Manganese in PDB 7l29: Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp, PDB code: 7l29 was solved by S.W.Horner, C.Garvie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	47.90 / 2.08
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	82.415, 58.783, 156.996, 90, 90.74, 90
*R / R_free (%)*	23.5 / 25.3

Other elements in 7l29:

The structure of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Calcium	(Ca)	1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp (pdb code 7l29). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp, PDB code: 7l29:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7l29

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Manganese Binding Sites List in 7l29

Manganese binding site 1 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mn1102 b:34.9 occ:1.00	OD2	A:ASP837	2.0	47.8	1.0
	OD1	A:ASP950	2.1	47.8	1.0
	NE2	A:HIS836	2.2	46.2	1.0
	NE2	A:HIS756	2.2	45.2	1.0
	O2P	A:AMP1101	2.3	52.9	1.0
	O3P	A:AMP1101	2.5	53.6	1.0
	P	A:AMP1101	2.8	80.0	1.0
	CD2	A:HIS836	3.1	42.7	1.0
	CG	A:ASP950	3.1	49.4	1.0
	CG	A:ASP837	3.1	48.4	1.0
	CD2	A:HIS756	3.1	49.4	1.0
	CE1	A:HIS836	3.2	45.9	1.0
	CE1	A:HIS756	3.2	49.4	1.0
	OD2	A:ASP950	3.4	52.1	1.0
	OD1	A:ASP837	3.6	50.4	1.0
	MG	A:MG1103	3.9	27.3	1.0
	O1P	A:AMP1101	3.9	48.2	1.0
	O	A:HOH1208	3.9	33.8	1.0
	O5'	A:AMP1101	4.1	81.5	1.0
	CG	A:HIS836	4.2	44.3	1.0
	ND1	A:HIS836	4.3	45.0	1.0
	CB	A:ASP837	4.3	47.0	1.0
	CG	A:HIS756	4.3	48.5	1.0
	ND1	A:HIS756	4.3	49.9	1.0
	CB	A:ASP950	4.5	49.0	1.0
	CD2	A:HIS752	4.5	50.8	1.0
	CG2	A:VAL760	4.7	47.0	1.0
	O	A:ASP950	4.7	53.5	1.0
	C5'	A:AMP1101	4.7	73.5	1.0
	O	A:HOH1218	4.8	31.1	1.0
	CA	A:ASP950	4.9	49.2	1.0

Manganese binding site 2 out of 4 in 7l29

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Manganese Binding Sites List in 7l29

Manganese binding site 2 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mn1102 b:33.0 occ:1.00	O1P	B:AMP1101	1.9	39.3	1.0
	OD2	B:ASP837	2.1	43.1	1.0
	OD1	B:ASP950	2.2	46.3	1.0
	NE2	B:HIS756	2.2	42.2	1.0
	NE2	B:HIS836	2.5	48.3	1.0
	O	B:HOH1201	2.6	30.0	1.0
	P	B:AMP1101	2.9	64.9	1.0
	O2P	B:AMP1101	2.9	81.5	1.0
	CG	B:ASP837	3.1	43.5	1.0
	CD2	B:HIS756	3.1	39.6	1.0
	CD2	B:HIS836	3.2	41.5	1.0
	CG	B:ASP950	3.2	46.9	1.0
	CE1	B:HIS756	3.3	39.5	1.0
	CE1	B:HIS836	3.5	44.2	1.0
	OD1	B:ASP837	3.5	41.0	1.0
	OD2	B:ASP950	3.6	45.1	1.0
	MG	B:MG1103	3.8	27.4	1.0
	O	B:HOH1209	3.9	34.7	1.0
	O3P	B:AMP1101	4.0	57.1	1.0
	O5'	B:AMP1101	4.0	63.9	1.0
	CB	B:ASP837	4.3	42.1	1.0
	CG	B:HIS756	4.3	44.7	1.0
	CG	B:HIS836	4.3	43.8	1.0
	ND1	B:HIS756	4.4	42.9	1.0
	ND1	B:HIS836	4.5	50.6	1.0
	CD2	B:HIS752	4.5	50.9	1.0
	CB	B:ASP950	4.6	44.7	1.0
	O	B:HOH1220	4.6	35.0	1.0
	CG2	B:VAL760	4.7	43.0	1.0
	O	B:ASP950	4.8	45.2	1.0
	CA	B:ASP950	5.0	44.2	1.0

