Ytterbium in PDB 5fgr: Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg

The structure of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom, PDB code: 5fgr was solved by P.Chaurasia, S.Pratap, I.Von Ossowski, A.Palva, V.Krishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	45.74 / 2.79
*Space group*	P 2₁ 2₁ 2
*Cell size a, b, c (Å), α, β, γ (°)*	57.603, 75.252, 117.388, 90.00, 90.00, 90.00
*R / R_free (%)*	19.7 / 23.6

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom (pdb code 5fgr). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 10 binding sites of Ytterbium where determined in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom, PDB code: 5fgr:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Ytterbium binding site 1 out of 10 in 5fgr

Ytterbium binding site 1 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

Ytterbium binding site 2 out of 10 in 5fgr

Ytterbium binding site 2 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Yb402 b:0.3 occ:0.59	OD2	A:ASP283	2.4	70.2	1.0
	OD1	A:ASP283	2.7	64.5	1.0
	CG	A:ASP283	2.9	63.2	1.0
	CB	A:ASP283	4.4	57.9	1.0
	OG1	A:THR266	4.8	50.1	1.0
	CG2	A:THR266	5.0	48.1	1.0

Ytterbium binding site 3 out of 10 in 5fgr

Ytterbium binding site 3 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Yb403 b:0.9 occ:0.48	OD2	A:ASP292	1.8	64.0	1.0
	NZ	A:LYS185	2.3	61.9	1.0
	CG	A:ASP292	2.7	60.9	1.0
	OD1	A:ASP292	3.0	64.2	1.0
	CE	A:LYS185	3.4	60.3	1.0
	CD	A:LYS185	4.0	59.7	1.0
	CB	A:ASP292	4.1	55.7	1.0
	CD	A:LYS190	5.0	84.7	1.0
	CE	A:LYS190	5.0	88.2	1.0

Ytterbium binding site 4 out of 10 in 5fgr

Ytterbium binding site 4 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Yb404 b:0.0 occ:0.36	OD2	A:ASP277	2.7	70.7	1.0
	CG	A:ASP277	3.5	66.5	1.0
	OD1	A:ASP277	3.7	70.2	1.0
	CB	A:ASP277	4.8	60.1	1.0
	O	A:HOH511	4.9	44.8	1.0
	O	A:PRO297	4.9	56.3	1.0
	O	A:HOH507	4.9	50.2	1.0

Ytterbium binding site 5 out of 10 in 5fgr

Ytterbium binding site 5 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Yb401 b:1.0 occ:0.59	NZ	B:LYS185	2.4	95.7	1.0
	OD2	B:ASP292	2.6	83.9	1.0
	OD1	B:ASP292	3.2	87.2	1.0
	CG	B:ASP292	3.3	85.4	1.0
	CE	B:LYS185	3.5	90.2	1.0
	CD	B:LYS185	4.5	88.2	1.0
	CB	B:ASP292	4.7	81.3	1.0

Ytterbium binding site 6 out of 10 in 5fgr

Ytterbium binding site 6 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Yb402 b:0.5 occ:0.74	OD1	D:ASP277	2.7	72.8	1.0
	CG	D:ASP277	3.1	68.6	1.0
	OD2	D:ASP277	3.1	73.6	1.0
	OD2	B:ASP204	3.3	0.3	1.0
	OD1	B:ASP204	3.7	98.3	1.0
	CG	B:ASP204	3.9	95.3	1.0
	CB	D:ASP277	4.4	62.7	1.0
	O	D:SER298	4.4	74.5	1.0
	C	D:SER298	4.4	83.2	1.0

Ytterbium binding site 7 out of 10 in 5fgr

Ytterbium binding site 7 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Yb401 b:0.2 occ:0.45	O	C:HOH501	2.6	54.0	1.0
	OD2	C:ASP283	3.2	98.1	1.0
	OD1	C:ASP283	3.3	93.4	1.0
	CG	C:ASP283	3.5	89.8	1.0
	O	C:ASN281	4.0	67.0	1.0
	CB	C:ASN281	4.2	64.8	1.0
	C	C:ASN281	4.4	61.6	1.0
	N	C:ASP283	4.6	68.8	1.0
	CB	C:ASP283	4.7	81.7	1.0
	CG2	C:THR266	4.8	65.9	1.0
	CA	C:ASN281	4.9	61.1	1.0
	N	C:THR282	5.0	62.6	1.0

Ytterbium binding site 8 out of 10 in 5fgr

Ytterbium binding site 8 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Yb402 b:0.9 occ:0.28	OD1	C:ASP214	2.2	97.1	1.0
	OD2	C:ASP214	2.9	91.0	1.0
	CG	C:ASP214	2.9	91.4	1.0
	CB	C:ASP214	4.4	87.2	1.0
	CD	C:LYS213	4.4	98.1	1.0
	CE	C:LYS213	4.9	99.4	1.0
	N	C:ASP214	4.9	80.5	1.0

Ytterbium binding site 9 out of 10 in 5fgr

Ytterbium binding site 9 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 9 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Yb403 b:81.5 occ:0.24	OD2	C:ASP277	2.4	80.5	1.0
	CG	C:ASP277	3.5	72.9	1.0
	OD1	C:ASP277	4.1	78.6	1.0
	O	C:PRO297	4.2	67.5	1.0
	CB	C:ASP277	4.5	64.2	1.0
	C	C:SER298	4.8	77.0	1.0

Ytterbium binding site 10 out of 10 in 5fgr

Ytterbium binding site 10 out of 10 in the Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Mono view

Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 10 of Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
D:Yb401 b:0.6 occ:0.46	OD2	D:ASP283	2.9	90.0	1.0
	CG	D:ASP283	3.4	85.8	1.0
	OD1	D:ASP283	3.5	88.7	1.0
	O	D:ASN281	4.1	63.0	1.0
	CB	D:ASP283	4.5	80.2	1.0
	N	D:ASP283	4.6	67.9	1.0
	C	D:ASN281	4.7	62.6	1.0
	CB	D:ASN281	4.8	69.0	1.0

Reference:

P.Chaurasia, S.Pratap, I.Von Ossowski, A.Palva, V.Krishnan. New Insights About Pilus Formation in Gut-Adapted Lactobacillus Rhamnosus Gg From the Crystal Structure of the Spaa Backbone-Pilin Subunit Sci Rep V. 6 28664 2016.
ISSN: ESSN 2045-2322
PubMed: 27349405
DOI: 10.1038/SREP28664

Ytterbium in PDB 5fgr: Crystal Structure of C-Terminal Domain of Shaft Pilin Spaa From Lactobacillus Rhamnosus Gg - P21212 Space Group with Yb Heavy Atom

Protein crystallography data

Ytterbium Binding Sites:

Ytterbium binding site 1 out of 10 in 5fgr

Ytterbium binding site 2 out of 10 in 5fgr

Ytterbium binding site 3 out of 10 in 5fgr

Ytterbium binding site 4 out of 10 in 5fgr

Ytterbium binding site 5 out of 10 in 5fgr

Ytterbium binding site 6 out of 10 in 5fgr

Ytterbium binding site 7 out of 10 in 5fgr

Ytterbium binding site 8 out of 10 in 5fgr

Ytterbium binding site 9 out of 10 in 5fgr

Ytterbium binding site 10 out of 10 in 5fgr

Reference:

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