Sodium in PDB 4n3p: Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396

The structure of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396, PDB code: 4n3p was solved by A.Kuzin, S.Lew, S.Rajagopalan, J.Seetharaman, L.Mao, R.Xiao, S.Kogan, M.Maglaqui, J.K.Everett, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.74 / 2.50
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	73.119, 73.119, 163.975, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 25.3

The structure of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 (pdb code 4n3p). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 18 binding sites of Sodium where determined in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396, PDB code: 4n3p:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:57.9 occ:1.00 O A:MSE77 2.5 44.2 1.0 OE1 A:GLN180 2.9 51.5 1.0 CG A:GLN180 3.1 47.5 1.0 CD A:GLN180 3.4 43.5 1.0 C A:MSE77 3.5 41.2 1.0 CA A:ALA78 3.7 36.1 1.0 CB A:GLN180 3.7 46.3 1.0 O A:HOH618 3.9 32.9 1.0 N A:ALA78 4.0 40.7 1.0 CB A:ALA78 4.0 37.7 1.0 CG A:MSE77 4.1 48.8 1.0 CA A:GLY105 4.5 35.1 1.0 CA A:MSE77 4.6 37.2 1.0 CA A:GLN180 4.6 46.1 1.0 NE2 A:GLN180 4.7 34.4 1.0 C A:GLY105 4.7 45.0 1.0 CB A:MSE77 4.7 36.5 1.0 O A:GLY105 4.8 49.1 1.0 C A:ALA78 4.9 36.0 1.0

Sodium binding site 2 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:55.2 occ:1.00 O A:GLY36 2.7 39.1 1.0 O A:GLY31 2.8 31.8 1.0 OG1 A:THR38 2.8 41.2 1.0 CA A:GLY225 3.4 37.7 1.0 CB A:ALA34 3.5 31.1 1.0 CB A:THR38 3.6 29.2 1.0 C A:GLY36 3.6 44.4 1.0 C A:GLY31 3.7 32.4 1.0 N A:THR38 3.7 42.4 1.0 CA A:GLY74 3.8 45.8 1.0 N A:GLY74 3.8 32.5 1.0 CA A:GLY31 3.9 30.1 1.0 C A:GLU37 3.9 43.4 1.0 N A:GLY225 4.0 32.1 1.0 C A:ALA34 4.0 42.4 1.0 O A:ALA34 4.0 47.7 1.0 CA A:THR38 4.2 30.0 1.0 O A:GLU35 4.2 34.2 1.0 N A:GLU37 4.2 44.3 1.0 CA A:ALA34 4.2 34.0 1.0 CA A:GLU37 4.2 45.0 1.0 O A:VAL72 4.3 32.9 1.0 C A:GLU35 4.3 41.1 1.0 O A:GLU37 4.4 46.8 1.0 N A:GLU35 4.4 45.5 1.0 N A:GLY36 4.5 39.1 1.0 CA A:GLY36 4.6 35.0 1.0 O A:PHE30 4.6 34.1 1.0 N A:ALA34 4.6 38.9 1.0 C A:GLY225 4.7 39.8 1.0 CA A:GLU35 4.8 45.4 1.0 CG2 A:THR38 4.9 28.3 1.0 C A:THR224 4.9 41.5 1.0 N A:GLN226 4.9 39.7 1.0 N A:SER32 4.9 33.9 1.0 CE1 A:PHE204 5.0 29.4 1.0

Sodium binding site 3 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:45.1 occ:1.00 O A:GLY258 2.7 36.8 1.0 O A:HOH601 2.8 26.2 1.0 OE2 A:GLU260 2.9 35.6 1.0 NA A:NA504 2.9 49.4 1.0 C A:GLY258 3.4 36.8 1.0 CG A:LEU263 3.5 36.0 1.0 CD2 A:LEU263 3.5 39.6 1.0 CG A:GLU260 3.5 31.8 1.0 CA A:GLY258 3.5 25.9 1.0 N A:GLY258 3.6 26.2 1.0 CD A:GLU260 3.6 38.8 1.0 CG1 A:ILE234 3.7 34.2 1.0 CB A:LEU263 3.7 35.7 1.0 CA A:ILE234 4.2 33.8 1.0 CB A:ILE234 4.5 26.1 1.0 CG1 A:VAL257 4.5 27.6 1.0 O A:GLY232 4.5 25.1 1.0 N A:ILE259 4.6 33.1 1.0 N A:GLU260 4.6 31.7 1.0 C A:VAL257 4.6 30.6 1.0 O A:ASP233 4.7 36.0 1.0 N A:LEU263 4.7 30.4 1.0 CD1 A:ILE234 4.8 29.8 1.0 OE1 A:GLU260 4.8 41.4 1.0 N A:ILE234 4.8 35.4 1.0 CA A:LEU263 4.9 38.4 1.0 CB A:GLU260 4.9 30.8 1.0 CD1 A:LEU263 4.9 37.6 1.0 CG2 A:ILE234 4.9 42.4 1.0 C A:ASP233 5.0 33.1 1.0

