Sodium in PDB 5cm6: Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate

The structure of Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate, PDB code: 5cm6 was solved by U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, 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, Enzymefunction Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 1.83
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.345, 83.345, 198.082, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 24.3

The binding sites of Sodium atom in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate (pdb code 5cm6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate, PDB code: 5cm6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate


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 Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:11.9 occ:1.00 O2 A:PYR401 2.2 17.4 1.0 O A:TRP211 2.3 17.0 1.0 OE1 A:GLN152 2.4 15.3 1.0 OE1 A:GLU235 2.5 25.6 1.0 OE2 A:GLU210 2.5 26.2 1.0 O3 A:PYR401 2.7 18.6 1.0 OE2 A:GLU235 3.0 15.9 1.0 CD A:GLU235 3.0 16.4 1.0 HE22 A:GLN152 3.1 18.5 1.0 C1 A:PYR401 3.2 22.7 1.0 HH A:TYR95 3.3 19.3 1.0 CD A:GLN152 3.4 17.3 1.0 C2 A:PYR401 3.4 25.1 1.0 C A:TRP211 3.5 18.8 1.0 HH12 A:ARG173 3.5 16.6 1.0 NE2 A:GLN152 3.6 15.4 1.0 CD A:GLU210 3.6 33.3 1.0 OH A:TYR95 3.7 16.1 1.0 HA A:TRP211 3.8 16.5 1.0 HA A:VAL212 3.9 9.9 1.0 OE1 A:GLU210 4.1 27.6 1.0 HG22 A:VAL212 4.1 20.7 1.0 HG3 A:PRO175 4.1 22.0 1.0 CA A:TRP211 4.1 13.8 1.0 O A:HOH632 4.2 23.3 1.0 NH1 A:ARG173 4.2 13.8 1.0 HH11 A:ARG173 4.3 16.6 1.0 CG A:GLU235 4.3 12.4 1.0 HD2 A:PRO175 4.3 22.2 1.0 O1 A:PYR401 4.4 15.3 1.0 HE21 A:GLN152 4.5 18.5 1.0 HG2 A:PRO175 4.5 22.0 1.0 HB2 A:GLU210 4.5 25.9 1.0 HB2 A:GLU235 4.5 12.6 1.0 N A:VAL212 4.5 10.6 1.0 HE21 A:GLN234 4.5 53.5 1.0 HG3 A:GLU235 4.5 14.9 1.0 N A:TRP211 4.6 13.9 1.0 HG21 A:THR238 4.6 10.3 1.0 HD3 A:PRO175 4.6 22.2 1.0 O A:GLU210 4.6 16.1 1.0 CG A:PRO175 4.6 18.4 1.0 C A:GLU210 4.6 17.9 1.0 CA A:VAL212 4.6 8.3 1.0 HB3 A:GLN152 4.7 19.6 1.0 CD A:PRO175 4.7 18.5 1.0 HE3 A:TRP211 4.7 19.6 1.0 HG23 A:VAL212 4.7 20.7 1.0 CG A:GLN152 4.8 15.0 1.0 HB3 A:GLU235 4.8 12.6 1.0 OG1 A:THR238 4.8 21.2 1.0 CB A:GLU235 4.8 10.5 1.0 CG2 A:VAL212 4.8 17.3 1.0 C3 A:PYR401 4.8 21.1 1.0 CG A:GLU210 4.9 22.1 1.0 HG1 A:THR238 4.9 25.4 1.0 CZ A:TYR95 5.0 13.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate


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 Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:17.9 occ:1.00 O B:TRP211 2.3 20.8 1.0 O2 B:PYR401 2.3 21.9 1.0 OE1 B:GLN152 2.4 19.1 1.0 OE2 B:GLU210 2.4 40.9 1.0 OE1 B:GLU235 2.5 28.4 1.0 O3 B:PYR401 2.5 27.9 1.0 CD B:GLU235 2.9 26.4 1.0 OE2 B:GLU235 3.0 20.7 1.0 HE22 B:GLN152 3.1 23.2 1.0 C1 B:PYR401 3.1 28.7 1.0 C2 B:PYR401 3.2 21.9 1.0 CD B:GLN152 3.3 21.1 1.0 HH B:TYR95 3.4 23.7 1.0 C B:TRP211 3.4 17.7 1.0 CD B:GLU210 3.5 49.7 1.0 NE2 B:GLN152 3.5 19.3 1.0 HH12 B:ARG173 3.6 25.8 1.0 OH B:TYR95 3.8 19.7 1.0 HA B:VAL212 3.8 21.5 1.0 HA B:TRP211 3.9 20.5 1.0 OE1 B:GLU210 4.0 48.3 1.0 O B:HOH595 4.1 21.9 1.0 CA B:TRP211 4.2 17.1 1.0 HG3 B:PRO175 4.2 38.0 1.0 HG22 B:VAL212 4.2 26.7 1.0 CG B:GLU235 4.3 26.2 1.0 NH1 B:ARG173 4.3 21.5 1.0 HG2 B:PRO175 4.3 38.0 1.0 O1 B:PYR401 4.3 19.6 1.0 HE21 B:GLN152 4.4 23.2 1.0 N B:VAL212 4.4 17.6 1.0 HG3 B:GLU235 4.4 31.5 1.0 HD2 B:PRO175 4.5 32.7 1.0 HH11 B:ARG173 4.5 25.8 1.0 N B:TRP211 4.5 18.5 1.0 HB2 B:GLU210 4.5 25.5 1.0 CA B:VAL212 4.6 17.9 1.0 HB2 B:GLU235 4.6 21.5 1.0 HE3 B:TRP211 4.6 29.3 1.0 CG B:PRO175 4.6 31.7 1.0 HB3 B:GLN152 4.6 20.0 1.0 HG21 B:THR238 4.6 18.7 1.0 C3 B:PYR401 4.7 18.5 1.0 CG B:GLN152 4.7 17.8 1.0 C B:GLU210 4.7 20.6 1.0 HB3 B:GLU235 4.7 21.5 1.0 OG1 B:THR238 4.8 19.1 1.0 CG B:GLU210 4.8 33.8 1.0 HD3 B:PRO175 4.8 32.7 1.0 O B:GLU210 4.8 22.3 1.0 HG23 B:VAL212 4.8 26.7 1.0 H B:TRP211 4.8 22.2 1.0 CB B:GLU235 4.8 17.9 1.0 CD B:PRO175 4.8 27.2 1.0 HE21 B:GLN234 4.9 45.9 1.0 CG2 B:VAL212 4.9 22.3 1.0 H33 B:PYR401 4.9 22.2 1.0 HG2 B:GLU235 5.0 31.5 1.0 HG3 B:GLU210 5.0 40.5 1.0

U.Yadava, M.W.Vetting, N.F.Al Obaidi, R.Toro, L.L.Morisco, J.Benach, 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. Crystal Structure of A Trap Periplasmic Solute Binding Protein From Pseudoalteromonas Atlantica T6C(PATL_2292, Target Efi-510180) with Bound Sodium and Pyruvate To Be Published.