Iodine in PDB 5kss: Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

Enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

All present enzymatic activity of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller):
3.1.3.5;

Protein crystallography data

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller), PDB code: 5kss was solved by A.T.P.Machado, E.M.B.Fonseca, M.A.Dos Reis, A.M.Saraiva, C.A.Dos Santos, A.M.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	43.94 / 2.82
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	86.941, 80.118, 71.511, 90.00, 95.51, 90.00
*R / R_free (%)*	27.2 / 32.9

Other elements in 5kss:

The structure of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Chlorine	(Cl)	2 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) (pdb code 5kss). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 3 binding sites of Iodine where determined in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller), PDB code: 5kss:
Jump to Iodine binding site number: 1; 2; 3;

Iodine binding site 1 out of 3 in 5kss

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Iodine Binding Sites List in 5kss

Iodine binding site 1 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I502 b:0.2 occ:0.54	ND2	A:ASN44	3.5	42.6	1.0
	N	A:ASN44	3.6	53.4	1.0
	CG	A:ASN44	3.8	44.8	1.0
	ND2	B:ASN44	3.8	46.8	1.0
	N	B:ASN44	4.0	61.4	1.0
	CB	A:ASN44	4.0	49.0	1.0
	CA	A:SER43	4.1	57.6	1.0
	CG	B:ASN44	4.1	66.5	1.0
	C	A:SER43	4.3	55.9	1.0
	O	A:TYR103	4.3	46.0	1.0
	CA	B:SER43	4.3	63.0	1.0
	O	B:TYR103	4.3	58.7	1.0
	OD1	A:ASN44	4.4	45.8	1.0
	CB	B:ASN44	4.4	66.4	1.0
	CA	A:ASN44	4.5	51.5	1.0
	O	A:HOH608	4.5	51.4	1.0
	OG	A:SER43	4.5	58.9	1.0
	CB	B:TYR103	4.5	72.5	1.0
	O	A:ALA42	4.5	63.3	1.0
	C	B:SER43	4.6	60.3	1.0
	CA	B:TYR103	4.6	64.8	1.0
	OG	B:SER43	4.7	67.2	1.0
	CA	A:TYR103	4.7	46.8	1.0
	CB	A:TYR103	4.7	47.1	1.0
	O	B:ALA42	4.7	68.9	1.0
	OD1	B:ASN44	4.7	46.7	1.0
	CD1	B:TYR103	4.7	77.7	1.0
	CA	B:ASN44	4.8	62.0	1.0
	CB	A:SER43	4.8	59.0	1.0
	C	A:TYR103	4.9	47.5	1.0
	C	B:TYR103	4.9	59.8	1.0
	CD1	A:TYR103	5.0	54.5	1.0
	CG	B:TYR103	5.0	77.6	1.0

Iodine binding site 2 out of 3 in 5kss

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Iodine Binding Sites List in 5kss

Iodine binding site 2 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I503 b:75.3 occ:0.41	NE2	B:HIS235	3.3	71.6	1.0
	N	A:TYR241	3.5	74.0	1.0
	CE1	B:HIS235	3.7	71.1	1.0
	CB	A:TYR241	3.9	75.4	1.0
	CD1	A:TYR241	4.0	69.1	1.0
	NE2	B:GLN242	4.1	77.8	0.0
	O	A:THR239	4.1	69.6	1.0
	N	A:GLN242	4.1	73.1	1.0
	CA	A:TYR241	4.1	75.5	1.0
	C	A:ARG240	4.3	74.8	1.0
	CA	A:ARG240	4.4	69.4	1.0
	CG	A:GLN242	4.4	68.0	0.0
	CG	A:TYR241	4.4	73.4	1.0
	I	A:IOD505	4.5	71.2	0.5
	CE1	A:HIS235	4.5	73.9	1.0
	NE2	A:GLN242	4.6	66.0	0.0
	CD2	B:HIS235	4.6	68.6	1.0
	C	A:TYR241	4.6	78.3	1.0
	CD	A:GLN242	4.8	67.8	0.0
	CB	A:GLN242	4.9	70.4	1.0
	ND1	B:HIS235	5.0	68.5	1.0
	NE2	A:HIS235	5.0	73.5	1.0

Iodine binding site 3 out of 3 in 5kss

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Iodine Binding Sites List in 5kss

Iodine binding site 3 out of 3 in the Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller)

Mono view

Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Stationary Phase Survival Protein E (Sure) From Xylella Fastidiosa - Xfsure-Ds (Dimer Smaller) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:I505 b:71.2 occ:0.48	NE2	A:HIS235	3.0	73.5	1.0
	CE1	A:HIS235	3.2	73.9	1.0
	N	B:TYR241	3.5	65.3	1.0
	CG	B:GLN242	3.9	78.2	1.0
	N	B:GLN242	3.9	79.8	1.0
	NE2	B:GLN242	4.0	77.8	0.0
	CA	B:ARG240	4.1	78.4	1.0
	C	B:ARG240	4.2	79.7	1.0
	CB	B:TYR241	4.2	66.6	1.0
	O	B:THR239	4.2	80.3	1.0
	CA	B:TYR241	4.2	66.9	1.0
	CD2	A:HIS235	4.3	69.9	1.0
	CD	B:GLN242	4.3	79.7	0.0
	CD1	B:TYR241	4.4	62.3	1.0
	NE2	A:GLN242	4.5	66.0	0.0
	I	A:IOD503	4.5	75.3	0.4
	ND1	A:HIS235	4.5	71.2	1.0
	CB	B:GLN242	4.6	80.8	1.0
	C	B:TYR241	4.6	81.0	1.0
	CG	B:ARG240	4.6	95.6	1.0
	CE1	B:HIS235	4.6	71.1	1.0
	CG	B:TYR241	4.8	75.8	1.0
	NE2	B:HIS235	4.9	71.6	1.0
	CA	B:GLN242	4.9	80.3	1.0
	CB	B:ARG240	5.0	64.5	1.0

Reference:

A.T.P.Machado, E.M.B.Fonseca, M.A.D.Reis, A.M.Saraiva, C.A.D.Santos, M.A.S.De Toledo, I.Polikarpov, A.P.De Souza, R.Aparicio, J.Iulek. Conformational Variability of the Stationary Phase Survival Protein E From Xylella Fastidiosa Revealed By X-Ray Crystallography, Small-Angle X-Ray Scattering Studies, and Normal Mode Analysis. Proteins V. 85 1931 2017.
ISSN: ESSN 1097-0134
PubMed: 28677327
DOI: 10.1002/PROT.25347

Page generated: Sun Aug 11 21:20:34 2024

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