Nickel in PDB 6jfr: K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

Enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

All present enzymatic activity of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus:
3.5.1.88;

Protein crystallography data

The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr was solved by I.H.Lee, T.H.Ho, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	49.99 / 2.40
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	95.792, 120.709, 47.281, 90.00, 90.00, 90.00
*R / R_free (%)*	20 / 25.4

Other elements in 6jfr:

The structure of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus (pdb code 6jfr). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus, PDB code: 6jfr:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6jfr

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Nickel Binding Sites List in 6jfr

Nickel binding site 1 out of 2 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni201 b:58.2 occ:1.00	F	A:K3U203	2.3	70.8	1.0
	NE2	A:HIS154	2.4	29.6	1.0
	SG	A:CYS111	2.4	26.5	1.0
	NE2	A:HIS158	2.4	40.7	1.0
	F1	A:K3U203	3.0	77.7	1.0
	CD2	A:HIS154	3.1	27.8	1.0
	C12	A:K3U203	3.1	88.2	1.0
	O	A:HOH316	3.3	35.4	1.0
	CB	A:CYS111	3.3	32.5	1.0
	CD2	A:HIS158	3.3	38.0	1.0
	CE1	A:HIS158	3.4	39.5	1.0
	CE1	A:HIS154	3.4	26.6	1.0
	NE2	A:GLN65	3.5	26.7	1.0
	OE2	A:GLU155	3.7	51.8	1.0
	CA	A:CYS111	3.7	33.1	1.0
	F2	A:K3U203	4.0	93.6	1.0
	CD	A:GLN65	4.1	29.4	1.0
	C4	A:K3U203	4.1	94.3	1.0
	OE1	A:GLN65	4.1	30.2	1.0
	C11	A:K3U203	4.3	86.5	1.0
	CG	A:HIS154	4.3	27.4	1.0
	O	A:GLY110	4.4	35.2	1.0
	ND1	A:HIS154	4.5	29.3	1.0
	ND1	A:HIS158	4.5	39.5	1.0
	CG	A:HIS158	4.5	35.9	1.0
	CD	A:GLU155	4.6	51.4	1.0
	O	A:HOH307	4.6	29.0	1.0
	C3	A:K3U203	4.6	89.5	1.0
	C	A:CYS111	4.7	36.0	1.0
	N	A:LEU112	4.7	35.4	1.0
	OE1	A:GLU155	4.8	55.9	1.0
	N	A:CYS111	4.9	32.9	1.0

Nickel binding site 2 out of 2 in 6jfr

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Nickel Binding Sites List in 6jfr

Nickel binding site 2 out of 2 in the K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus

Mono view

Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Ni202 b:0.3 occ:1.00	NE2	A:HIS177	2.4	45.0	1.0
	CE1	A:HIS177	3.2	43.7	1.0
	OD2	A:ASP169	3.5	60.3	1.0
	CD2	A:HIS177	3.5	42.4	1.0
	ND1	A:HIS177	4.4	42.9	1.0
	CB	A:ASP169	4.4	46.9	1.0
	CG	A:ASP169	4.4	51.1	1.0
	CG	A:HIS177	4.6	43.6	1.0
	ND1	A:HIS123	4.9	36.8	1.0

Reference:

I.H.Lee, T.H.Ho, L.W.Kang. K3U Bound Crystal Structure of Class II Peptide Deformylase From Methicillin Resistant Staphylococcus Aureus To Be Published.

Page generated: Thu Oct 10 08:34:41 2024

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