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Sodium in PDB 4xcz: X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with Tdp-QUI3N and N5-Thf

Enzymatic activity of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with Tdp-QUI3N and N5-Thf

All present enzymatic activity of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 in Complex with Tdp-QUI3N and N5-Thf, PDB code: 4xcz 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) 37.90 / 1.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.235, 78.235, 151.131, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.5

Other elements in 4xcz:

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

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

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with Tdp-QUI3N and N5-Thf (pdb code 4xcz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with Tdp-QUI3N and N5-Thf, PDB code: 4xcz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 4xcz

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Sodium binding site 1 out of 5 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 in Complex with Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:27.5
occ:1.00
 O A:HOH960 2.5 44.0 1.0
O A:ASN39 2.6 21.1 1.0
O A:HOH685 2.7 27.5 1.0
O A:GLN43 2.8 18.1 1.0
O A:HOH690 2.9 34.1 1.0
OG A:SER41 3.0 26.0 1.0
N A:SER41 3.5 20.7 1.0
CB A:SER41 3.7 23.6 1.0
C A:ASN39 3.8 23.2 1.0
C A:GLN43 3.9 15.4 1.0
C A:ASP40 3.9 22.7 1.0
N A:SER45 4.0 16.9 1.0
CA A:ASP40 4.0 23.7 1.0
C A:LEU44 4.0 19.9 1.0
O A:HOH684 4.1 23.9 1.0
O A:LEU44 4.1 18.9 1.0
CA A:SER41 4.2 19.8 1.0
N A:ASP40 4.3 22.0 1.0
CA A:SER45 4.4 17.2 1.0
CB A:SER45 4.6 15.3 1.0
N A:LEU44 4.7 19.4 1.0
O A:ASP40 4.7 26.0 1.0
O A:HOH683 4.7 14.0 1.0
CA A:LEU44 4.7 18.1 1.0
OD1 A:ASN9 4.8 15.6 1.0
O A:HOH689 4.8 25.4 1.0
CA A:GLN43 4.8 15.0 1.0
N A:GLN43 4.9 14.8 1.0
CB A:GLN43 4.9 16.3 1.0
CA A:ASN39 5.0 24.0 1.0

Sodium binding site 2 out of 5 in 4xcz

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Sodium binding site 2 out of 5 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 in Complex with Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:16.8
occ:1.00
 O A:HOH616 2.2 26.2 1.0
O A:ILE135 2.3 13.7 1.0
O A:HOH721 2.4 17.0 1.0
OG A:SER176 2.4 18.9 1.0
O A:HOH561 2.5 16.4 1.0
O A:SER176 2.5 16.8 1.0
C A:SER176 3.2 15.6 1.0
C A:ILE135 3.3 13.3 1.0
CB A:SER176 3.5 19.4 1.0
N A:SER176 3.6 15.0 1.0
CA A:SER176 3.6 16.5 1.0
CA A:ILE135 3.7 14.2 1.0
CG2 A:ILE135 4.1 16.1 1.0
N A:ILE177 4.3 16.9 1.0
O A:HOH566 4.3 16.9 1.0
O A:HOH1015 4.4 37.5 1.0
O A:ILE134 4.5 13.2 1.0
N A:ASP136 4.5 14.2 1.0
CB A:ILE135 4.5 14.5 1.0
O A:HOH720 4.7 19.0 1.0
CA A:ILE177 4.7 16.2 1.0
N A:ILE135 4.8 13.7 1.0
C A:TYR175 4.9 17.5 1.0

Sodium binding site 3 out of 5 in 4xcz

Go back to Sodium Binding Sites List in 4xcz
Sodium binding site 3 out of 5 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 in Complex with Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:18.3
occ:1.00
 O A:LYS190 2.3 13.4 1.0
O A:ILE193 2.4 13.6 1.0
O A:HOH781 2.4 28.6 1.0
O A:HOH773 2.4 19.0 1.0
O A:HOH630 2.4 22.6 1.0
OH A:TYR105 2.5 14.9 1.0
C A:LYS190 3.5 14.2 1.0
CZ A:TYR105 3.5 12.2 1.0
C A:ILE193 3.6 12.3 1.0
CE2 A:TYR105 3.8 11.4 1.0
O A:HOH511 3.9 27.6 1.0
O A:HOH918 4.1 33.8 1.0
CA A:ASP194 4.1 15.1 1.0
O A:HOH780 4.1 25.6 1.0
CA A:LYS190 4.2 15.6 1.0
N A:ASP194 4.3 13.4 1.0
O A:HOH783 4.4 21.9 1.0
N A:LYS191 4.5 14.6 1.0
CB A:LYS190 4.5 21.0 1.0
N A:TYR195 4.5 12.2 1.0
N A:ILE193 4.6 12.1 1.0
CA A:LYS191 4.6 16.1 1.0
CE1 A:TYR105 4.7 11.6 1.0
CA A:ILE193 4.7 11.3 1.0
O A:HOH555 4.8 24.7 1.0
CD2 A:TYR195 4.8 12.5 1.0
C A:ASP194 4.9 13.2 1.0
C A:LYS191 4.9 15.2 1.0

Sodium binding site 4 out of 5 in 4xcz

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Sodium binding site 4 out of 5 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 in Complex with Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:16.8
occ:1.00
 O A:HOH636 2.6 32.5 1.0
O A:LYS196 2.6 21.1 1.0
OD1 A:ASN197 3.0 20.7 0.5
C A:LYS196 3.8 19.4 1.0
CG A:ASN197 4.0 22.4 0.5
O A:HOH554 4.3 40.3 1.0
CA A:ASN197 4.4 18.6 0.5
CA A:ASN197 4.4 18.1 0.5
N A:ASN197 4.6 16.9 1.0
CB A:ASN197 4.8 19.8 0.5
ND2 A:ASN197 4.8 25.2 0.5
CB A:ASN197 4.8 21.1 0.5
O A:HOH802 4.8 31.8 1.0
CA A:LYS196 4.8 17.1 1.0
OD1 A:ASN197 4.9 21.2 0.5

Sodium binding site 5 out of 5 in 4xcz

Go back to Sodium Binding Sites List in 4xcz
Sodium binding site 5 out of 5 in the X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with 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 5 of X-Ray Structure of the N-Formyltransferase Qdtf From Providencia Alcalifaciens in Complex with Tdp-QUI3N and N5-Thf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:25.2
occ:1.00
 O A:HOH508 1.7 27.3 1.0
O A:HOH512 2.2 1.0 1.0
O A:LEU291 2.6 15.2 1.0
O A:SER288 2.8 14.9 1.0
O A:HOH632 2.9 22.3 1.0
O A:HOH648 2.9 42.7 1.0
O A:HOH838 3.1 25.1 1.0
CD1 A:LEU291 3.7 14.8 1.0
C A:LEU291 3.7 15.3 1.0
O A:HOH577 3.9 24.6 1.0
C A:SER288 4.0 14.4 1.0
CG A:LEU291 4.1 14.9 1.0
O A:LYS289 4.4 16.7 1.0
CA A:LYS292 4.5 12.0 1.0
CA A:LYS289 4.5 15.0 1.0
N A:LYS292 4.5 12.0 1.0
O A:HOH581 4.6 22.7 1.0
C A:LYS289 4.6 15.3 1.0
CA A:LEU291 4.7 14.9 1.0
O A:HOH567 4.7 18.3 1.0
N A:LYS289 4.8 16.0 1.0
N A:LEU291 4.8 14.8 1.0
C A:LYS292 4.9 13.6 1.0
CB A:LEU291 4.9 14.6 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 19:03:05 2024

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