Cadmium in PDB 5cwx: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

Enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134:
3.5.1.88;

Protein crystallography data

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134, PDB code: 5cwx was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.40 / 2.20
*Space group*	P 6₁ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	58.528, 58.528, 264.214, 90.00, 90.00, 120.00
*R / R_free (%)*	20.7 / 25.9

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 (pdb code 5cwx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 4 binding sites of Cadmium where determined in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134, PDB code: 5cwx:
Jump to Cadmium binding site number: 1; 2; 3; 4;

Cadmium binding site 1 out of 4 in 5cwx

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Cadmium Binding Sites List in 5cwx

Cadmium binding site 1 out of 4 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

Mono view

Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cd201 b:31.9 occ:0.50	CD	A:CD201	0.0	31.9	0.5
	SG	A:CYS99	2.0	33.4	1.0
	CD	A:CD201	2.1	34.9	0.5
	NE2	A:HIS141	2.2	33.5	1.0
	NE2	A:HIS145	2.4	24.4	1.0
	CB	A:CYS99	3.0	32.4	1.0
	CD2	A:HIS141	3.1	38.1	1.0
	CE1	A:HIS145	3.1	25.1	1.0
	CE1	A:HIS141	3.3	38.2	1.0
	O	A:HOH348	3.4	41.6	1.0
	CD2	A:HIS145	3.6	28.0	1.0
	CA	A:CYS99	3.7	33.4	1.0
	O	A:HOH337	3.7	32.6	1.0
	NE2	A:GLN51	3.8	28.2	1.0
	OE1	A:GLN51	3.8	31.1	1.0
	CD	A:GLN51	4.0	30.9	1.0
	OE2	A:GLU142	4.0	35.9	1.0
	CG	A:HIS141	4.3	29.2	1.0
	N7	A:56K205	4.3	50.1	1.0
	ND1	A:HIS141	4.4	31.2	1.0
	ND1	A:HIS145	4.4	25.9	1.0
	O	A:HOH355	4.4	36.6	1.0
	C	A:CYS99	4.5	34.0	1.0
	N	A:LEU100	4.5	34.2	1.0
	O	A:GLY98	4.5	39.0	1.0
	OE1	A:GLU142	4.6	34.6	1.0
	CG	A:HIS145	4.6	26.8	1.0
	CD	A:GLU142	4.7	28.8	1.0
	N	A:CYS99	4.9	36.7	1.0

Cadmium binding site 2 out of 4 in 5cwx

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Cadmium Binding Sites List in 5cwx

Cadmium binding site 2 out of 4 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

Mono view

Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cd201 b:34.9 occ:0.50	CD	A:CD201	0.0	34.9	0.5
	CD	A:CD201	2.1	31.9	0.5
	OE1	A:GLN51	2.4	31.1	1.0
	OE2	A:GLU142	2.5	35.9	1.0
	O	A:HOH348	2.5	41.6	1.0
	NE2	A:HIS145	2.6	24.4	1.0
	OE1	A:GLU142	2.7	34.6	1.0
	CD	A:GLU142	3.0	28.8	1.0
	CD2	A:HIS145	3.1	28.0	1.0
	CD	A:GLN51	3.1	30.9	1.0
	NE2	A:HIS141	3.3	33.5	1.0
	NE2	A:GLN51	3.4	28.2	1.0
	CD2	A:HIS141	3.4	38.1	1.0
	SG	A:CYS99	3.8	33.4	1.0
	CE1	A:HIS145	3.8	25.1	1.0
	N7	A:56K205	3.9	50.1	1.0
	O	A:GLY46	4.0	27.6	1.0
	CG	A:HIS145	4.4	26.8	1.0
	CG	A:GLN51	4.4	26.2	1.0
	CA	A:LEU47	4.5	26.0	1.0
	CG	A:GLU142	4.5	26.7	1.0
	C	A:GLY46	4.5	27.8	1.0
	CE1	A:HIS141	4.6	38.2	1.0
	N	A:ALA48	4.7	22.9	1.0
	ND1	A:HIS145	4.7	25.9	1.0
	CG	A:HIS141	4.7	29.2	1.0
	N	A:LEU47	4.8	24.8	1.0
	CB	A:CYS99	4.8	32.4	1.0
	O	A:HOH362	4.9	33.1	1.0
	CA	A:GLU142	5.0	27.2	1.0

Cadmium binding site 3 out of 4 in 5cwx

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Cadmium Binding Sites List in 5cwx

Cadmium binding site 3 out of 4 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

Mono view

Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cd202 b:38.2 occ:1.00	OE1	A:GLU128	2.3	31.0	1.0
	OE2	A:GLU130	2.5	36.4	1.0
	OE1	A:GLU130	2.6	41.3	1.0
	OE2	A:GLU128	2.8	36.4	1.0
	CD	A:GLU130	2.9	36.6	1.0
	CD	A:GLU128	2.9	32.8	1.0
	NE	A:ARG116	4.3	36.1	1.0
	CG	A:GLU130	4.3	37.0	1.0
	O	A:GLU128	4.4	36.0	1.0
	N	A:GLU130	4.4	30.6	1.0
	CG	A:GLU128	4.4	33.4	1.0
	CA	A:ARG129	4.7	31.4	1.0
	C	A:ARG129	4.8	29.1	1.0
	C	A:GLU128	4.8	34.2	1.0
	CD	A:ARG116	4.9	31.1	1.0
	N	A:ARG129	5.0	30.7	1.0

Cadmium binding site 4 out of 4 in 5cwx

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Cadmium Binding Sites List in 5cwx

Cadmium binding site 4 out of 4 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134

Mono view

Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Cd203 b:58.8 occ:1.00	OE2	A:GLU37	2.6	37.2	1.0
	O	A:HOH369	2.9	44.0	1.0
	OE1	A:GLU37	3.0	28.6	1.0
	CD	A:GLU37	3.1	36.8	1.0
	N	A:MET1	4.0	34.5	1.0
	CA	A:MET1	4.0	37.7	1.0
	O	A:HOH311	4.1	33.2	1.0
	CG	A:GLU37	4.5	34.5	1.0
	N	A:ILE2	4.6	42.7	1.0
	C	A:MET1	4.7	42.3	1.0

Reference:

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae, in Complex with Fragment 134 To Be Published.

Page generated: Thu Jul 10 14:15:21 2025

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