Sodium in PDB 3i24: Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176

The structure of Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176, PDB code: 3i24 was solved by J.Seetharaman, M.Abashidze, F.Forouhar, H.Janjua, R.Xiao, C.Ciccosanti, E.L.Foote, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong, Northeaststructural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.74 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.433, 69.312, 49.077, 90.00, 109.44, 90.00
R / Rfree (%)	19.7 / 21.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 (pdb code 3i24). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 19 binding sites of Sodium where determined in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176, PDB code: 3i24:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na150 b:5.9 occ:1.00 O A:HOH183 3.0 13.3 1.0 N A:GLY84 3.1 10.6 1.0 O A:HOH312 3.1 28.8 1.0 CE1 A:HIS93 3.2 5.0 1.0 O A:HOH213 3.2 16.8 1.0 O A:HOH217 3.3 15.3 1.0 NA A:NA153 3.3 7.5 1.0 NE2 A:HIS91 3.5 8.2 1.0 CB A:LEU83 3.6 13.4 1.0 CA A:GLY84 3.6 10.3 1.0 NE2 A:HIS93 3.9 9.8 1.0 CE1 A:HIS91 4.0 9.4 1.0 C A:LEU83 4.1 9.7 1.0 ND1 A:HIS93 4.2 9.7 1.0 CD1 A:LEU83 4.3 17.2 1.0 CA A:LEU83 4.3 10.7 1.0 CG A:LEU83 4.4 15.3 1.0 O A:HOH258 4.4 24.9 1.0 CD2 A:HIS91 4.5 8.6 1.0 O A:HOH416 4.5 31.8 1.0 N A:LEU83 4.6 9.0 1.0 N A:ASN85 4.6 11.3 1.0 C A:GLY84 4.6 10.4 1.0 O A:HOH256 4.8 23.6 1.0

Sodium binding site 2 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na151 b:5.7 occ:1.00 O A:ILE27 2.8 6.1 1.0 O A:ILE31 2.9 11.6 1.0 NH2 A:ARG117 2.9 13.2 1.0 N A:TRP34 3.0 6.4 1.0 O A:GLU29 3.2 9.0 1.0 CB A:TRP34 3.4 4.7 1.0 NH1 A:ARG117 3.5 12.6 1.0 CD1 A:LEU26 3.6 7.7 1.0 O A:TRP34 3.6 6.1 1.0 CZ A:ARG117 3.6 11.3 1.0 CA A:TRP34 3.7 6.4 1.0 C A:ILE27 3.8 6.3 1.0 C A:PRO33 3.9 7.8 1.0 CA A:PRO33 4.0 8.8 1.0 C A:TRP34 4.1 6.6 1.0 C A:ILE31 4.1 10.4 1.0 CB A:ILE27 4.1 7.7 1.0 N A:ILE27 4.2 5.4 1.0 CG2 A:ILE27 4.3 7.2 1.0 CA A:ILE27 4.3 6.7 1.0 C A:GLU29 4.4 10.3 1.0 CG A:LEU26 4.5 6.2 1.0 N A:ILE31 4.5 10.6 1.0 CG A:TRP34 4.6 7.3 1.0 CA A:GLY32 4.8 8.4 1.0 N A:GLU29 4.8 6.6 1.0 CB A:PRO33 4.8 12.0 1.0 N A:GLY32 4.9 9.9 1.0 NE A:ARG117 4.9 12.5 1.0 N A:LYS28 5.0 6.9 1.0 CA A:ILE31 5.0 10.5 1.0