Sodium binding site 4 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:49.4 occ:1.00 O A:GLY232 2.6 25.1 1.0 NA A:NA503 2.9 45.1 1.0 CA A:GLY258 3.6 25.9 1.0 O A:HOH601 3.6 26.2 1.0 CG1 A:ILE234 3.7 34.2 1.0 C A:GLY232 3.8 36.1 1.0 CG A:GLU260 3.8 31.8 1.0 CB A:PRO231 4.0 24.9 1.0 N A:GLY258 4.1 26.2 1.0 N A:GLY232 4.2 26.4 1.0 C A:GLY258 4.3 36.8 1.0 O A:GLY258 4.4 36.8 1.0 CD1 A:ILE234 4.5 29.8 1.0 CA A:GLY232 4.5 25.5 1.0 N A:ILE234 4.5 35.4 1.0 C A:PRO231 4.5 30.5 1.0 C A:ASP233 4.6 33.1 1.0 O A:HOH634 4.6 41.8 1.0 CD A:GLU260 4.6 38.8 1.0 CG A:PRO231 4.6 25.2 1.0 OE2 A:GLU260 4.7 35.6 1.0 CA A:ILE234 4.7 33.8 1.0 O A:ASP233 4.8 36.0 1.0 N A:ASP233 4.8 34.8 1.0 CB A:ILE234 4.9 26.1 1.0 CA A:PRO231 4.9 26.9 1.0 O A:PRO231 5.0 34.7 1.0 CB A:GLU260 5.0 30.8 1.0

Sodium binding site 5 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:35.0 occ:1.00 O A:GLY68 2.6 31.2 1.0 O A:VAL40 2.8 27.8 1.0 N A:ILE43 3.2 26.9 1.0 N A:ASP42 3.3 32.7 1.0 CG2 A:ILE43 3.5 26.2 1.0 O A:HOH627 3.5 43.7 1.0 CB A:ILE43 3.5 27.3 1.0 C A:VAL40 3.5 27.4 1.0 CA A:TYR41 3.5 33.3 1.0 C A:TYR41 3.6 26.8 1.0 C A:GLY68 3.7 39.2 1.0 CA A:VAL69 3.8 34.3 1.0 N A:ILE70 3.9 28.9 1.0 N A:TYR41 3.9 30.0 1.0 CA A:ILE43 4.0 27.7 1.0 CG1 A:ILE70 4.1 27.4 1.0 C A:ASP42 4.1 27.5 1.0 CA A:ASP42 4.2 35.4 1.0 NH2 A:ARG45 4.2 60.5 1.0 N A:VAL69 4.2 39.8 1.0 C A:VAL69 4.2 35.0 1.0 O A:TYR41 4.4 26.2 1.0 CB A:VAL40 4.6 26.6 1.0 CA A:VAL40 4.7 27.2 1.0 CD1 A:ILE70 4.7 27.9 1.0 CG1 A:VAL40 4.8 26.0 1.0 CB A:ILE70 4.8 33.3 1.0 CG1 A:ILE43 4.9 25.3 1.0 CA A:ILE70 4.9 31.7 1.0 O A:ILE43 4.9 26.0 1.0 CB A:TYR41 4.9 37.2 1.0 CA A:GLY68 4.9 30.6 1.0 C A:ILE43 4.9 29.6 1.0

Sodium binding site 6 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:75.7 occ:1.00 O A:HIS10 2.4 48.1 1.0 O A:ILE426 2.7 77.0 1.0 CD2 A:HIS10 3.1 80.7 1.0 N A:HIS10 3.2 57.2 1.0 C A:HIS10 3.2 53.6 1.0 CG2 A:ILE426 3.3 80.7 1.0 NE2 A:HIS10 3.3 85.4 1.0 CG A:HIS10 3.3 80.4 1.0 CE1 A:HIS10 3.5 88.1 1.0 ND1 A:HIS10 3.5 86.4 1.0 C A:ILE426 3.5 73.8 1.0 CA A:ILE426 3.5 67.8 1.0 CA A:HIS10 3.6 62.5 1.0 CB A:ILE426 3.9 83.5 1.0 CB A:ILE8 3.9 61.2 1.0 N A:ARG9 3.9 64.8 1.0 CB A:HIS10 4.0 72.0 1.0 CG1 A:ILE426 4.3 82.6 1.0 C A:ARG9 4.3 63.8 1.0 N A:LEU11 4.4 53.0 1.0 CA A:ILE8 4.6 59.2 1.0 C A:ILE8 4.6 66.3 1.0 CA A:ARG9 4.6 62.8 1.0 CG2 A:ILE8 4.6 61.6 1.0 CG1 A:ILE8 4.6 64.9 1.0 O A:LEU425 4.7 53.4 1.0 CD1 A:ILE8 4.7 64.3 1.0 N A:HIS427 4.8 78.5 1.0 N A:ILE426 4.9 59.0 1.0 CA A:LEU11 5.0 50.7 1.0

