Sodium in PDB 4ys6: Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose, PDB code: 4ys6 was solved by M.W.Vetting, Y.Patskovsky, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.94 / 1.70
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	80.686, 80.686, 170.004, 90.00, 90.00, 120.00
R / Rfree (%)	15 / 18.3

The structure of Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose (pdb code 4ys6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose, PDB code: 4ys6:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:18.9 occ:1.00 O A:HOH662 2.3 24.1 1.0 O A:GLY291 2.3 18.4 1.0 O A:ALA286 2.4 16.7 1.0 H A:GLY291 2.9 20.8 1.0 C A:ALA286 3.2 16.3 1.0 HA A:ILE287 3.3 19.5 1.0 N A:GLY291 3.4 17.3 1.0 C A:GLY291 3.4 17.3 1.0 HA2 A:GLY290 3.4 22.2 1.0 HB1 A:ALA286 3.5 21.7 1.0 N A:ILE287 3.9 16.1 1.0 CA A:GLY291 3.9 17.1 1.0 CA A:ILE287 4.0 16.2 1.0 C A:GLY290 4.1 21.4 1.0 CA A:ALA286 4.1 16.1 1.0 HA A:ALA286 4.1 19.4 1.0 CA A:GLY290 4.2 18.5 1.0 CB A:ALA286 4.2 18.1 1.0 H A:GLY290 4.4 25.0 1.0 HB3 A:ALA286 4.5 21.7 1.0 O A:HOH610 4.5 23.2 1.0 HA A:GLU292 4.6 18.7 1.0 HA3 A:GLY291 4.6 20.5 1.0 N A:GLU292 4.6 17.1 1.0 HA2 A:GLY291 4.6 20.5 1.0 C A:ILE287 4.7 16.9 1.0 H A:ILE287 4.7 19.3 1.0 O A:ILE287 4.7 17.9 1.0 N A:GLY290 4.8 20.9 1.0 H A:ALA293 4.8 20.4 1.0 HG13 A:ILE287 4.8 20.6 1.0 HA3 A:GLY290 4.9 22.2 1.0 HG12 A:ILE287 5.0 20.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:36.8 occ:1.00 O A:GLU133 2.4 14.4 1.0 O A:HOH667 2.4 56.1 1.0 OD1 A:ASN136 2.4 25.0 1.0 O A:HOH680 3.0 41.3 1.0 OE1 A:GLU133 3.2 61.7 1.0 O A:HOH677 3.3 62.5 1.0 HA A:ASN136 3.3 17.8 1.0 C A:GLU133 3.4 16.4 1.0 HA A:GLU133 3.5 18.6 1.0 CG A:ASN136 3.5 22.9 1.0 O A:HOH657 3.7 23.6 1.0 H A:ASN136 3.7 17.0 1.0 CA A:GLU133 4.0 15.5 1.0 HB3 A:GLU133 4.0 22.4 1.0 CA A:ASN136 4.0 14.8 1.0 HA A:LYS134 4.2 16.0 1.0 N A:ASN136 4.2 14.1 1.0 CD A:GLU133 4.3 62.4 1.0 CB A:ASN136 4.3 16.1 1.0 N A:LYS134 4.5 13.8 1.0 CB A:GLU133 4.5 18.6 1.0 O A:HOH621 4.5 26.3 1.0 ND2 A:ASN136 4.5 27.3 1.0 HD21 A:ASN136 4.5 32.7 1.0 HB3 A:ASN136 4.6 19.3 1.0 CA A:LYS134 4.7 13.3 1.0 C A:LYS134 5.0 13.3 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:32.4 occ:1.00 O A:HOH655 2.2 41.5 1.0 O A:HOH513 2.4 33.6 1.0 O A:SER54 2.4 17.8 0.4 O A:SER54 2.4 17.4 0.6 OD1 A:ASP56 2.5 23.3 1.0 O A:HOH528 2.5 27.9 1.0 CG A:ASP56 3.2 28.4 1.0 HG A:SER54 3.2 35.6 0.6 OD2 A:ASP56 3.5 23.5 1.0 O A:HOH507 3.6 34.8 1.0 C A:SER54 3.6 18.7 0.4 C A:SER54 3.6 19.1 0.6 HB3 A:ASN55 3.6 20.4 1.0 O A:HOH570 3.8 25.2 1.0 HB2 A:ASN55 3.8 20.4 1.0 C A:ASN55 3.8 15.2 1.0 O A:ASN55 3.9 17.5 1.0 HB3 A:SER54 3.9 26.9 0.4 OG A:SER54 4.0 29.6 0.6 CB A:ASN55 4.1 17.0 1.0 N A:ASP56 4.1 15.5 1.0 HB3 A:SER54 4.1 27.1 0.6 O A:HOH537 4.2 30.2 1.0 CA A:ASN55 4.3 14.9 1.0 HA A:ASP56 4.3 19.5 1.0 HB2 A:SER54 4.3 26.9 0.4 CB A:ASP56 4.3 17.6 1.0 H A:ASP56 4.4 18.6 1.0 N A:ASN55 4.4 16.9 1.0 CB A:SER54 4.5 22.4 0.4 CA A:ASP56 4.5 16.3 1.0 CB A:SER54 4.5 22.6 0.6 CA A:SER54 4.7 17.8 0.4 HB2 A:ASP56 4.7 21.1 1.0 CA A:SER54 4.7 17.1 0.6 O A:HOH681 4.7 38.9 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:37.0 occ:1.00 O A:HOH651 2.3 24.3 1.0 O A:HOH671 2.3 36.6 1.0 O A:VAL295 2.4 16.5 1.0 O A:HOH674 2.7 51.5 1.0 H A:VAL295 3.0 19.5 1.0 C A:VAL295 3.6 13.8 1.0 N A:VAL295 3.8 16.3 1.0 HG22 A:VAL295 4.0 32.8 1.0 O A:HOH501 4.0 35.7 1.0 HA A:PRO294 4.1 22.5 1.0 HG23 A:VAL295 4.1 32.8 1.0 HA A:ASN296 4.1 17.4 1.0 CA A:VAL295 4.3 14.6 1.0 CG2 A:VAL295 4.5 27.4 1.0 N A:ASN296 4.6 14.1 1.0 HB3 A:ASN296 4.6 20.8 1.0 C A:PRO294 4.7 18.3 1.0 CA A:ASN296 4.8 14.5 1.0 CA A:PRO294 4.8 18.7 1.0 HB3 A:PRO294 4.9 30.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose


