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Sodium in PDB 4xd1: X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf

Enzymatic activity of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf

All present enzymatic activity of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf:
2.1.2.9;

Protein crystallography data

The structure of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf, PDB code: 4xd1 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) 35.03 / 1.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.279, 78.279, 151.105, 90.00, 90.00, 90.00
R / Rfree (%) 18 / 20.8

Other elements in 4xd1:

The structure of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf also contains other interesting chemical elements:

Potassium (K) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf (pdb code 4xd1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf, PDB code: 4xd1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4xd1

Go back to Sodium Binding Sites List in 4xd1
Sodium binding site 1 out of 4 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf


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, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:42.2
occ:1.00
 O A:GLN43 2.7 19.2 1.0
O A:HOH713 2.8 29.9 1.0
O A:HOH971 3.0 34.7 1.0
O A:HOH716 3.0 29.5 1.0
O A:ASN39 3.1 23.8 1.0
OG A:SER41 3.1 25.5 1.0
C A:GLN43 3.7 14.6 1.0
N A:SER41 3.7 22.8 1.0
O A:HOH712 3.8 24.0 1.0
O A:LEU44 3.8 17.6 1.0
N A:SER45 3.8 17.4 1.0
C A:LEU44 3.9 21.4 1.0
CB A:SER41 3.9 23.2 1.0
C A:ASP40 4.2 27.9 1.0
C A:ASN39 4.2 25.6 1.0
CA A:SER45 4.2 17.3 1.0
CA A:ASP40 4.2 24.2 1.0
O A:HOH711 4.4 13.6 1.0
OD1 A:ASN9 4.4 16.4 1.0
CA A:SER41 4.4 20.4 1.0
N A:LEU44 4.5 19.6 1.0
CA A:LEU44 4.6 18.3 1.0
CA A:GLN43 4.6 14.1 1.0
CB A:SER45 4.6 16.4 1.0
CB A:GLN43 4.6 13.6 1.0
N A:ASP40 4.7 23.7 1.0
N A:GLN43 4.7 15.0 1.0
O A:HOH1031 4.8 46.0 1.0
O A:ASP40 4.9 24.9 1.0

Sodium binding site 2 out of 4 in 4xd1

Go back to Sodium Binding Sites List in 4xd1
Sodium binding site 2 out of 4 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf


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, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:15.8
occ:1.00
 O A:ILE135 2.3 11.6 1.0
O A:HOH630 2.3 19.3 1.0
OG A:SER176 2.4 15.1 1.0
O A:SER176 2.5 13.8 1.0
O A:HOH748 2.5 14.7 1.0
O A:HOH578 2.5 11.4 1.0
C A:SER176 3.2 13.9 1.0
C A:ILE135 3.3 11.6 1.0
CB A:SER176 3.5 16.0 1.0
CA A:SER176 3.6 13.5 1.0
N A:SER176 3.6 13.5 1.0
CA A:ILE135 3.7 11.8 1.0
N A:ILE177 4.2 14.1 1.0
CG2 A:ILE135 4.2 14.1 1.0
O A:HOH1010 4.4 35.0 1.0
O A:HOH546 4.4 15.1 1.0
O A:ILE134 4.4 11.8 1.0
N A:ASP136 4.5 11.1 1.0
CB A:ILE135 4.5 12.1 1.0
CA A:ILE177 4.7 15.1 1.0
O A:HOH747 4.8 17.0 1.0
N A:ILE135 4.8 11.9 1.0
C A:TYR175 4.8 15.8 1.0
C A:ILE134 5.0 11.2 1.0

Sodium binding site 3 out of 4 in 4xd1

Go back to Sodium Binding Sites List in 4xd1
Sodium binding site 3 out of 4 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf


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, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:19.0
occ:1.00
 O A:LYS190 2.3 13.1 1.0
O A:ILE193 2.3 12.4 1.0
O A:HOH798 2.4 17.4 1.0
O A:HOH644 2.4 19.8 1.0
O A:HOH805 2.5 28.9 1.0
OH A:TYR105 2.5 15.6 1.0
C A:LYS190 3.4 13.7 1.0
CZ A:TYR105 3.5 12.2 1.0
C A:ILE193 3.5 11.9 1.0
CE2 A:TYR105 3.7 10.9 1.0
O A:HOH503 4.0 24.4 1.0
CA A:ASP194 4.1 13.4 1.0
CA A:LYS190 4.2 15.9 1.0
O A:HOH804 4.2 25.8 1.0
O A:HOH932 4.3 31.5 1.0
N A:ASP194 4.3 12.6 1.0
CB A:LYS190 4.4 23.2 1.0
N A:LYS191 4.4 13.4 1.0
N A:ILE193 4.5 11.1 1.0
O A:HOH807 4.5 21.0 1.0
N A:TYR195 4.5 13.2 1.0
CA A:ILE193 4.6 10.0 1.0
CA A:LYS191 4.6 15.6 1.0
CE1 A:TYR105 4.7 10.6 1.0
O A:HOH799 4.7 25.1 1.0
CD2 A:TYR195 4.8 12.8 1.0
C A:LYS191 4.8 14.3 1.0
C A:ASP194 4.9 12.4 1.0

Sodium binding site 4 out of 4 in 4xd1

Go back to Sodium Binding Sites List in 4xd1
Sodium binding site 4 out of 4 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens, W305A Mutant, in the Presence of Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:31.7
occ:1.00
 O A:LEU291 2.5 14.9 1.0
O A:HOH643 2.7 21.2 1.0
O A:SER288 3.0 12.2 1.0
O A:HOH693 3.0 38.5 1.0
O A:HOH594 3.5 26.9 1.0
O A:HOH859 3.5 21.9 1.0
C A:LEU291 3.7 15.2 1.0
CD1 A:LEU291 3.9 13.6 1.0
C A:SER288 4.2 14.2 1.0
O A:LYS289 4.2 15.1 1.0
CG A:LEU291 4.3 13.2 1.0
CA A:LYS292 4.3 10.9 1.0
CA A:LYS289 4.3 13.6 1.0
C A:LYS289 4.4 13.8 1.0
N A:LYS292 4.5 12.6 1.0
O A:HOH559 4.6 20.2 1.0
O A:HOH607 4.6 22.3 1.0
CA A:LEU291 4.7 13.5 1.0
N A:LEU291 4.7 13.0 1.0
N A:LYS289 4.8 13.7 1.0
C A:LYS292 4.8 12.4 1.0

Reference:

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
Page generated: Mon Oct 7 19:03:43 2024

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