Sodium in PDB 8p3d: Full Length Structure of Tcmip with Bound Inhibitor NJS224.

All present enzymatic activity of Full Length Structure of Tcmip with Bound Inhibitor NJS224.:
5.2.1.8;

The structure of Full Length Structure of Tcmip with Bound Inhibitor NJS224., PDB code: 8p3d was solved by J.J.Whittaker, A.Guskov, B.Goretzki, U.A.Hellmich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.77 / 1.71
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.858, 34.696, 53.081, 90, 93.53, 90
R / Rfree (%)	18.2 / 21.7

The structure of Full Length Structure of Tcmip with Bound Inhibitor NJS224. also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Full Length Structure of Tcmip with Bound Inhibitor NJS224. (pdb code 8p3d). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Full Length Structure of Tcmip with Bound Inhibitor NJS224., PDB code: 8p3d:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Full Length Structure of Tcmip with Bound Inhibitor NJS224.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Full Length Structure of Tcmip with Bound Inhibitor NJS224. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:26.2 occ:1.00 H A:SER130 2.2 22.8 1.0 O A:GLY118 2.7 20.6 1.0 O A:PRO127 2.8 21.6 1.0 NA A:NA203 2.8 28.1 1.0 HA2 A:GLY121 2.8 25.6 1.0 H A:TYR129 2.8 22.1 1.0 HB2 A:SER130 3.0 22.9 1.0 N A:SER130 3.0 19.0 1.0 N A:TYR129 3.2 18.4 1.0 HG22 A:ILE126 3.2 25.4 1.0 HA A:PRO128 3.3 22.3 1.0 HB2 A:TYR117 3.4 26.9 1.0 HB2 A:TYR113 3.5 24.8 1.0 H A:GLY121 3.5 24.6 1.0 H A:GLY118 3.5 23.5 1.0 N A:GLY118 3.6 19.6 1.0 C A:PRO128 3.6 19.5 1.0 CA A:GLY121 3.7 21.3 1.0 HG A:SER130 3.7 24.9 1.0 CB A:SER130 3.7 19.1 1.0 C A:TYR117 3.7 23.4 1.0 C A:GLY118 3.8 23.1 1.0 CA A:PRO128 3.8 18.6 1.0 C A:PRO127 3.8 20.8 1.0 CA A:SER130 3.9 17.0 1.0 HA A:TYR129 3.9 24.6 1.0 N A:GLY121 3.9 20.5 1.0 CA A:TYR129 3.9 20.5 1.0 C A:TYR129 3.9 16.4 1.0 O A:SER130 4.0 19.2 1.0 HG21 A:ILE126 4.0 25.4 1.0 O A:TYR117 4.0 25.6 1.0 H A:TYR117 4.0 22.0 1.0 HA3 A:GLY121 4.0 25.6 1.0 CG2 A:ILE126 4.0 21.1 1.0 CB A:TYR117 4.1 22.4 1.0 OG A:SER130 4.1 20.7 1.0 CA A:GLY118 4.2 21.9 1.0 HB3 A:TYR117 4.2 26.9 1.0 N A:PRO128 4.3 19.4 1.0 CA A:TYR117 4.3 19.9 1.0 O A:PRO128 4.4 19.6 1.0 HG23 A:ILE126 4.4 25.4 1.0 CB A:TYR113 4.4 20.7 1.0 C A:SER130 4.4 16.3 1.0 N A:TYR117 4.5 18.4 1.0 HA2 A:GLY118 4.5 26.3 1.0 HB3 A:SER130 4.5 22.9 1.0 HB3 A:TYR113 4.5 24.8 1.0 HA A:TYR113 4.6 21.4 1.0 HA A:SER130 4.7 20.4 1.0 O A:ILE126 4.8 22.2 1.0 C A:GLY121 4.8 24.0 1.0 N A:VAL119 4.9 21.5 1.0 HD2 A:TYR113 5.0 34.3 1.0

