Magnesium in PDB 4jiw: C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

All present enzymatic activity of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5:
3.2.1.17;

Protein crystallography data

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw was solved by S.A.Buth, P.G.Leiman, M.M.Shneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	48.57 / 3.40
*Space group*	P 6₁ 2 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	184.157, 184.157, 238.893, 90.00, 90.00, 120.00
*R / R_free (%)*	18.4 / 24.3

Other elements in 4jiw:

The structure of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 also contains other interesting chemical elements:

Chlorine	(Cl)	3 atoms
Zinc	(Zn)	4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 (pdb code 4jiw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 4jiw

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Magnesium Binding Sites List in 4jiw

Magnesium binding site 1 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg601 b:0.3 occ:1.00	O	A:HOH602	2.1	85.3	1.0
	O	B:HOH702	2.1	0.3	1.0
	O	A:HOH601	2.1	0.5	1.0
	O	C:HOH602	2.1	0.4	1.0
	O	C:HOH601	2.1	88.8	1.0
	O	B:HOH701	2.1	0.5	1.0
	OE1	C:GLU552	3.6	0.2	1.0
	OE2	A:GLU552	3.9	1.0	1.0
	OE1	B:GLU552	4.1	0.7	1.0
	OE2	C:GLU552	4.2	0.1	1.0
	CD	C:GLU552	4.3	0.7	1.0
	OE2	B:GLU552	4.6	0.3	1.0
	CD	B:GLU552	4.8	0.6	1.0
	CD	A:GLU552	4.8	0.8	1.0
	OE1	A:GLU552	4.8	0.9	1.0
	CE	B:MET557	4.8	0.2	1.0
	CE	C:MET557	4.9	0.9	1.0

Magnesium binding site 2 out of 4 in 4jiw

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Magnesium Binding Sites List in 4jiw

Magnesium binding site 2 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
F:Mg601 b:0.5 occ:1.00	O	G:HOH602	2.1	0.6	1.0
	O	F:HOH701	2.1	0.1	1.0
	O	E:HOH701	2.1	0.8	1.0
	O	F:HOH702	2.1	99.0	1.0
	O	E:HOH702	2.1	0.7	1.0
	O	G:HOH601	2.1	0.4	1.0
	OE2	F:GLU552	3.7	0.1	1.0
	OE1	G:GLU552	3.8	0.3	1.0
	OE2	G:GLU552	4.3	0.7	1.0
	OE1	E:GLU552	4.4	0.9	1.0
	CD	G:GLU552	4.4	0.6	1.0
	OE1	F:GLU552	4.5	0.4	1.0
	CE	E:MET557	4.5	0.8	1.0
	CD	F:GLU552	4.5	0.3	1.0
	CE	F:MET557	4.6	0.7	1.0
	OE2	E:GLU552	4.8	0.7	1.0
	CE	G:MET557	4.9	0.4	1.0

Magnesium binding site 3 out of 4 in 4jiw

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Magnesium Binding Sites List in 4jiw

Magnesium binding site 3 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
I:Mg601 b:0.1 occ:1.00	O	I:HOH702	2.1	88.2	1.0
	O	J:HOH602	2.1	82.4	1.0
	O	I:HOH701	2.1	0.3	1.0
	O	K:HOH601	2.1	85.1	1.0
	O	K:HOH602	2.1	0.3	1.0
	O	J:HOH601	2.1	0.6	1.0
	OE1	I:GLU552	3.9	0.5	1.0
	OE1	K:GLU552	3.9	0.2	1.0
	OE2	J:GLU552	4.3	0.5	1.0
	OE2	I:GLU552	4.5	0.3	1.0
	OE2	K:GLU552	4.5	0.4	1.0
	CE	K:MET557	4.6	0.6	1.0
	OE1	J:GLU552	4.6	0.2	1.0
	CD	I:GLU552	4.6	0.8	1.0
	CD	K:GLU552	4.6	0.0	1.0
	CD	J:GLU552	4.9	0.8	1.0
	CE	I:MET557	4.9	0.8	1.0

Magnesium binding site 4 out of 4 in 4jiw

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Magnesium Binding Sites List in 4jiw

Magnesium binding site 4 out of 4 in the C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of C1882 Paar-Repeat Protein From Escherichia Coli in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
O:Mg601 b:0.0 occ:1.00	O	O:HOH701	2.1	0.3	1.0
	O	N:HOH601	2.1	1.0	1.0
	O	O:HOH703	2.1	0.8	1.0
	O	M:HOH701	2.1	0.7	1.0
	O	N:HOH602	2.1	79.0	1.0
	O	O:HOH702	2.1	0.6	1.0
	OE2	O:GLU552	3.4	0.7	1.0
	OE1	O:GLU552	4.2	0.7	1.0
	CE	O:MET557	4.2	0.4	1.0
	OE2	M:GLU552	4.2	0.3	1.0
	CD	O:GLU552	4.2	0.8	1.0
	OE1	N:GLU552	4.3	0.2	1.0
	OE1	M:GLU552	4.6	0.4	1.0
	OE2	N:GLU552	4.8	0.8	1.0
	CD	M:GLU552	4.8	1.0	1.0
	CD	N:GLU552	4.9	0.7	1.0

Reference:

M.M.Shneider, S.A.Buth, B.T.Ho, M.Basler, J.J.Mekalanos, P.G.Leiman. Paar-Repeat Proteins Sharpen and Diversify the Type VI Secretion System Spike. Nature V. 500 350 2013.
ISSN: ISSN 0028-0836
PubMed: 23925114
DOI: 10.1038/NATURE12453

Page generated: Sat Aug 17 02:19:16 2024

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