Sodium binding site 7 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:66.0 occ:1.00 OD1 A:ASP268 3.0 40.0 1.0 CG2 A:ILE267 3.4 39.8 1.0 O A:THR264 3.5 48.9 1.0 CG A:ASP268 3.8 42.2 1.0 NA A:NA508 3.9 53.1 1.0 CB A:ILE267 3.9 45.6 1.0 OD2 A:ASP268 4.1 44.7 1.0 C A:THR264 4.3 45.9 1.0 CG2 A:THR264 4.4 58.4 1.0 CA A:THR264 4.4 41.0 1.0 N A:ASP268 4.5 47.0 1.0 CD1 A:ILE267 4.7 29.5 1.0 CB A:THR264 4.8 43.3 1.0 OG1 A:THR264 4.8 48.8 1.0 C A:ILE267 4.8 49.8 1.0 CG1 A:ILE267 4.9 42.6 1.0 CD1 A:ILE279 4.9 30.4 1.0 CA A:ILE267 4.9 46.4 1.0 CB A:ASP268 5.0 39.1 1.0 CA A:ASP268 5.0 42.9 1.0

Sodium binding site 8 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:53.1 occ:1.00 OD1 A:ASP268 2.6 40.0 1.0 NE A:ARG271 3.4 44.2 1.0 CG A:ASP268 3.7 42.2 1.0 CA A:ASP268 3.9 42.9 1.0 NA A:NA507 3.9 66.0 1.0 CG A:ARG271 4.0 41.5 1.0 CB A:ARG271 4.0 40.0 1.0 CD A:ARG271 4.1 36.6 1.0 CG2 A:ILE267 4.2 39.8 1.0 NH2 A:ARG271 4.3 41.0 1.0 CB A:ASP268 4.3 39.1 1.0 CZ A:ARG271 4.3 41.1 1.0 N A:ASP268 4.3 47.0 1.0 O A:ILE267 4.4 57.0 1.0 C A:ILE267 4.6 49.8 1.0 OD2 A:ASP268 4.7 44.7 1.0 C A:ASP268 5.0 44.7 1.0 O A:ASP268 5.0 47.5 1.0

Sodium binding site 9 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:63.1 occ:1.00 O A:GLY114 2.7 36.2 1.0 OG A:SER119 3.5 44.6 1.0 C A:ASP115 3.6 44.0 1.0 C A:GLY114 3.8 31.5 1.0 CA A:ASP115 3.8 40.9 1.0 O A:ASP115 3.8 49.5 1.0 O A:HOH615 3.9 45.3 1.0 N A:ASP116 3.9 41.3 1.0 N A:ASP115 4.3 32.0 1.0 CB B:LEU50 4.4 25.8 1.0 CA A:ASP116 4.5 41.6 1.0 CB A:SER119 4.5 51.6 1.0 CD2 B:LEU50 4.6 48.9 1.0 CG B:LEU50 4.6 47.1 1.0

Sodium binding site 10 out of 18 in the Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na510 b:61.5 occ:1.00 OE1 A:GLN73 2.6 38.0 1.0 CD A:GLN73 3.7 41.8 1.0 CB A:GLN73 3.8 37.5 1.0 C A:GLY36 3.9 44.4 1.0 CA A:GLN73 3.9 32.9 1.0 N A:GLU37 4.0 44.3 1.0 CB A:GLU37 4.1 33.9 1.0 O A:GLY36 4.1 39.1 1.0 CA A:GLU37 4.2 45.0 1.0 CG A:GLN73 4.3 38.5 1.0 CA A:GLY36 4.3 35.0 1.0 C A:GLN73 4.4 32.6 1.0 N A:GLY74 4.4 32.5 1.0 N A:GLY36 4.8 39.1 1.0 O A:GLY74 4.8 46.1 1.0 NE2 A:GLN73 4.8 48.1 1.0 OE2 A:GLU37 4.9 42.4 1.0

A.Kuzin, S.Lew, S.Rajagopalan, J.Seetharaman, L.Mao, R.Xiao, S.Kogan, M.Maglaqui, J.K.Everett, T.B.Acton, G.T.Montelione, L.Tong, J.F.Hunt, Northeast Structural Genomics Consortium (Nesg). Crystal Structure of De Novo Designed Serine Hydrolase OSH18, Northeast Structural Genomics Consortium (Nesg) Target OR396 To Be Published.