Ytterbium in PDB 1s26: Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

Enzymatic activity of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

All present enzymatic activity of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site:
4.6.1.1;

Protein crystallography data

The structure of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site, PDB code: 1s26 was solved by Y.Shen, N.L.Zhukovskaya, A.Bohm, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	29.78 / 3.00
*Space group*	I 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	117.555, 167.605, 345.346, 90.00, 90.00, 90.00
*R / R_free (%)*	26.4 / 30.4

Other elements in 1s26:

Calcium

(Ca)

6 atoms

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site (pdb code 1s26). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 3 binding sites of Ytterbium where determined in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site, PDB code: 1s26:
Jump to Ytterbium binding site number: 1; 2; 3;

Ytterbium binding site 1 out of 3 in 1s26

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Ytterbium Binding Sites List in 1s26

Ytterbium binding site 1 out of 3 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Yb901 b:85.3 occ:1.00	OD1	A:ASP493	2.2	43.0	1.0
	CG	A:ASP493	2.9	40.5	1.0
	OD2	A:ASP493	2.9	45.3	1.0
	OD2	A:ASP491	2.9	46.4	1.0
	NE2	A:HIS577	3.0	31.6	1.0
	O2B	A:APC1139	3.2	75.2	1.0
	OD1	A:ASP491	3.3	50.2	1.0
	O1A	A:APC1139	3.4	85.7	1.0
	CG	A:ASP491	3.4	46.0	1.0
	C3A	A:APC1139	3.7	80.9	1.0
	PB	A:APC1139	3.9	76.0	1.0
	PA	A:APC1139	3.9	85.6	1.0
	CD2	A:HIS577	4.0	30.4	1.0
	CE1	A:HIS577	4.0	31.5	1.0
	O5'	A:APC1139	4.1	89.2	1.0
	O1B	A:APC1139	4.1	75.4	1.0
	CB	A:ASP493	4.4	38.5	1.0
	O	A:LYS346	4.4	38.2	1.0
	CB	A:ASP491	4.8	44.1	1.0
	CE	A:LYS346	4.9	29.8	1.0
	CA	A:ASP493	5.0	37.7	1.0

Ytterbium binding site 2 out of 3 in 1s26

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Ytterbium Binding Sites List in 1s26

Ytterbium binding site 2 out of 3 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Yb902 b:1.0 occ:1.00	OD2	B:ASP493	2.3	57.0	1.0
	OD1	B:ASP493	2.6	59.3	1.0
	OD1	B:ASP491	2.6	36.8	1.0
	CG	B:ASP493	2.8	55.5	1.0
	CE1	B:HIS577	3.0	50.0	1.0
	CG	B:ASP491	3.4	37.2	1.0
	OD2	B:ASP491	3.4	42.9	1.0
	O1A	B:APC2139	3.6	98.2	1.0
	O2B	B:APC2139	3.6	86.6	1.0
	NE2	B:HIS577	3.7	52.9	1.0
	O5'	B:APC2139	3.9	0.8	1.0
	PA	B:APC2139	4.0	99.0	1.0
	ND1	B:HIS577	4.0	50.2	1.0
	C3A	B:APC2139	4.0	92.6	1.0
	PB	B:APC2139	4.1	87.9	1.0
	O1B	B:APC2139	4.2	85.0	1.0
	CB	B:ASP493	4.3	49.8	1.0
	O	B:LYS346	4.5	46.6	1.0
	CB	B:ASP491	4.7	35.4	1.0
	CA	B:ASP493	5.0	46.1	1.0
	CD2	B:HIS577	5.0	51.1	1.0

Ytterbium binding site 3 out of 3 in 1s26

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Ytterbium Binding Sites List in 1s26

Ytterbium binding site 3 out of 3 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Yb903 b:95.7 occ:1.00	OD1	C:ASP493	2.3	39.4	1.0
	OD2	C:ASP491	2.8	48.6	1.0
	OD2	C:ASP493	3.0	49.5	1.0
	CG	C:ASP493	3.0	41.9	1.0
	OD1	C:ASP491	3.0	51.4	1.0
	NE2	C:HIS577	3.1	43.6	1.0
	CG	C:ASP491	3.3	46.7	1.0
	O1A	C:APC3139	3.6	96.7	1.0
	O2B	C:APC3139	3.6	84.7	1.0
	O5'	C:APC3139	3.8	99.0	1.0
	CD2	C:HIS577	4.0	41.2	1.0
	PA	C:APC3139	4.1	96.8	1.0
	CE1	C:HIS577	4.1	43.4	1.0
	O	C:LYS346	4.2	40.2	1.0
	C3A	C:APC3139	4.3	91.0	1.0
	PB	C:APC3139	4.4	86.8	1.0
	CB	C:ASP493	4.5	38.2	1.0
	CB	C:ASP491	4.7	44.3	1.0
	O1B	C:APC3139	4.8	88.0	1.0

Reference:

Y.Shen, Q.Guo, N.L.Zhukovskaya, C.L.Drum, A.Bohm, W.-J.Tang. Structure of Anthrax Edema Factor-Calmodulin-Adenosine-5'-(Alpha,Beta-Methylene) -Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site Biochem.Biophys.Res.Commun. V. 317 309 2004.
ISSN: ISSN 0006-291X
PubMed: 15063758
DOI: 10.1016/J.BBRC.2004.03.046

Page generated: Sat Oct 12 20:56:43 2024

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