Sodium binding site 3 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na152 b:7.5 occ:1.00 O A:HOH171 2.8 11.7 1.0 O B:HOH177 2.9 12.6 1.0 NA A:NA153 3.0 7.5 1.0 N A:HIS91 3.0 5.7 1.0 O A:HIS91 3.1 8.7 1.0 ND1 A:HIS91 3.4 6.1 1.0 CA A:LEU90 3.6 8.5 1.0 CD2 A:LEU90 3.7 13.4 1.0 CE1 A:HIS91 3.8 9.4 1.0 C A:LEU90 3.8 6.7 1.0 CA A:GLY84 3.8 10.3 1.0 N A:GLY84 3.9 10.6 1.0 O A:GLN89 3.9 8.6 1.0 C A:HIS91 4.0 5.7 1.0 C A:LEU83 4.0 9.7 1.0 CA A:HIS91 4.0 6.8 1.0 CG A:HIS91 4.1 5.7 1.0 O A:LEU83 4.1 11.4 1.0 N A:LEU83 4.1 9.0 1.0 O A:LYS45 4.3 11.9 1.0 NZ B:LYS77 4.4 16.6 1.0 N A:LEU90 4.4 7.7 1.0 C A:ALA82 4.5 7.3 1.0 C A:GLN89 4.5 8.8 1.0 CA A:ALA82 4.5 6.5 1.0 NE2 A:HIS91 4.5 8.2 1.0 O A:VAL87 4.6 14.5 1.0 CB A:LEU90 4.6 8.8 1.0 CB A:HIS91 4.6 7.2 1.0 CG A:LEU90 4.6 15.8 1.0 CB A:ALA82 4.7 8.3 1.0 CD2 A:HIS91 4.7 8.6 1.0 CA A:LEU83 4.7 10.7 1.0 CE B:LYS77 4.8 14.1 1.0 O A:LEU90 5.0 8.0 1.0

Sodium binding site 4 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na153 b:7.5 occ:1.00 O A:HIS91 2.8 8.7 1.0 N A:LEU83 2.8 9.0 1.0 NA A:NA152 3.0 7.5 1.0 N A:GLY84 3.1 10.6 1.0 NE2 A:HIS91 3.2 8.2 1.0 CE1 A:HIS93 3.3 5.0 1.0 NA A:NA150 3.3 5.9 1.0 CE1 A:HIS91 3.4 9.4 1.0 CD2 A:HIS91 3.4 8.6 1.0 ND1 A:HIS93 3.5 9.7 1.0 C A:LEU83 3.6 9.7 1.0 CA A:LEU83 3.6 10.7 1.0 ND1 A:HIS91 3.7 6.1 1.0 CG A:HIS91 3.7 5.7 1.0 C A:ALA82 3.7 7.3 1.0 CA A:ALA82 3.8 6.5 1.0 C A:HIS91 3.9 5.7 1.0 CA A:GLY84 3.9 10.3 1.0 CB A:LEU83 4.0 13.4 1.0 O A:GLY81 4.1 8.5 1.0 NE2 A:HIS93 4.4 9.8 1.0 O A:LEU83 4.5 11.4 1.0 CG A:LEU83 4.5 15.3 1.0 N A:HIS91 4.5 5.7 1.0 CA A:HIS91 4.6 6.8 1.0 N A:ALA82 4.7 6.0 1.0 CB A:HIS91 4.7 7.2 1.0 C A:GLY81 4.7 6.3 1.0 CG A:HIS93 4.8 5.5 1.0 CB A:ALA82 4.8 8.3 1.0 N A:ILE92 4.8 5.5 1.0 O A:ALA82 4.9 7.8 1.0 CA A:ILE92 4.9 5.8 1.0 O B:HOH177 5.0 12.6 1.0

Sodium binding site 5 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na154 b:8.4 occ:1.00 N A:VAL108 3.0 7.8 1.0 ND2 A:ASN79 3.0 4.8 1.0 CZ3 A:TRP109 3.3 8.0 1.0 CH2 A:TRP109 3.4 7.2 1.0 CA A:PRO107 3.6 8.2 1.0 CE3 A:TRP109 3.6 9.0 1.0 NH1 A:ARG97 3.7 7.5 1.0 CB A:VAL108 3.7 9.6 1.0 CG2 A:VAL108 3.7 13.8 1.0 C A:PRO107 3.8 8.8 1.0 CB A:ASN79 3.8 7.0 1.0 CZ2 A:TRP109 3.8 8.7 1.0 CG A:ASN79 3.9 7.0 1.0 CA A:VAL108 3.9 9.1 1.0 CD2 A:TRP109 4.0 9.3 1.0 CB A:PRO107 4.1 8.3 1.0 CE2 A:TRP109 4.1 8.8 1.0 CD1 A:ILE95 4.2 9.6 1.0 CD2 B:LEU83 4.4 18.0 1.0 N A:TRP109 4.5 10.0 1.0 CZ A:ARG97 4.6 7.2 1.0 CD A:ARG97 4.6 8.0 1.0 CG B:LEU83 4.7 15.4 1.0 C A:VAL108 4.8 8.5 1.0 N A:PRO107 5.0 8.1 1.0 CG A:TRP109 5.0 10.0 1.0 O A:PRO107 5.0 8.8 1.0 O A:GLY106 5.0 6.7 1.0

