Manganese in PDB 8k05: Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme

Enzymatic activity of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme

All present enzymatic activity of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme:
4.2.1.70;

Protein crystallography data

The structure of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme, PDB code: 8k05 was solved by J.Y.Lee, S.H.Kim, S.K.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	28.55 / 1.45
*Space group*	P 2₁ 3
*Cell size a, b, c (Å), α, β, γ (°)*	121.126, 121.126, 121.126, 90, 90, 90
*R / R_free (%)*	20.6 / 21.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme (pdb code 8k05). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme, PDB code: 8k05:

Manganese binding site 1 out of 1 in 8k05

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Manganese Binding Sites List in 8k05

Manganese binding site 1 out of 1 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Sulfate Bound Holoenzyme within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn401 b:34.9 occ:1.00	O	A:HOH594	2.0	29.2	1.0
	OD1	A:ASP164	2.2	23.9	1.0
	O	A:HOH600	2.3	34.1	1.0
	O	A:HOH672	2.3	23.4	1.0
	O	A:HOH502	2.5	35.5	1.0
	CG	A:ASP164	3.2	24.6	1.0
	OD2	A:ASP164	3.6	27.8	1.0
	NE2	A:HIS156	3.9	27.3	1.0
	O	A:HOH782	4.0	48.3	1.0
	O2	A:SO4403	4.1	32.2	1.0
	CD2	A:HIS156	4.4	22.7	1.0
	O1	A:SO4403	4.5	24.7	1.0
	N	A:ILE165	4.5	18.7	1.0
	CB	A:ASP164	4.5	21.4	1.0
	O4	A:SO4403	4.6	28.4	1.0
	CE1	A:HIS156	4.6	26.7	1.0
	S	A:SO4403	4.6	26.6	1.0
	O	A:ILE165	4.6	18.0	1.0
	C	A:ASP164	4.7	20.2	1.0
	C	A:ILE165	4.7	15.7	1.0
	CA	A:ASP164	4.8	19.7	1.0
	N	A:SER166	4.9	16.6	1.0

Reference:

J.Lee, S.H.Kim, S.Rhee. Structure and Function of the Pseudouridine 5'-Monophosphate Glycosylase Pumy From Arabidopsis Thaliana. Rna Biol. V. 21 1 2024.
ISSN: ESSN 1555-8584
PubMed: 38117089
DOI: 10.1080/15476286.2023.2293340

Page generated: Sun Oct 6 13:22:21 2024

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