 B:VAL60 4.5 26.4 1.0 CB B:ASP59 4.7 25.0 1.0 N B:THR61 4.7 22.8 1.0 N B:ASP59 4.8 23.5 1.0 C B:LEU58 4.8 23.0 1.0 O B:HOH333 4.8 31.5 1.0 C B:VAL60 4.8 22.9 1.0

Sodium binding site 3 out of 4 in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A within 5.0Å range: probe atom residue distance (Å) B Occ D:Na282 b:28.9 occ:1.00 O D:HOH857 2.4 46.6 1.0 O D:HOH428 2.4 31.3 1.0 O D:LYS227 2.8 34.8 1.0 O E:HOH471 3.4 26.8 1.0 N D:ALA231 3.4 23.6 1.0 CB D:ALA230 3.7 27.5 1.0 C D:LYS227 3.8 33.8 1.0 CB D:ALA231 3.9 23.3 1.0 CA D:ALA231 3.9 24.2 1.0 C D:ALA230 4.0 24.5 1.0 CA D:LYS227 4.2 33.5 1.0 CG2 E:THR276 4.3 27.4 1.0 CA D:ALA230 4.4 26.0 1.0 O D:HOH969 4.4 38.9 1.0 CB D:LYS227 4.4 35.1 1.0 O D:ALA230 4.7 25.0 1.0 N D:ALA230 4.9 25.3 1.0 CG D:LYS227 5.0 37.3 1.0 N D:ALA228 5.0 23.6 1.0

Sodium binding site 4 out of 4 in the The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A within 5.0Å range: probe atom residue distance (Å) B Occ E:Na282 b:25.4 occ:1.00 NZ E:LYS191 2.8 52.9 1.0 NE2 B:GLN215 3.1 36.7 1.0 CE E:LYS191 3.4 51.6 1.0 CB E:ALA194 3.7 22.4 1.0 CZ E:PHE196 4.0 21.9 1.0 CD B:GLN215 4.0 37.1 1.0 CE2 E:PHE196 4.1 20.4 1.0 CD B:ARG211 4.1 52.3 1.0 OE1 B:GLN215 4.1 39.0 1.0 CG E:GLN215 4.2 40.1 1.0 O E:VAL214 4.2 36.6 1.0 CA E:GLN215 4.5 38.1 1.0 CB E:GLN215 4.8 40.4 1.0 CG B:ARG211 4.9 47.1 1.0 CD E:LYS191 4.9 45.0 1.0 C E:VAL214 4.9 33.9 1.0 NH2 B:ARG211 5.0 63.3 1.0 N E:GLN215 5.0 34.1 1.0

A.J.Stein, E.Evdokimova, O.Egorova, A.Savchenko, A.Joachimiak. The Crystal Structure of A Short-Chain Dehydrogenase From Streptomyces Avermitilis to 2A To Be Published.