Sodium in PDB 3u1o: Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49

The structure of Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49, PDB code: 3u1o was solved by A.Kuzin, M.Su, S.Lew, F.Forouhar, J.Seetharaman, P.Daya, R.Xiao, C.Ciccosanti, F.Richter, J.K.Everett, T.B.Acton, D.Baker, G.T.Montelione, J.F.Hunt, L.Tong, Northeast Structural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.03 / 2.49
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	109.135, 129.200, 72.178, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 26.2

The binding sites of Sodium atom in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49 (pdb code 3u1o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49, PDB code: 3u1o:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na425 b:32.1 occ:1.00 ND2 A:ASN183 2.8 14.8 1.0 O A:GLN180 2.9 13.6 1.0 N A:LYS277 3.0 31.8 1.0 OD1 A:ASN183 3.2 30.5 1.0 N A:ASP278 3.2 34.7 1.0 CG A:ASN183 3.3 25.6 1.0 C A:GLN180 3.6 11.7 1.0 CB A:ASP278 3.7 26.7 1.0 CA A:GLN180 3.7 9.7 1.0 O A:ASP278 3.8 29.7 1.0 CA A:ALA276 3.8 27.0 1.0 CA A:LYS277 3.8 39.4 1.0 C A:ALA276 3.8 26.8 1.0 O A:THR179 3.8 23.8 1.0 C A:LYS277 3.9 37.6 1.0 CA A:ASP278 3.9 25.6 1.0 CB A:ALA276 3.9 26.9 1.0 CB A:LYS277 4.0 49.7 1.0 C A:ASP278 4.3 21.7 1.0 N A:GLN180 4.6 20.4 1.0 C A:THR179 4.6 20.9 1.0 CB A:ASN183 4.7 23.1 1.0 CB A:GLN180 4.7 9.8 1.0 N A:LYS181 4.8 10.7 1.0 O A:LYS277 4.9 37.6 1.0 O A:ALA276 5.0 23.6 1.0

Sodium binding site 2 out of 4 in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na426 b:36.8 occ:1.00 O A:VAL315 2.8 13.9 1.0 O A:GLY319 2.9 9.7 1.0 O A:HOH449 3.0 9.6 1.0 N A:GLY319 3.4 16.1 1.0 C A:VAL315 3.6 14.3 1.0 CD1 A:LEU334 3.7 9.8 1.0 CG1 A:VAL315 3.7 15.6 1.0 CA A:VAL315 3.7 14.9 1.0 C A:GLY319 3.7 12.8 1.0 CB A:LEU318 3.8 14.9 1.0 CA A:GLY319 3.8 13.4 1.0 CG A:PRO325 3.8 9.7 1.0 C A:LEU318 3.9 13.6 1.0 O A:HOH438 4.2 9.5 1.0 CB A:VAL315 4.2 15.4 1.0 CA A:LEU318 4.2 13.1 1.0 CD2 A:LEU334 4.5 10.0 1.0 O A:LEU318 4.5 17.4 1.0 CG A:LEU334 4.6 12.5 1.0 O A:HOH518 4.6 26.0 1.0 N A:LEU318 4.6 13.7 1.0 CG2 A:VAL315 4.7 12.1 1.0 CB A:PRO325 4.8 9.6 1.0 O A:GLY314 4.8 9.7 1.0 O A:HOH456 4.8 9.6 1.0 N A:GLU316 4.8 16.9 1.0 CD A:PRO325 4.9 15.4 1.0 N A:VAL315 5.0 16.1 1.0 CG A:LEU318 5.0 15.7 1.0 N A:LEU320 5.0 9.7 1.0

Sodium binding site 3 out of 4 in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na427 b:41.1 occ:1.00 O A:SER3 3.0 31.2 1.0 O A:GLY2 3.6 75.7 1.0 NE2 A:HIS4 3.8 39.6 1.0 C A:SER3 3.9 37.0 1.0 C A:GLY2 4.0 70.3 1.0 CD2 A:HIS4 4.0 37.7 1.0 CE1 A:HIS4 4.2 37.2 1.0 CA A:SER3 4.4 42.9 1.0 N A:SER3 4.4 54.7 1.0 CG A:HIS4 4.5 34.5 1.0 ND1 A:HIS4 4.6 36.2 1.0 CA A:GLY2 4.8 76.7 1.0 N A:HIS4 4.9 33.4 1.0

Sodium binding site 4 out of 4 in the Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Three Dimensional Structure of De Novo Designed Cysteine Esterase ECH19, Northeast Structural Genomics Consortium Target OR49 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na421 b:39.8 occ:1.00 O B:VAL119 2.8 12.4 1.0 O B:HOH508 3.0 17.3 1.0 ND2 B:ASN249 3.1 10.5 1.0 O B:HOH566 3.4 19.6 1.0 O B:HOH463 3.5 15.3 1.0 CD2 B:LEU350 3.6 8.4 1.0 CD1 B:LEU350 3.8 17.5 1.0 CG B:LEU350 4.0 21.2 1.0 C B:VAL119 4.0 13.4 1.0 CB B:LEU350 4.0 16.0 1.0 CG B:ASN249 4.0 16.0 1.0 OD1 B:ASN249 4.0 14.0 1.0 CB B:VAL324 4.2 13.3 1.0 CA B:THR120 4.3 14.8 1.0 CB B:THR120 4.4 16.8 1.0 CB B:SER250 4.4 12.6 1.0 CG2 B:VAL324 4.5 12.5 1.0 O B:VAL324 4.5 17.9 1.0 N B:VAL324 4.5 16.5 1.0 N B:THR120 4.6 14.6 1.0 OG1 B:THR120 4.7 19.4 1.0 N B:VAL119 4.9 8.5 1.0 CA B:SER250 4.9 17.1 1.0 CA B:VAL324 4.9 15.5 1.0 OG B:SER118 5.0 20.3 1.0

F.Richter, R.Blomberg, S.D.Khare, G.Kiss, A.P.Kuzin, A.J.Smith, J.Gallaher, Z.Pianowski, R.C.Helgeson, A.Grjasnow, R.Xiao, J.Seetharaman, M.Su, S.Vorobiev, S.Lew, F.Forouhar, G.J.Kornhaber, J.F.Hunt, G.T.Montelione, L.Tong, K.N.Houk, D.Hilvert, D.Baker. Computational Design of Catalytic Dyads and Oxyanion Holes For Ester Hydrolysis. J.Am.Chem.Soc. V. 134 16197 2012.
ISSN: ISSN 0002-7863
PubMed: 22871159
DOI: 10.1021/JA3037367