Magnesium in PDB 4jiv: VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

Enzymatic activity of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5

All present enzymatic activity of VCA0105 Paar-Repeat Protein From Vibrio Cholerae 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 VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiv 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)*	80.40 / 1.90
*Space group*	P 4₂ 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	113.703, 113.703, 76.897, 90.00, 90.00, 90.00
*R / R_free (%)*	16.4 / 20.8

Other elements in 4jiv:

The structure of VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5 (pdb code 4jiv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the VCA0105 Paar-Repeat Protein From Vibrio Cholerae in Complex with A Vgrg-Like Beta-Helix That Is Based on A Fragment of T4 GP5, PDB code: 4jiv:

Magnesium binding site 1 out of 1 in 4jiv

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Magnesium Binding Sites List in 4jiv

Magnesium binding site 1 out of 1 in the VCA0105 Paar-Repeat Protein From Vibrio Cholerae 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 VCA0105 Paar-Repeat Protein From Vibrio Cholerae 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
A:Mg601 b:36.6 occ:1.00	O	B:HOH751	2.1	35.9	1.0
	O	C:HOH794	2.1	36.7	1.0
	O	A:HOH702	2.1	37.0	1.0
	O	B:HOH722	2.1	35.9	1.0
	O	A:HOH701	2.1	37.4	1.0
	O	C:HOH702	2.1	36.5	1.0
	OE1	C:GLU552	4.1	35.1	1.0
	OE1	A:GLU552	4.1	41.0	1.0
	OE2	B:GLU552	4.1	37.4	1.0
	O	C:HOH756	4.2	56.2	1.0
	OE1	B:GLU552	4.2	32.4	1.0
	OE2	C:GLU552	4.2	32.8	1.0
	OE2	A:GLU552	4.2	41.9	1.0
	O	A:HOH743	4.2	48.1	1.0
	O	B:HOH737	4.2	36.2	0.7
	CD	C:GLU552	4.6	30.3	1.0
	CD	B:GLU552	4.6	30.2	1.0
	CD	A:GLU552	4.6	40.2	1.0
	CE	B:MET557	4.8	38.2	1.0
	CE	A:MET557	4.8	38.3	1.0
	CZ2	B:TRP550	4.8	32.0	1.0
	CE	C:MET557	4.9	32.3	1.0
	CZ2	A:TRP550	4.9	39.2	1.0
	CZ2	C:TRP550	4.9	30.5	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 02:18:54 2024

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