Magnesium in PDB 1ze1: Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

Enzymatic activity of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

All present enzymatic activity of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate:
4.2.1.70;

Protein crystallography data

The structure of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate, PDB code: 1ze1 was solved by K.Phannachet, R.H.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	50.00 / 2.90
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	44.650, 64.170, 176.070, 87.48, 86.44, 79.35
*R / R_free (%)*	23.5 / 28.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate (pdb code 1ze1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate, PDB code: 1ze1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ze1

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Magnesium Binding Sites List in 1ze1

Magnesium binding site 1 out of 4 in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg310 b:14.9 occ:1.00	O	A:HOH328	2.6	20.1	1.0
	NE2	A:HIS34	2.6	40.8	1.0
	NE2	A:HIS17	2.7	42.1	1.0
	CE1	A:HIS17	2.8	41.8	1.0
	CE1	A:HIS34	3.4	40.7	1.0
	CD2	A:HIS34	3.7	39.7	1.0
	CD2	A:HIS17	3.9	41.9	1.0
	ND1	A:HIS17	4.0	41.8	1.0
	CG	A:HIS17	4.5	39.4	1.0
	ND1	A:HIS34	4.6	40.9	1.0
	CG	A:HIS34	4.7	37.8	1.0

Magnesium binding site 2 out of 4 in 1ze1

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Magnesium Binding Sites List in 1ze1

Magnesium binding site 2 out of 4 in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg310 b:14.4 occ:1.00	NE2	B:HIS17	2.3	49.7	1.0
	CE1	B:HIS17	2.3	48.8	1.0
	NE2	B:HIS34	2.3	42.6	1.0
	O	B:HOH316	2.8	21.8	1.0
	CE1	B:HIS34	3.2	42.5	1.0
	CD2	B:HIS34	3.4	43.2	1.0
	ND1	B:HIS17	3.4	48.6	1.0
	CD2	B:HIS17	3.5	49.2	1.0
	CG	B:HIS17	4.0	47.5	1.0
	ND1	B:HIS34	4.4	42.1	1.0
	CG	B:HIS34	4.5	41.6	1.0

Magnesium binding site 3 out of 4 in 1ze1

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Magnesium Binding Sites List in 1ze1

Magnesium binding site 3 out of 4 in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg310 b:47.3 occ:1.00	CE1	C:HIS17	2.3	49.3	1.0
	NE2	C:HIS17	2.4	49.5	1.0
	NE2	C:HIS34	2.4	43.1	1.0
	CE1	C:HIS34	3.2	43.4	1.0
	ND1	C:HIS17	3.4	49.5	1.0
	CD2	C:HIS34	3.6	42.0	1.0
	CD2	C:HIS17	3.6	49.3	1.0
	CG	C:HIS17	4.1	48.5	1.0
	ND1	C:HIS34	4.4	42.2	1.0
	CG	C:HIS34	4.6	40.6	1.0

Magnesium binding site 4 out of 4 in 1ze1

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Magnesium Binding Sites List in 1ze1

Magnesium binding site 4 out of 4 in the Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mg310 b:41.5 occ:1.00	CE1	D:HIS17	2.4	50.7	1.0
	NE2	D:HIS34	2.4	42.9	1.0
	NE2	D:HIS17	2.6	51.4	1.0
	CE1	D:HIS34	3.0	42.0	1.0
	ND1	D:HIS17	3.6	49.1	1.0
	CD2	D:HIS34	3.6	41.6	1.0
	CD2	D:HIS17	3.9	50.1	1.0
	ND1	D:HIS34	4.3	40.1	1.0
	CG	D:HIS17	4.3	47.2	1.0
	CG	D:HIS34	4.6	39.3	1.0

Reference:

K.Phannachet, R.H.Huang. Conformational Change of Pseudouridine 55 Synthase Upon Its Association with Rna Substrate Nucleic Acids Res. V. 32 1422 2004.
ISSN: ISSN 0305-1048
PubMed: 14990747
DOI: 10.1093/NAR/GKH287

Page generated: Sun Aug 10 08:51:34 2025

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