Sodium in PDB 2im3: Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+

Enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+

All present enzymatic activity of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+, PDB code: 2im3 was solved by A.A.Thompson, O.B.Peersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.70 / 2.60
*Space group*	P 6₅
*Cell size a, b, c (Å), α, β, γ (°)*	128.115, 128.115, 112.833, 90.00, 90.00, 120.00
*R / R_free (%)*	23.7 / 26.9

Other elements in 2im3:

The structure of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+ also contains other interesting chemical elements:

Arsenic	(As)	4 atoms
Manganese	(Mn)	2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+ (pdb code 2im3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+, PDB code: 2im3:

Sodium binding site 1 out of 1 in 2im3

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Sodium Binding Sites List in 2im3

Sodium binding site 1 out of 1 in the Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Poliovirus Polymerase Complexed with Utp and MN2+ within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na3001 b:47.5 occ:1.00	OG	A:SER271	2.7	44.5	1.0
	O	A:GLY284	2.7	44.5	1.0
	O	A:GLY285	2.8	44.1	1.0
	CB	A:SER271	3.1	44.8	1.0
	O	A:LEU268	3.1	37.2	1.0
	O	A:ASN269	3.2	40.7	1.0
	CG1	A:VAL282	3.6	43.4	1.0
	C	A:GLY285	3.7	42.9	1.0
	C	A:GLY284	3.7	44.2	1.0
	CB	A:VAL282	3.8	44.4	1.0
	NE2	A:HIS273	3.9	52.9	1.0
	N	A:SER271	4.0	42.9	1.0
	C	A:ASN269	4.1	40.2	1.0
	CG	A:PRO287	4.1	46.2	1.0
	O	A:VAL282	4.1	43.1	1.0
	CA	A:GLY285	4.1	43.5	1.0
	CA	A:SER271	4.1	44.2	1.0
	C	A:LEU268	4.2	39.3	1.0
	N	A:GLY285	4.3	44.5	1.0
	CD	A:PRO287	4.3	46.2	1.0
	C	A:VAL282	4.6	44.0	1.0
	N	A:GLY284	4.6	44.4	1.0
	CA	A:ASN269	4.6	40.9	1.0
	N	A:MET286	4.7	42.3	1.0
	CA	A:GLY284	4.7	44.6	1.0
	CE1	A:HIS273	4.7	54.0	1.0
	N	A:PRO287	4.8	45.9	1.0
	CG2	A:VAL282	4.8	44.6	1.0
	CA	A:VAL282	4.8	44.7	1.0
	N	A:ASN269	4.9	39.7	1.0
	C	A:HIS270	4.9	42.2	1.0
	CD2	A:HIS273	5.0	54.5	1.0

Reference:

A.A.Thompson, R.A.Albertini, O.B.Peersen. Stabilization of Poliovirus Polymerase By Ntp Binding and Fingers-Thumb Interactions. J.Mol.Biol. V. 366 1459 2007.
ISSN: ISSN 0022-2836
PubMed: 17223130
DOI: 10.1016/J.JMB.2006.11.070

Page generated: Mon Oct 7 02:53:51 2024

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