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 An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi- 511156) with Bound Beta-D-Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:58.7 occ:1.00 OG A:SER35 2.3 34.1 1.0 O A:HOH685 2.4 48.0 1.0 O A:HOH629 2.4 48.3 1.0 O A:HOH607 2.5 40.4 1.0 O A:ASN31 2.9 17.1 1.0 HB3 A:ASN31 3.2 17.8 1.0 O A:HOH648 3.5 39.8 1.0 CB A:SER35 3.6 22.9 1.0 HA A:ASN31 3.6 19.5 1.0 C A:ASN31 3.7 16.1 1.0 HB2 A:SER35 3.7 27.5 1.0 CA A:ASN31 4.0 16.2 1.0 H A:SER35 4.0 17.7 1.0 CB A:ASN31 4.0 14.8 1.0 HB3 A:SER35 4.2 27.5 1.0 OH A:TYR52 4.4 20.5 1.0 N A:SER35 4.5 14.7 1.0 CA A:SER35 4.5 15.4 1.0 OD1 A:ASN31 4.5 21.4 1.0 HA A:SER35 4.5 18.5 1.0 HH A:TYR52 4.6 24.6 1.0 HB2 A:ASN31 4.7 17.8 1.0 HA A:GLN32 4.7 17.6 1.0 N A:GLN32 4.8 13.9 1.0 CG A:ASN31 4.8 18.3 1.0

M.W.Vetting, Y.Patskovsky, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, J.Koss, S.R.Wasserman, J.D.Attonito, A.Scott Glenn, S.Chamala, S.Chowdhury, J.Lafleur, J.Love, R.D.Seidel, K.L.Whalen, J.A.Gerlt, S.C.Almo, Enzyme Function Initiative (Efi). Crystal Structure of An Abc Transporter Solute Binding Protein (IPR025997) From Clostridium Phytofermentans (CPHY_1585, Target Efi-511156) with Bound Beta-D-Glucose To Be Published.