Sodium binding site 2 out of 4 in the Full Length Structure of Tcmip with Bound Inhibitor NJS224.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Full Length Structure of Tcmip with Bound Inhibitor NJS224. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:28.1 occ:1.00 H A:TYR117 2.1 22.0 1.0 HB3 A:ALA116 2.7 19.6 1.0 HB2 A:TYR117 2.7 26.9 1.0 O A:SER130 2.8 19.2 1.0 NA A:NA202 2.8 26.2 1.0 N A:TYR117 2.9 18.4 1.0 HB1 A:ALA116 3.0 19.6 1.0 HG21 A:ILE126 3.1 25.4 1.0 HB2 A:SER130 3.1 22.9 1.0 CB A:ALA116 3.2 16.3 1.0 H A:GLY118 3.3 23.5 1.0 HD21 A:LEU132 3.3 22.4 1.0 HG A:LEU132 3.3 19.1 1.0 HD2 A:TYR117 3.4 23.6 1.0 HA A:TYR113 3.4 21.4 1.0 HD11 A:LEU132 3.5 20.4 1.0 CB A:TYR117 3.5 22.4 1.0 H A:SER130 3.6 22.8 1.0 HG22 A:ILE126 3.6 25.4 1.0 CA A:TYR117 3.6 19.9 1.0 CG2 A:ILE126 3.7 21.1 1.0 N A:GLY118 3.8 19.6 1.0 C A:SER130 3.8 16.3 1.0 HG23 A:ILE126 3.9 25.4 1.0 CB A:SER130 3.9 19.1 1.0 HB2 A:TYR113 3.9 24.8 1.0 C A:TYR117 3.9 23.4 1.0 CG A:LEU132 3.9 15.9 1.0 C A:ALA116 3.9 20.0 1.0 HB2 A:ALA116 4.0 19.6 1.0 CD2 A:LEU132 4.0 18.6 1.0 CD1 A:LEU132 4.1 17.0 1.0 CD2 A:TYR117 4.1 19.6 1.0 CA A:ALA116 4.2 21.0 1.0 N A:SER130 4.2 19.0 1.0 CA A:SER130 4.2 17.0 1.0 HB3 A:TYR117 4.2 26.9 1.0 HB3 A:SER130 4.2 22.9 1.0 CA A:TYR113 4.3 17.8 1.0 O A:TYR113 4.3 20.8 1.0 HD23 A:LEU132 4.3 22.4 1.0 CG A:TYR117 4.3 21.9 1.0 HA2 A:GLY121 4.4 25.6 1.0 HA A:TYR117 4.5 23.9 1.0 CB A:TYR113 4.5 20.7 1.0 HD13 A:ILE126 4.5 24.7 1.0 HD12 A:LEU132 4.5 20.4 1.0 HB3 A:TYR113 4.7 24.8 1.0 H A:ALA116 4.8 25.7 1.0 HD22 A:LEU132 4.8 22.4 1.0 C A:TYR113 4.8 22.6 1.0 O A:GLY118 4.8 20.6 1.0 O A:TYR117 4.8 25.6 1.0 HA A:ALA116 4.9 25.2 1.0 O A:PRO127 4.9 21.6 1.0 HD13 A:LEU132 4.9 20.4 1.0 HA A:PRO131 4.9 20.6 1.0 N A:PRO131 5.0 19.8 1.0 OG A:SER130 5.0 20.7 1.0

