Magnesium in PDB 5vcp: Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.54 / 1.95
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	63.110, 90.330, 140.210, 90.00, 90.00, 90.00
*R / R_free (%)*	16.2 / 19.2

Other elements in 5vcp:

The structure of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin (pdb code 5vcp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin, PDB code: 5vcp:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5vcp

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Magnesium Binding Sites List in 5vcp

Magnesium binding site 1 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg203 b:50.2 occ:1.00	O	A:HOH386	2.0	68.5	1.0
	OD1	A:ASP21	2.7	56.2	1.0
	OD2	A:ASP21	2.7	74.1	1.0
	O	A:HOH340	2.7	41.9	1.0
	CG	A:ASP21	3.1	66.7	1.0
	CB	A:ASP21	4.6	44.7	1.0
	CG	A:PRO19	4.6	41.0	1.0
	O	A:HOH304	4.7	61.1	1.0
	O	A:HOH367	4.9	43.4	0.5
	O	A:HOH346	4.9	41.1	1.0

Magnesium binding site 2 out of 3 in 5vcp

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Magnesium Binding Sites List in 5vcp

Magnesium binding site 2 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg203 b:52.0 occ:1.00	O	C:HOH338	2.1	63.9	1.0
	O	C:HOH362	2.2	68.7	1.0
	O	B:HOH343	2.6	43.2	1.0
	OD1	B:ASP21	2.7	82.7	1.0
	OD1	C:ASN156	2.7	63.5	1.0
	O	C:HOH366	3.1	70.6	1.0
	OD2	B:ASP21	3.3	84.2	1.0
	CG	B:ASP21	3.3	77.6	1.0
	CG	C:ASN156	3.9	69.1	1.0
	O	C:HOH336	4.3	28.8	0.3
	O	A:HOH396	4.4	59.6	1.0
	O	C:ILE155	4.5	42.4	1.0
	CG	B:PRO19	4.6	40.1	1.0
	CD	B:PRO19	4.6	36.8	1.0
	ND2	C:ASN156	4.7	78.7	1.0
	O	C:MET153	4.7	39.3	1.0
	O	B:PRO19	4.8	34.1	1.0
	CB	B:ASP21	4.8	58.1	1.0
	CB	B:PRO19	4.8	35.7	1.0
	O	B:HOH321	4.9	44.1	1.0

Magnesium binding site 3 out of 3 in 5vcp

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Magnesium Binding Sites List in 5vcp

Magnesium binding site 3 out of 3 in the Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg204 b:47.4 occ:1.00	O	B:HOH384	2.3	50.2	1.0
	O	B:MET92	2.4	45.3	1.0
	O	B:HOH312	2.8	49.2	1.0
	C	B:MET92	3.5	44.4	1.0
	N	B:MET92	4.1	44.2	1.0
	N	B:GLU93	4.4	38.8	1.0
	CA	B:MET92	4.4	41.0	1.0
	CA	B:GLU93	4.4	45.0	1.0
	CB	B:GLU93	4.7	59.2	1.0
	OG	B:SER113	4.8	56.8	1.0
	O	B:HOH355	4.9	50.6	1.0
	C	B:ASP91	5.0	45.1	1.0

Reference:

D.G.Conrady, J.Abendroth, D.D.Lorimer, T.E.Edwards. Crystal Structure of A Peptide Deformylase From Burkholderia Xenovorans in Complex with Actinonin To Be Published.

Page generated: Tue Aug 12 21:05:53 2025

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