Manganese binding site 3 out of 4 in 7l29

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Manganese Binding Sites List in 7l29

Manganese binding site 3 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Mn1102 b:33.4 occ:1.00	OD2	C:ASP837	2.1	46.7	1.0
	OD1	C:ASP950	2.2	47.1	1.0
	O3P	C:AMP1101	2.2	38.3	1.0
	NE2	C:HIS756	2.2	52.4	1.0
	O2P	C:AMP1101	2.4	47.1	1.0
	NE2	C:HIS836	2.5	46.6	1.0
	P	C:AMP1101	2.7	81.2	1.0
	CG	C:ASP837	3.1	47.4	1.0
	CD2	C:HIS836	3.1	42.0	1.0
	CD2	C:HIS756	3.1	50.6	1.0
	CE1	C:HIS756	3.3	49.6	1.0
	CG	C:ASP950	3.3	51.3	1.0
	OD1	C:ASP837	3.5	54.0	1.0
	CE1	C:HIS836	3.5	45.1	1.0
	O5'	C:AMP1101	3.8	61.1	1.0
	MG	C:MG1103	3.9	27.8	1.0
	O	C:HOH1239	3.9	45.4	1.0
	O1P	C:AMP1101	3.9	46.1	1.0
	OD2	C:ASP950	3.9	52.8	1.0
	CD2	C:HIS752	4.3	56.2	1.0
	CB	C:ASP837	4.3	46.5	1.0
	CG	C:HIS836	4.3	41.4	1.0
	CG	C:HIS756	4.3	52.4	1.0
	ND1	C:HIS756	4.3	52.7	1.0
	CB	C:ASP950	4.4	48.3	1.0
	ND1	C:HIS836	4.5	43.8	1.0
	CG2	C:VAL760	4.7	45.8	1.0
	NE2	C:HIS752	4.7	56.0	1.0
	O	C:HOH1223	4.9	32.3	1.0
	O	C:ASP950	5.0	51.2	1.0
	CA	C:ASP950	5.0	49.0	1.0

Manganese binding site 4 out of 4 in 7l29

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Manganese Binding Sites List in 7l29

Manganese binding site 4 out of 4 in the Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp

Mono view

Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the Catalytic Domain of Human PDE3A Bound to Amp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Mn1102 b:29.7 occ:1.00	O1P	D:AMP1101	2.0	41.1	1.0
	OD2	D:ASP837	2.1	39.3	1.0
	OD1	D:ASP950	2.2	41.5	1.0
	NE2	D:HIS756	2.2	35.7	1.0
	NE2	D:HIS836	2.4	38.7	1.0
	O	D:HOH1201	2.4	30.0	1.0
	O2P	D:AMP1101	2.8	72.2	1.0
	P	D:AMP1101	2.9	60.8	1.0
	CD2	D:HIS836	3.1	36.4	1.0
	CD2	D:HIS756	3.1	35.8	1.0
	CG	D:ASP837	3.1	39.1	1.0
	CG	D:ASP950	3.1	46.6	1.0
	CE1	D:HIS756	3.2	36.1	1.0
	OD2	D:ASP950	3.4	47.8	1.0
	CE1	D:HIS836	3.5	38.4	1.0
	OD1	D:ASP837	3.6	33.6	1.0
	MG	D:MG1103	3.9	25.6	1.0
	O5'	D:AMP1101	4.0	55.3	1.0
	O	D:HOH1229	4.0	28.0	1.0
	O3P	D:AMP1101	4.0	42.7	1.0
	CG	D:HIS836	4.3	39.1	1.0
	CB	D:ASP837	4.3	37.9	1.0
	CG	D:HIS756	4.3	37.4	1.0
	ND1	D:HIS756	4.3	37.2	1.0
	ND1	D:HIS836	4.4	43.2	1.0
	CB	D:ASP950	4.5	44.2	1.0
	CD2	D:HIS752	4.6	40.1	1.0
	CG2	D:VAL760	4.6	38.6	1.0
	O	D:ASP950	4.7	46.9	1.0
	O	D:HOH1238	4.8	27.6	1.0
	CA	D:ASP950	5.0	43.5	1.0

Reference:

C.W.Garvie, S.W.Horner. Structure of PDE3A-SLFN12 Complex Reveals Requirements For Activation of SLFN12 Rnase To Be Published.

Page generated: Sun Oct 6 09:48:47 2024

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