Sodium binding site 6 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na155 b:8.5 occ:1.00 O B:HOH230 2.8 15.5 1.0 OG A:SER63 3.0 8.9 1.0 OG A:SER62 3.1 8.2 1.0 CA A:SER63 3.4 7.9 1.0 N A:SER63 3.4 7.2 1.0 CD1 A:ILE80 3.5 10.2 1.0 C A:SER62 3.6 7.4 1.0 CG2 B:ILE47 3.7 12.8 1.0 CB B:ILE47 3.8 10.4 1.0 O A:SER62 3.8 7.8 1.0 CB A:SER63 3.8 7.6 1.0 CB A:SER62 3.9 7.5 1.0 N B:HIS48 3.9 9.3 1.0 CB B:HIS48 4.0 11.5 1.0 CB A:ALA66 4.1 7.3 1.0 CA B:HIS48 4.4 10.3 1.0 CA A:SER62 4.5 7.3 1.0 C B:ILE47 4.5 10.5 1.0 CD1 A:ILE59 4.6 11.9 1.0 CD1 B:ILE47 4.7 10.8 1.0 CA B:ILE47 4.7 10.9 1.0 CD2 B:HIS48 4.7 15.2 1.0 C A:SER63 4.7 8.1 1.0 O A:ILE59 4.8 6.3 1.0 CG B:HIS48 4.8 14.0 1.0 CG1 B:ILE47 4.8 11.3 1.0 O B:HOH255 5.0 25.3 1.0 CG1 A:ILE80 5.0 9.8 1.0

Sodium binding site 7 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na156 b:8.2 occ:1.00 O A:HOH221 2.8 13.4 1.0 NA B:NA151 3.0 7.3 1.0 N A:HIS48 3.0 8.3 1.0 CD2 A:HIS48 3.1 12.9 1.0 N A:ILE47 3.3 6.8 1.0 CB B:ALA66 3.5 6.8 1.0 CB A:ILE47 3.5 7.7 1.0 CD1 B:ILE80 3.5 7.1 1.0 CB A:HIS48 3.6 11.8 1.0 CG A:HIS48 3.7 10.6 1.0 CA A:ILE47 3.7 7.0 1.0 C A:ILE47 3.7 7.3 1.0 CA A:HIS48 3.9 9.1 1.0 CB A:GLU46 3.9 9.2 1.0 C A:GLU46 4.1 7.4 1.0 NE2 A:HIS48 4.3 13.9 1.0 CG1 A:ILE47 4.4 8.9 1.0 CA A:GLU46 4.5 9.1 1.0 CG2 A:ILE47 4.5 8.1 1.0 OE1 A:GLU46 4.5 11.3 1.0 OG B:SER63 4.7 7.8 1.0 CG1 B:ILE80 4.7 7.0 1.0 CA B:SER63 4.9 7.3 1.0 O A:ILE47 4.9 7.6 1.0 CD1 A:ILE47 4.9 9.9 1.0 O A:GLU46 4.9 7.3 1.0 ND1 A:HIS48 5.0 13.2 1.0 CG A:GLU46 5.0 9.4 1.0 CA B:ALA66 5.0 7.2 1.0

