Magnesium in PDB 3uie: Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps

Enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps

All present enzymatic activity of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps:
2.7.1.25;

Protein crystallography data

The structure of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps, PDB code: 3uie was solved by G.E.Ravilious, J.M.Jez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	30.50 / 1.79
*Space group*	C 1 2 1
*Cell size a, b, c (Å), α, β, γ (°)*	121.137, 95.313, 73.327, 90.00, 114.08, 90.00
*R / R_free (%)*	17.3 / 20.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps (pdb code 3uie). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps, PDB code: 3uie:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3uie

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Magnesium Binding Sites List in 3uie

Magnesium binding site 1 out of 3 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg403 b:32.4 occ:1.00	O	A:HOH541	2.0	27.1	1.0
	O2G	A:ANP402	2.1	28.9	1.0
	O	A:HOH575	2.1	27.1	1.0
	O1B	A:ANP402	2.2	26.3	1.0
	OG	A:SER115	2.2	30.9	1.0
	O	A:HOH509	2.3	27.9	1.0
	CB	A:SER115	3.2	31.1	1.0
	PG	A:ANP402	3.2	36.4	1.0
	PB	A:ANP402	3.3	28.6	1.0
	N3B	A:ANP402	3.4	27.6	1.0
	OD1	A:ASP136	3.8	35.9	1.0
	O	A:HOH571	3.8	36.6	1.0
	O3G	A:ANP402	3.9	32.4	1.0
	O1A	A:ANP402	4.1	27.4	1.0
	N	A:SER115	4.1	24.4	1.0
	CA	A:SER115	4.2	29.2	1.0
	O3A	A:ANP402	4.3	27.8	1.0
	NZ	A:LYS218	4.3	75.8	1.0
	OD2	A:ASP136	4.3	44.9	1.0
	O2B	A:ANP402	4.5	26.1	1.0
	CG	A:ASP136	4.5	34.9	1.0
	O	A:HOH563	4.5	50.7	1.0
	O1G	A:ANP402	4.5	31.3	1.0
	O	A:HOH552	4.5	49.3	1.0
	PA	A:ANP402	4.5	28.8	1.0
	OG	A:SER179	4.6	28.3	0.5
	O2A	A:ANP402	4.7	29.0	1.0

Magnesium binding site 2 out of 3 in 3uie

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Magnesium Binding Sites List in 3uie

Magnesium binding site 2 out of 3 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg303 b:34.3 occ:1.00	O2B	B:ANP302	2.1	32.8	1.0
	O	B:HOH443	2.1	28.2	1.0
	O3G	B:ANP302	2.1	34.1	1.0
	OG	B:SER115	2.1	31.3	1.0
	O	B:HOH439	2.1	36.5	1.0
	O	B:HOH474	2.3	34.5	1.0
	CB	B:SER115	3.2	30.3	1.0
	PB	B:ANP302	3.2	33.0	1.0
	PG	B:ANP302	3.3	38.7	1.0
	O	B:HOH433	3.6	50.6	1.0
	N3B	B:ANP302	3.7	29.9	1.0
	OD1	B:ASP136	3.8	48.6	1.0
	O	B:HOH427	4.0	37.0	1.0
	O1G	B:ANP302	4.0	36.1	1.0
	N	B:SER115	4.0	28.9	1.0
	OD2	B:ASP136	4.1	45.0	1.0
	O1A	B:ANP302	4.1	34.7	1.0
	CA	B:SER115	4.2	31.9	1.0
	O	B:HOH550	4.3	67.3	1.0
	O3A	B:ANP302	4.4	33.7	1.0
	CG	B:ASP136	4.4	39.3	1.0
	O1B	B:ANP302	4.5	31.9	1.0
	NZ	B:LYS218	4.5	73.0	1.0
	OG	B:SER179	4.5	27.9	0.4
	O2G	B:ANP302	4.6	37.0	1.0
	PA	B:ANP302	4.6	32.0	1.0
	O2A	B:ANP302	4.8	31.1	1.0
	O	B:HOH571	5.0	57.9	1.0
	CE	B:LYS114	5.0	29.8	1.0

Magnesium binding site 3 out of 3 in 3uie

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Magnesium Binding Sites List in 3uie

Magnesium binding site 3 out of 3 in the Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Adenosine 5'-Phosphosulfate Kinase From Arabidopsis Thaliana in Complex with Amppnp and Aps within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mg303 b:44.6 occ:1.00	O	C:HOH471	1.8	33.8	1.0
	O	C:HOH446	2.1	39.9	1.0
	O	C:HOH431	2.2	35.6	1.0
	OG	C:SER115	2.2	37.1	1.0
	O2G	C:ANP302	2.2	48.6	1.0
	O1B	C:ANP302	2.3	39.5	1.0
	CB	C:SER115	3.3	34.8	1.0
	PG	C:ANP302	3.3	51.7	1.0
	PB	C:ANP302	3.5	37.9	1.0
	N3B	C:ANP302	3.6	31.7	1.0
	OD1	C:ASP136	3.8	46.3	1.0
	OD2	C:ASP138	3.9	49.4	1.0
	O3G	C:ANP302	3.9	38.2	1.0
	O	C:HOH475	4.0	50.8	1.0
	OD2	C:ASP136	4.1	45.6	1.0
	N	C:SER115	4.2	33.4	1.0
	O1A	C:ANP302	4.2	39.3	1.0
	CA	C:SER115	4.3	39.3	1.0
	CG	C:ASP136	4.4	42.6	1.0
	O3A	C:ANP302	4.4	38.7	1.0
	O2B	C:ANP302	4.6	37.4	1.0
	O1G	C:ANP302	4.6	43.6	1.0
	OG	C:SER179	4.6	35.6	0.7
	PA	C:ANP302	4.7	39.4	1.0
	ND1	B:HIS84	4.7	60.3	1.0
	O2A	C:ANP302	4.8	35.2	1.0
	O3'	C:ADX301	4.8	47.1	1.0
	CG	C:ASP138	4.9	55.1	1.0
	CB	B:HIS84	4.9	42.0	1.0
	CE	C:LYS114	5.0	35.2	1.0
	CG	B:HIS84	5.0	55.5	1.0

Reference:

G.E.Ravilious, A.Nguyen, J.A.Francois, J.M.Jez. Structural Basis and Evolution of Redox Regulation in Plant Adenosine-5'-Phosphosulfate Kinase. Proc.Natl.Acad.Sci.Usa V. 109 309 2012.
ISSN: ISSN 0027-8424
PubMed: 22184237
DOI: 10.1073/PNAS.1115772108

Page generated: Thu Aug 15 12:31:23 2024

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