Chlorine 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 / R_free (%)*	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
Sodium	(Na)	4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 3 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 4xd1

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Chlorine Binding Sites List in 4xd1

Chlorine binding site 1 out of 3 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 Chlorine with other atoms in the Cl 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:Cl413 b:36.1 occ:1.00	N	A:ILE387	3.3	18.1	1.0
	N	A:GLU388	3.3	17.3	1.0
	O	A:HOH898	3.4	20.0	1.0
	O	A:LYS385	3.7	18.0	1.0
	CB	A:GLU388	3.8	21.8	1.0
	C	A:ASN386	4.0	15.7	1.0
	CA	A:ILE387	4.0	17.5	1.0
	O	A:HOH624	4.1	45.1	1.0
	C	A:ILE387	4.1	16.1	1.0
	CA	A:ASN386	4.1	16.1	1.0
	CA	A:GLU388	4.2	19.8	1.0
	CB	A:ILE387	4.2	19.3	1.0
	O	A:HOH542	4.5	46.3	1.0
	C	A:LYS385	4.7	15.3	1.0
	CG1	A:ILE387	4.9	22.5	1.0
	N	A:ASN386	4.9	15.2	1.0
	O	A:ASN386	5.0	13.4	1.0

Chlorine binding site 2 out of 3 in 4xd1

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Chlorine Binding Sites List in 4xd1

Chlorine binding site 2 out of 3 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 Chlorine with other atoms in the Cl 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:Cl414 b:17.0 occ:1.00	O	A:HOH903	3.1	23.8	1.0
	NZ	A:LYS345	3.1	16.3	1.0
	ND2	A:ASN386	3.3	17.3	1.0
	ND2	A:ASN384	3.3	16.8	1.0
	CA	A:MET381	3.7	12.4	1.0
	CE	A:LYS345	3.8	15.3	1.0
	CD	A:LYS345	3.8	13.0	1.0
	CB	A:ASN384	3.8	18.0	1.0
	O	A:TYR380	3.8	14.7	1.0
	CG	A:MET381	3.8	11.2	1.0
	N	A:MET381	3.9	11.8	1.0
	C	A:TYR380	4.0	12.9	1.0
	CG	A:ASN384	4.1	21.2	1.0
	CB	A:MET381	4.3	12.7	1.0
	CG	A:ASN386	4.3	17.0	1.0
	CD2	A:LEU349	4.3	19.8	1.0
	CB	A:ASN386	4.5	17.2	1.0
	CB	A:TYR380	4.5	12.8	1.0
	O	A:HOH871	4.7	35.1	1.0
	C	A:MET381	4.8	12.1	1.0
	O	A:HOH603	4.9	23.5	1.0
	CA	A:TYR380	4.9	12.8	1.0
	O	A:MET381	5.0	13.4	1.0

Chlorine binding site 3 out of 3 in 4xd1

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Chlorine Binding Sites List in 4xd1

Chlorine binding site 3 out of 3 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 Chlorine with other atoms in the Cl 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:Cl415 b:30.5 occ:1.00	O	A:HOH963	2.9	46.3	1.0
	O	A:HOH962	3.1	38.4	1.0
	NZ	A:LYS8	3.1	18.4	1.0
	O	A:HOH715	3.2	23.1	1.0
	ND2	A:ASN33	3.3	14.6	1.0
	O	A:HOH961	3.4	27.5	1.0
	CE	A:LYS8	3.6	15.8	1.0
	CD	A:LYS8	3.8	13.9	1.0
	CB	A:ASN33	4.0	12.8	1.0
	CG	A:ASN33	4.1	13.5	1.0
	CB	A:ASN35	4.4	27.6	1.0
	CB	A:ASP77	4.4	17.5	1.0
	C6Q	A:T3Q402	4.5	23.2	1.0
	OD1	A:ASN35	4.5	54.8	1.0
	CG	A:ASN35	4.7	39.4	1.0
	OD1	A:ASP77	4.9	21.1	1.0
	CG	A:LYS8	5.0	12.5	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: Fri Jul 26 03:22:31 2024

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