Sodium in PDB 6srf: Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones

All present enzymatic activity of Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones:
3.4.13.9;

The structure of Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones, PDB code: 6srf was solved by E.Wator, P.Wilk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.86 / 1.85
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	103.557, 106.692, 216.699, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 21.7

The structure of Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones (pdb code 6srf). 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 Human Prolidase G278N Variant Expressed in the Presence of Chaperones, PDB code: 6srf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones


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 Human Prolidase G278N Variant Expressed in the Presence of Chaperones within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:32.1 occ:0.87 HA2 A:GLY504 2.4 44.9 1.0 MN A:MN501 2.4 20.3 0.4 OE1 A:GLU412 2.6 23.2 1.0 OD2 A:ASP276 2.6 23.9 1.0 C A:GLY504 2.7 24.4 1.0 H2 A:GLY504 2.7 40.0 1.0 CA A:GLY504 2.8 37.5 1.0 OE1 A:GLU452 2.8 19.5 1.0 OE2 A:GLU452 3.1 19.3 1.0 O A:GLY504 3.1 24.0 1.0 N A:GLY504 3.2 33.3 1.0 CD A:GLU452 3.2 27.3 1.0 N A:PRO505 3.2 24.2 1.0 OD1 A:ASP276 3.3 24.4 1.0 CG A:ASP276 3.3 30.4 1.0 HD3 A:PRO505 3.4 46.2 1.0 OD2 A:ASP287 3.4 32.9 1.0 OD1 A:ASP287 3.4 25.4 1.0 CD A:GLU412 3.4 22.9 1.0 H3 A:GLY504 3.5 40.0 1.0 HG1 A:THR289 3.5 25.4 1.0 OE2 A:GLU412 3.5 24.2 1.0 HE A:ARG450 3.6 23.1 1.0 CG A:ASP287 3.7 30.4 1.0 O A:HOH605 3.7 19.3 1.0 HA3 A:GLY504 3.7 44.9 1.0 HA A:PRO505 3.7 30.9 1.0 CD A:PRO505 3.8 38.5 1.0 HG3 A:PRO505 3.9 49.3 1.0 OG1 A:THR289 3.9 21.2 1.0 H1 A:GLY504 4.0 40.0 1.0 CA A:PRO505 4.0 25.7 1.0 NE A:ARG450 4.3 19.2 1.0 CG A:PRO505 4.3 41.1 1.0 HH21 A:ARG450 4.3 35.0 1.0 HB2 A:GLU452 4.4 18.9 1.0 HH A:TYR241 4.5 1.0 1.0 HD2 A:ARG450 4.5 30.4 1.0 CG A:GLU452 4.6 17.1 1.0 HD2 A:PRO505 4.6 46.2 1.0 NE2 A:HIS370 4.7 16.7 1.0 CB A:ASP276 4.7 27.8 1.0 CB A:PRO505 4.7 26.0 1.0 HB2 A:GLU412 4.8 25.3 1.0 HB3 A:GLU412 4.8 25.3 1.0 CG A:GLU412 4.8 24.9 1.0 OH A:TYR241 4.8 0.7 1.0 HB3 A:PRO505 4.9 31.2 1.0 HB2 A:ASP276 4.9 33.3 1.0 NH2 A:ARG450 4.9 29.2 1.0 CB A:GLU452 4.9 15.8 1.0 HG3 A:GLU452 4.9 20.5 1.0 HE2 A:HIS377 4.9 27.5 1.0 HD12 A:ILE244 5.0 52.1 1.0 CD A:ARG450 5.0 25.3 1.0 CZ A:ARG450 5.0 26.1 1.0 CB A:ASP287 5.0 27.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Prolidase G278N Variant Expressed in the Presence of Chaperones


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 Human Prolidase G278N Variant Expressed in the Presence of Chaperones within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:36.1 occ:1.00 HA2 B:GLY503 2.3 44.2 1.0 OE1 B:GLU412 2.4 24.7 1.0 MN B:MN501 2.6 25.6 0.6 OD2 B:ASP276 2.7 22.0 1.0 C B:GLY503 2.7 26.2 1.0 OE1 B:GLU452 2.8 23.3 1.0 CA B:GLY503 2.8 36.8 1.0 H1 B:GLY503 2.9 55.0 1.0 OE2 B:GLU452 3.0 27.7 1.0 HD3 B:PRO504 3.1 34.5 1.0 N B:PRO504 3.1 26.1 1.0 O B:GLY503 3.1 26.5 1.0 N B:GLY503 3.2 45.9 1.0 CD B:GLU452 3.2 26.8 1.0 H2 B:GLY503 3.2 55.0 1.0 CD B:GLU412 3.3 29.9 1.0 CG B:ASP276 3.4 30.6 1.0 OE2 B:GLU412 3.5 23.0 1.0 OD1 B:ASP276 3.5 27.8 1.0 OD2 B:ASP287 3.5 33.1 1.0 HE B:ARG450 3.5 21.6 1.0 CD B:PRO504 3.5 28.8 1.0 OD1 B:ASP287 3.6 22.2 1.0 HG1 B:THR289 3.7 31.6 1.0 HA3 B:GLY503 3.7 44.2 1.0 HA B:PRO504 3.7 37.5 1.0 HG3 B:PRO504 3.8 36.4 1.0 CG B:ASP287 3.8 27.6 1.0 O B:HOH602 3.9 18.0 1.0 OG1 B:THR289 4.0 26.3 1.0 CA B:PRO504 4.0 31.3 1.0 H3 B:GLY503 4.0 55.0 1.0 NE B:ARG450 4.1 18.0 1.0 CG B:PRO504 4.2 30.3 1.0 HD2 B:ARG450 4.2 26.7 1.0 HH21 B:ARG450 4.3 31.7 1.0 HD2 B:PRO504 4.4 34.5 1.0 HB2 B:GLU452 4.4 22.9 1.0 CG B:GLU452 4.5 25.2 1.0 HB2 B:GLU412 4.7 26.8 1.0 CG B:GLU412 4.7 25.9 1.0 NE2 B:HIS370 4.7 17.9 1.0 CB B:PRO504 4.7 27.2 1.0 HB3 B:GLU412 4.7 26.8 1.0 CD B:ARG450 4.8 22.3 1.0 NH2 B:ARG450 4.8 26.4 1.0 CB B:ASP276 4.8 19.7 1.0 OH B:TYR241 4.9 61.5 1.0 CZ B:ARG450 4.9 21.7 1.0 HG3 B:GLU452 4.9 30.3 1.0 CB B:GLU452 4.9 19.1 1.0 HB2 B:ASP276 4.9 23.7 1.0 HE2 B:HIS377 5.0 24.0 1.0 CB B:GLU412 5.0 22.3 1.0

E.Wator, M.Rutkiewicz, M.S.Weiss, P.Wilk. Co-Expression with Chaperones Can Affect Protein 3D-Structure As Exemplified By Loss-of-Function Variants of Human Prolidase. Febs Lett. 2020.
ISSN: ISSN 0014-5793
PubMed: 32598484
DOI: 10.1002/1873-3468.13877