Chlorine in PDB 5ktr: Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster

Enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster

All present enzymatic activity of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster:
2.5.1.72;

Protein crystallography data

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster, PDB code: 5ktr was solved by M.K.Fenwick, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.62 / 1.34
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	47.256, 52.605, 55.510, 90.00, 111.70, 90.00
*R / R_free (%)*	12.5 / 15.6

Other elements in 5ktr:

The structure of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster (pdb code 5ktr). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster, PDB code: 5ktr:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5ktr

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Chlorine Binding Sites List in 5ktr

Chlorine binding site 1 out of 3 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl403 b:13.7 occ:1.00	N	A:ASP49	3.1	10.8	1.0
	NH2	A:ARG44	3.2	16.0	1.0
	O	A:HOH868	3.3	15.1	0.7
	CD1	A:ILE17	3.5	14.3	1.0
	N	A:ALA50	3.6	10.1	1.0
	NH1	A:ARG44	3.7	12.6	1.0
	CA	A:VAL48	3.8	10.0	1.0
	C	A:VAL48	3.9	10.5	1.0
	CZ	A:ARG44	3.9	12.5	1.0
	CA	A:ASP49	4.0	13.6	1.0
	O	A:ARG47	4.1	12.2	1.0
	CG1	A:VAL48	4.1	11.4	1.0
	CB	A:ASP49	4.1	19.0	1.0
	CB	A:ALA50	4.2	10.7	1.0
	C	A:ASP49	4.3	13.0	1.0
	CB	A:ILE17	4.4	9.1	1.0
	CB	A:VAL48	4.5	11.6	1.0
	CG2	A:ILE17	4.5	8.8	1.0
	CA	A:ALA50	4.5	10.1	1.0
	CG1	A:ILE17	4.5	11.6	1.0
	O	A:HOH598	4.7	18.0	1.0
	OD2	A:ASP49	4.8	26.8	1.0
	N	A:VAL48	4.8	9.3	1.0
	CG	A:ASP49	4.9	25.0	1.0
	C	A:ARG47	4.9	9.9	1.0
	CG2	A:VAL48	4.9	13.3	1.0

Chlorine binding site 2 out of 3 in 5ktr

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Chlorine Binding Sites List in 5ktr

Chlorine binding site 2 out of 3 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl404 b:10.5 occ:1.00	NE2	A:GLN244	3.3	13.7	1.0
	CD1	A:TYR242	3.8	7.8	1.0
	CE1	A:TYR242	4.0	8.1	1.0
	CD	A:GLN244	4.3	12.9	1.0
	OE1	A:GLN244	4.5	13.3	1.0

Chlorine binding site 3 out of 3 in 5ktr

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Chlorine Binding Sites List in 5ktr

Chlorine binding site 3 out of 3 in the Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster

Mono view

Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Pyrococcus Horikoshii Quinolinate Synthase (Nada) with Bound Maleate and FE4S4 Cluster within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cl405 b:11.3 occ:0.80	FE4	A:SF4401	2.3	8.7	0.9
	O	A:HOH825	2.9	30.9	1.0
	O	A:HOH547	3.2	31.5	1.0
	O	A:HOH503	3.4	38.8	0.8
	C3	A:MAE402	3.6	8.6	1.0
	S3	A:SF4401	3.7	9.3	1.0
	CE2	A:TYR23	3.7	6.7	1.0
	S2	A:SF4401	3.8	10.2	1.0
	ND2	A:ASN111	3.9	12.7	0.5
	CE	A:MET61	3.9	13.8	1.0
	C2	A:MAE402	4.0	8.8	1.0
	S1	A:SF4401	4.0	8.0	1.0
	OH	A:TYR109	4.1	9.4	0.5
	CE	A:MET259	4.1	7.6	1.0
	CD2	A:TYR23	4.2	7.1	1.0
	CE1	A:HIS21	4.3	6.4	1.0
	NE2	A:HIS21	4.4	7.0	1.0
	FE1	A:SF4401	4.5	9.5	1.0
	CZ	A:TYR23	4.7	6.1	1.0
	CZ	A:PHE60	4.7	16.6	0.7
	FE2	A:SF4401	4.8	7.7	1.0
	C4	A:MAE402	4.8	8.6	1.0
	FE3	A:SF4401	4.9	7.4	1.0
	OH	A:TYR23	4.9	7.2	1.0
	CG	A:ASN111	4.9	11.8	0.5
	OE2	A:GLU198	4.9	13.1	1.0
	OG	A:SER38	4.9	7.4	0.6

Reference:

M.K.Fenwick, S.E.Ealick. Crystal Structures of the Iron-Sulfur Cluster-Dependent Quinolinate Synthase in Complex with Dihydroxyacetone Phosphate, Iminoaspartate Analogues, and Quinolinate. Biochemistry V. 55 4135 2016.
ISSN: ISSN 0006-2960
PubMed: 27404889
DOI: 10.1021/ACS.BIOCHEM.6B00626

Page generated: Fri Jul 26 10:53:47 2024

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