Sodium binding site 3 out of 4 in the Full Length Structure of Tcmip with Bound Inhibitor NJS224.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Full Length Structure of Tcmip with Bound Inhibitor NJS224. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:34.9 occ:1.00 HH11 A:ARG102 2.5 41.4 1.0 HZ2 A:TRP107 2.5 28.6 1.0 OD2 A:ASP105 2.7 24.9 1.0 O A:HOH400 2.7 27.9 1.0 O A:LEU100 2.9 26.0 1.0 NH1 A:ARG102 2.9 34.5 1.0 HA A:MET101 3.1 26.2 1.0 HD3 A:ARG102 3.1 50.1 1.0 HH12 A:ARG102 3.1 41.4 1.0 HG11 A:VAL153 3.2 35.4 1.0 CZ2 A:TRP107 3.3 23.8 1.0 HG12 A:VAL153 3.5 35.4 1.0 HD11 A:LEU157 3.5 34.6 1.0 CG A:ASP105 3.7 26.8 1.0 HD12 A:LEU157 3.7 34.6 1.0 HE1 A:TRP107 3.8 28.5 1.0 CG1 A:VAL153 3.8 29.5 1.0 H A:ARG102 3.8 32.6 1.0 CZ A:ARG102 3.8 36.6 1.0 CD A:ARG102 3.9 41.8 1.0 O A:HOH342 3.9 34.0 1.0 CA A:MET101 4.0 21.9 1.0 C A:LEU100 4.0 24.3 1.0 CE2 A:TRP107 4.0 20.2 1.0 HD2 A:ARG102 4.0 50.1 1.0 CD1 A:LEU157 4.1 28.8 1.0 OD1 A:ASP105 4.1 28.4 1.0 NE A:ARG102 4.2 44.1 1.0 NE1 A:TRP107 4.2 23.8 1.0 CH2 A:TRP107 4.2 24.4 1.0 HH2 A:TRP107 4.2 29.3 1.0 HG13 A:VAL153 4.2 35.4 1.0 N A:ARG102 4.4 27.2 1.0 HD13 A:LEU157 4.4 34.6 1.0 HG2 A:MET101 4.4 24.3 1.0 N A:MET101 4.5 25.1 1.0 C A:MET101 4.6 25.9 1.0 HE A:ARG43 4.6 30.1 1.0 O A:HOH341 4.7 45.4 1.0 HB3 A:ASP105 4.7 24.2 1.0 NH2 A:ARG102 4.8 34.9 1.0 CB A:ASP105 4.8 20.2 1.0 HB2 A:ARG102 4.8 30.9 1.0 HB3 A:LEU100 4.8 29.9 1.0 OD1 A:ASP154 4.9 37.7 1.0 HH22 A:ARG102 4.9 41.8 1.0 HB A:VAL153 4.9 35.1 1.0 HE A:ARG102 4.9 52.9 1.0 CB A:MET101 5.0 22.4 1.0 CB A:VAL153 5.0 29.2 1.0

Sodium binding site 4 out of 4 in the Full Length Structure of Tcmip with Bound Inhibitor NJS224.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Full Length Structure of Tcmip with Bound Inhibitor NJS224. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:33.9 occ:1.00 O A:HOH439 2.4 42.0 1.0 OE1 A:GLU133 2.7 24.8 1.0 O A:LEU67 2.8 20.5 1.0 HA2 A:GLY70 3.1 25.5 1.0 H A:GLY70 3.2 24.0 1.0 HB3 A:ARG66 3.5 24.0 1.0 CD A:GLU133 3.5 33.0 1.0 HB3 A:GLU133 3.6 22.9 1.0 HA A:ARG68 3.6 23.9 1.0 HB2 A:ARG66 3.6 24.0 1.0 N A:GLY70 3.7 20.0 1.0 HE1 A:PHE22 3.7 31.0 1.0 HZ A:PHE22 3.7 27.8 1.0 CA A:GLY70 3.8 21.3 1.0 O A:ARG68 3.9 24.0 1.0 HD3 A:ARG66 3.9 35.5 1.0 C A:LEU67 3.9 15.3 1.0 HB2 A:GLU133 3.9 22.9 1.0 CB A:ARG66 4.0 20.0 1.0 C A:ARG68 4.0 21.2 1.0 OE2 A:GLU133 4.1 33.3 1.0 CB A:GLU133 4.1 19.0 1.0 O A:HOH353 4.2 45.0 1.0 CA A:ARG68 4.2 19.9 1.0 CE1 A:PHE22 4.3 25.8 1.0 HA3 A:GLY70 4.3 25.5 1.0 CZ A:PHE22 4.3 23.2 1.0 HD2 A:ARG66 4.3 35.5 1.0 CG A:GLU133 4.4 17.9 1.0 CD A:ARG66 4.5 29.6 1.0 N A:ARG68 4.5 17.8 1.0 N A:ASP69 4.7 20.8 1.0 C A:ASP69 4.7 27.7 1.0 C A:ARG66 4.8 18.4 1.0 HE3 A:LYS26 4.8 38.6 1.0 HG2 A:GLU133 4.8 21.4 1.0 O A:ARG66 4.9 17.5 1.0 C A:GLY70 4.9 23.5 1.0 CG A:ARG66 4.9 24.0 1.0 N A:LEU67 5.0 18.6 1.0

J.J.Whittaker, A.Guskov, B.Goretzki, U.A.Hellmich. Structural Dynamics of Macrophage Infectivity Potentiator Proteins (Mips) Are Differentially Modulated By Inhibitors and Appendage Domains To Be Published.