Sodium in PDB 8afv: DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I)

All present enzymatic activity of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I):
1.2.1.38;

The structure of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I), PDB code: 8afv was solved by P.Pfister, M.Nattermann, J.Zarzycki, T.J.Erb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.36 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	91.877, 109.55, 133.225, 90, 90, 90
R / Rfree (%)	18.9 / 20.7

The binding sites of Sodium atom in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I) (pdb code 8afv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I), PDB code: 8afv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:25.6 occ:1.00 O A:HOH541 2.4 22.3 1.0 O B:HOH562 2.5 23.1 1.0 O D:HOH440 2.5 31.8 1.0 O A:PRO235 2.5 18.2 1.0 O B:PRO235 2.6 19.5 1.0 C A:PRO235 3.7 21.0 1.0 C B:PRO235 3.8 20.4 1.0 CB A:PRO235 4.0 18.8 1.0 CB B:PRO235 4.1 19.0 1.0 OE2 B:GLU198 4.4 25.4 1.0 OE2 A:GLU198 4.4 21.3 1.0 CG A:PRO235 4.4 19.8 1.0 OD1 A:ASN197 4.4 21.6 1.0 CG B:PRO235 4.5 17.0 1.0 CA A:PRO235 4.5 20.5 1.0 CA B:PRO235 4.6 18.5 1.0 OD1 B:ASN197 4.7 17.5 1.0 N A:ALA236 4.7 17.2 1.0 N B:ALA236 4.8 17.4 1.0 CA A:ALA236 4.9 20.6 1.0 CA B:ALA236 4.9 17.5 1.0 CZ D:PHE193 5.0 22.6 1.0

Sodium binding site 2 out of 4 in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:30.1 occ:1.00 OD2 A:ASP282 2.7 21.5 1.0 CE1 A:HIS276 2.7 25.6 1.0 OD2 A:ASP290 2.7 23.1 1.0 CA A:PRO278 3.3 19.7 1.0 CB A:PRO278 3.4 23.8 1.0 CG A:ASP282 3.4 21.7 1.0 CB A:ASP282 3.5 22.4 1.0 O A:HOH515 3.5 20.1 1.0 NE2 A:HIS276 3.6 26.0 1.0 CG A:ASP290 3.6 23.1 1.0 ND1 A:HIS276 3.7 25.5 1.0 CB A:ASP290 3.8 18.9 1.0 CG A:PRO278 3.9 20.1 1.0 CE1 A:TYR272 4.0 25.8 1.0 CB C:PRO46 4.1 22.8 1.0 N A:PRO278 4.2 20.9 1.0 O A:HOH506 4.2 23.0 1.0 N A:SER279 4.3 20.9 1.0 C A:PRO278 4.4 21.7 1.0 CZ A:TYR272 4.4 24.4 1.0 OH A:TYR272 4.5 27.2 1.0 OD1 A:ASP282 4.5 19.9 1.0 CD1 A:TYR272 4.6 25.0 1.0 O A:ILE277 4.7 19.9 1.0 CD A:PRO278 4.7 19.0 1.0 C A:ILE277 4.8 20.3 1.0 CD2 A:HIS276 4.8 19.6 1.0 OD1 A:ASP290 4.8 21.3 1.0 CG A:HIS276 4.8 23.1 1.0 CG C:PRO46 5.0 24.3 1.0 CA A:ASP282 5.0 17.3 1.0

Sodium binding site 3 out of 4 in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:51.5 occ:1.00 O B:HOH656 2.4 42.4 1.0 O B:HOH631 2.4 52.3 1.0 OD1 B:ASP282 2.5 26.2 1.0 O B:HOH535 2.7 29.8 1.0 OG B:SER279 2.7 27.0 1.0 CG B:ASP282 3.2 26.2 1.0 OD2 B:ASP282 3.3 26.3 1.0 O A:HOH624 3.3 45.2 1.0 CB B:SER279 3.8 24.7 1.0 O B:HOH576 4.2 32.5 1.0 O B:HOH648 4.3 52.2 1.0 O B:HOH538 4.3 29.8 1.0 CG D:PRO46 4.5 31.4 1.0 N B:SER279 4.6 21.0 1.0 CB B:ASP282 4.6 24.8 1.0 OD2 A:ASP199 4.7 26.0 1.0 N B:ASP282 4.7 26.5 1.0 CD D:PRO46 4.8 27.7 1.0 CA B:SER279 4.8 22.8 1.0 O A:HOH623 4.9 55.5 1.0 OD1 A:ASP199 4.9 25.3 1.0 CB B:ALA281 5.0 26.4 1.0

Sodium binding site 4 out of 4 in the DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of DAARGC3 - Engineered Formyl Phosphate Reductase with 3 Substitutions (S178V, G182V, L233I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na401 b:24.7 occ:1.00 O D:HOH438 2.3 20.7 1.0 O C:HOH544 2.4 22.1 1.0 O C:PRO235 2.6 22.0 1.0 O D:PRO235 2.6 22.5 1.0 C C:PRO235 3.8 22.7 1.0 C D:PRO235 3.8 24.5 1.0 CB C:PRO235 4.1 20.5 1.0 CB D:PRO235 4.1 22.4 1.0 OE2 D:GLU198 4.3 23.1 1.0 OE2 C:GLU198 4.4 24.1 1.0 O D:HOH440 4.5 31.8 1.0 CG D:PRO235 4.5 22.2 1.0 OD1 C:ASN197 4.5 19.9 1.0 CG C:PRO235 4.5 22.2 1.0 OD1 D:ASN197 4.5 20.7 1.0 CA C:PRO235 4.6 23.1 1.0 CA D:PRO235 4.6 22.1 1.0 N C:ALA236 4.8 20.9 1.0 N D:ALA236 4.8 22.1 1.0 CA C:ALA236 4.9 21.2 1.0 CZ B:PHE193 5.0 21.7 1.0 CZ A:PHE193 5.0 19.3 1.0 CA D:ALA236 5.0 23.3 1.0

M.Nattermann, S.Wenk, P.Pfister, N.Guntermann, L.Nickel, J.Zarzycki, G.Francio, W.Leitner, A.Bar-Even, T.J.Erb. N-Acetyl-Gamma-Glutamyl-Phosphate Reductase of Denitrovibrio Acetiphilus To Be Published.