Sodium in PDB 4xd0: X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens

All present enzymatic activity of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens:
2.1.2.9;

The structure of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, PDB code: 4xd0 was solved by J.B.Thoden, C.R.Woodford, H.M.Holden, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.97 / 1.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.134, 78.134, 151.424, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.5

The structure of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens (pdb code 4xd0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, PDB code: 4xd0:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:22.1 occ:1.00 O A:HOH569 2.8 32.6 1.0 O A:ASN384 2.8 26.7 1.0 O A:LYS385 2.9 25.5 1.0 OD1 A:ASN386 3.1 24.7 1.0 C A:LYS385 3.5 22.5 1.0 O A:HOH552 3.9 24.1 1.0 CG A:ASN386 3.9 22.4 1.0 C A:ASN384 3.9 25.9 1.0 CB A:LYS385 4.0 28.1 1.0 CA A:LYS385 4.2 25.4 1.0 N A:ASN386 4.3 22.3 1.0 ND2 A:ASN386 4.4 23.0 1.0 N A:LYS385 4.5 25.0 1.0 CA A:ASN386 4.6 22.5 1.0 O A:HOH716 4.9 29.3 1.0 CB A:ASN386 4.9 22.0 1.0

Sodium binding site 2 out of 3 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:26.4 occ:1.00 O A:ILE193 2.3 20.7 1.0 O A:HOH754 2.3 38.4 1.0 O A:HOH753 2.3 23.6 1.0 O A:LYS190 2.4 21.2 1.0 O A:HOH579 2.6 32.4 1.0 OH A:TYR105 2.6 20.9 1.0 C A:ILE193 3.5 20.7 1.0 C A:LYS190 3.6 23.5 1.0 CZ A:TYR105 3.6 22.6 1.0 CE2 A:TYR105 3.8 19.2 1.0 O A:HOH501 3.9 37.6 1.0 CA A:ASP194 4.0 22.0 1.0 N A:ASP194 4.2 20.6 1.0 N A:TYR195 4.4 19.6 1.0 CA A:LYS190 4.4 23.9 1.0 O A:HOH547 4.5 37.8 1.0 N A:LYS191 4.5 23.0 1.0 CA A:ILE193 4.6 18.5 1.0 CA A:LYS191 4.6 23.8 1.0 N A:ILE193 4.6 17.9 1.0 C A:ASP194 4.8 20.2 1.0 CB A:LYS190 4.8 32.2 1.0 CE1 A:TYR105 4.8 19.3 1.0 C A:LYS191 4.9 22.1 1.0 CD2 A:TYR195 5.0 19.7 1.0

Sodium binding site 3 out of 3 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:24.0 occ:1.00 O A:HOH540 2.1 25.1 1.0 OG A:SER176 2.4 25.8 1.0 O A:SER176 2.4 23.6 1.0 O A:ILE135 2.4 20.1 1.0 O A:HOH673 2.5 26.6 1.0 O A:HOH531 2.6 23.4 1.0 C A:SER176 3.1 25.0 1.0 C A:ILE135 3.3 19.9 1.0 CB A:SER176 3.5 26.0 1.0 N A:SER176 3.5 28.9 1.0 CA A:SER176 3.5 26.6 1.0 CA A:ILE135 3.6 21.3 1.0 N A:ILE177 4.1 22.9 1.0 CG2 A:ILE135 4.1 21.6 1.0 O A:ILE134 4.4 21.1 1.0 CA A:ILE177 4.4 22.9 1.0 CB A:ILE135 4.5 21.9 1.0 O A:HOH545 4.5 26.5 1.0 N A:ASP136 4.6 20.1 1.0 C A:TYR175 4.7 29.5 1.0 N A:ILE135 4.7 21.5 1.0 O A:HOH699 4.8 23.9 1.0 C A:ILE134 5.0 21.1 1.0

C.R.Woodford, J.B.Thoden, H.M.Holden. New Role For the Ankyrin Repeat Revealed By A Study of the N-Formyltransferase From Providencia Alcalifaciens. Biochemistry V. 54 631 2015.
ISSN: ISSN 0006-2960
PubMed: 25574689
DOI: 10.1021/BI501539A