Magnesium in PDB 2f8e: Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein

Enzymatic activity of Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein

All present enzymatic activity of Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein:
2.7.7.48;

Protein crystallography data

The structure of Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein, PDB code: 2f8e was solved by C.Ferrer-Orta, A.Arias, R.Perez-Luque, C.Escarmis, E.Domingo, N.Verdaguer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.00 / 2.90
*Space group*	P 3₂ 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	94.381, 94.381, 99.726, 90.00, 90.00, 120.00
*R / R_free (%)*	23.4 / 28.4

Other elements in 2f8e:

The structure of Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein (pdb code 2f8e). 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 Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein, PDB code: 2f8e:

Magnesium binding site 1 out of 1 in 2f8e

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Magnesium Binding Sites List in 2f8e

Magnesium binding site 1 out of 1 in the Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Foot and Mouth Disease Virus Rna-Dependent Rna Polymerase in Complex with Uridylylated Vpg Protein within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
X:Mg502 b:67.3 occ:0.70	O1P	A:U5P2003	2.8	60.3	0.7
	OH	A:TYR1003	3.1	69.8	0.7
	OG	X:SER298	3.4	71.6	1.0
	P	A:U5P2003	3.4	60.3	0.7
	C5'	A:U5P2003	3.6	60.1	0.7
	CB	X:SER298	3.7	71.1	1.0
	O5'	A:U5P2003	3.8	60.3	0.7
	O	X:ILE180	4.3	60.5	1.0
	CZ	A:TYR1003	4.3	69.5	0.7
	NH1	X:ARG179	4.4	62.4	1.0
	OD2	X:ASP245	4.4	60.9	1.0
	NZ	X:LYS59	4.5	65.2	1.0
	CG	X:ASP245	4.8	60.1	1.0
	CD	X:ARG179	4.8	60.6	1.0
	CB	X:ARG179	4.9	60.3	1.0
	O2P	A:U5P2003	4.9	60.3	0.7
	CE1	A:TYR1003	5.0	69.4	0.7
	N	X:ILE180	5.0	60.5	1.0

Reference:

C.Ferrer-Orta, A.Arias, R.Agudo, R.Perez-Luque, C.Escarmis, E.Domingo, N.Verdaguer. The Structure of A Protein Primer-Polymerase Complex in the Initiation of Genome Replication Embo J. V. 25 880 2006.
ISSN: ISSN 0261-4189
PubMed: 16456546
DOI: 10.1038/SJ.EMBOJ.7600971

Page generated: Tue Aug 13 23:04:52 2024

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