Sodium binding site 8 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na157 b:9.0 occ:1.00 O A:PRO39 2.9 8.8 1.0 O A:LEU90 2.9 8.0 1.0 O A:HOH197 3.0 14.2 1.0 CB A:LEU90 3.6 8.8 1.0 N A:LEU90 3.7 7.7 1.0 C A:LEU90 3.7 6.7 1.0 CG A:GLN89 3.8 8.9 1.0 CG1 A:VAL38 3.8 5.2 1.0 CA A:LEU90 3.9 8.5 1.0 O A:ILE41 3.9 10.4 1.0 CD A:PRO39 3.9 6.7 1.0 C A:PRO39 3.9 8.5 1.0 N A:PRO39 4.0 6.1 1.0 CB A:LEU44 4.0 11.7 1.0 CB A:PRO39 4.1 7.4 1.0 CD1 A:LEU44 4.1 12.8 1.0 CE1 A:PHE3 4.2 11.0 1.0 CA A:PRO39 4.3 6.4 1.0 O A:LEU44 4.3 11.2 1.0 C A:GLN89 4.4 8.8 1.0 C A:VAL38 4.5 5.8 1.0 CG A:PRO39 4.5 8.3 1.0 CD A:GLN89 4.6 8.3 1.0 CG A:LEU44 4.6 11.6 1.0 O A:HOH261 4.8 16.3 1.0 CD1 A:LEU90 4.8 12.6 1.0 CG A:LEU90 4.8 15.8 1.0 CA A:VAL38 4.9 5.6 1.0 N A:ILE41 4.9 8.3 1.0 CA A:GLN89 4.9 10.3 1.0 CD1 A:PHE3 4.9 10.1 1.0 CB A:GLN89 4.9 10.8 1.0 C A:LEU44 4.9 11.4 1.0 CA A:LEU44 5.0 11.9 1.0 NE2 A:GLN89 5.0 9.9 1.0 CB A:VAL38 5.0 5.3 1.0

Sodium binding site 9 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na158 b:9.3 occ:1.00 O A:HOH174 2.8 10.7 1.0 O A:HOH204 2.8 16.9 1.0 OG1 A:THR113 2.9 10.4 1.0 N A:THR113 2.9 9.2 1.0 CB A:THR112 3.6 10.5 1.0 CB A:THR113 3.6 9.0 1.0 CG2 A:THR113 3.6 9.6 1.0 CG2 A:VAL102 3.7 9.9 1.0 CA A:THR113 3.8 8.2 1.0 CA A:THR112 3.8 10.6 1.0 C A:THR112 3.8 9.5 1.0 N A:GLY114 4.1 8.1 1.0 O A:HOH296 4.1 25.5 1.0 C A:THR113 4.4 9.2 1.0 OG1 A:THR112 4.4 11.3 1.0 O A:HOH206 4.4 14.1 1.0 CG2 A:THR112 4.5 12.4 1.0 O A:ASP30 4.6 12.7 1.0 OE1 A:GLU29 4.6 12.7 1.0 CB A:ILE31 4.7 12.5 1.0 CG1 A:VAL102 4.7 12.2 1.0 CD1 A:ILE31 4.8 15.3 1.0 CB A:VAL102 4.8 10.4 1.0 N A:VAL115 4.8 9.0 1.0 O A:HOH187 4.9 13.7 1.0 O A:VAL115 5.0 8.4 1.0

Sodium binding site 10 out of 19 in the Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176


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 A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na159 b:8.8 occ:1.00 OG1 A:THR99 2.8 7.7 1.0 CB A:THR99 3.4 7.0 1.0 CG2 A:THR100 3.6 10.7 1.0 C A:THR99 3.9 7.3 1.0 O A:THR99 4.0 8.8 1.0 N A:THR100 4.2 8.2 1.0 CA A:THR99 4.3 8.2 1.0 CG2 A:THR99 4.5 6.5 1.0 CA A:THR100 4.6 8.5 1.0 CB A:THR100 4.7 9.0 1.0

J.Seetharaman, M.Abashidze, F.Forouhar, H.Janjua, R.Xiao, C.Ciccosanti, E.L.Foote, T.B.Acton, B.Rost, G.T.Montelione, J.F.Hunt, L.Tong. Crystal Structure of A Hit Family Hydrolase Protein From Vibrio Fischeri. Northeast Structural Genomics Consortium Target Id VFR176 To Be Published.