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Ytterbium in PDB 1ggy: Human Factor XIII with Ytterbium Bound in the Ion Site

Enzymatic activity of Human Factor XIII with Ytterbium Bound in the Ion Site

All present enzymatic activity of Human Factor XIII with Ytterbium Bound in the Ion Site:
2.3.2.13;

Protein crystallography data

The structure of Human Factor XIII with Ytterbium Bound in the Ion Site, PDB code: 1ggy was solved by B.A.Fox, V.C.Yee, L.C.Pederson, I.L.Trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 101.060, 72.390, 135.990, 90.00, 106.09, 90.00
R / Rfree (%) 18.8 / 28.1

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Human Factor XIII with Ytterbium Bound in the Ion Site (pdb code 1ggy). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 8 binding sites of Ytterbium where determined in the Human Factor XIII with Ytterbium Bound in the Ion Site, PDB code: 1ggy:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Ytterbium binding site 1 out of 8 in 1ggy

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Ytterbium binding site 1 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb732

b:50.1
occ:1.00
 OE1 A:GLU485 2.1 35.0 1.0
O A:HOH5034 2.1 22.0 1.0
OE2 A:GLU485 2.2 47.3 1.0
O A:HOH3006 2.3 37.5 1.0
CD A:GLU485 2.5 45.4 1.0
OE1 A:GLU490 3.4 62.3 1.0
OD1 A:ASN436 3.6 33.1 1.0
OE2 A:GLU490 3.7 65.1 1.0
CD A:GLU490 3.9 60.7 1.0
CG A:GLU485 4.0 44.0 1.0
O A:ASN436 4.2 30.7 1.0
OD1 A:ASP438 4.2 38.9 1.0
CG A:ASN436 4.6 31.9 1.0
CB A:GLU485 4.8 43.4 1.0
O A:ALA457 4.8 32.2 1.0
OD2 A:ASP438 4.8 40.6 1.0
CB A:ASN436 4.9 29.1 1.0
CG A:ASP438 4.9 34.4 1.0
C A:ASN436 5.0 27.5 1.0

Ytterbium binding site 2 out of 8 in 1ggy

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Ytterbium binding site 2 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb733

b:12.2
occ:0.25
 OD1 A:ASP270 2.1 79.3 1.0
OD1 A:ASP271 3.0 72.1 1.0
CG A:ASP270 3.4 80.3 1.0
YB A:YB740 3.4 22.4 0.2
YB A:YB741 3.4 23.3 0.2
O A:ASP270 3.5 67.7 1.0
YB B:YB742 3.7 11.5 0.2
OD2 A:ASP270 4.1 85.4 1.0
CG A:ASP271 4.3 68.6 1.0
CB A:ASP270 4.5 74.5 1.0
C A:ASP270 4.6 64.8 1.0
OE1 A:GLU272 4.9 66.4 1.0

Ytterbium binding site 3 out of 8 in 1ggy

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Ytterbium binding site 3 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb740

b:22.4
occ:0.25
 OD1 A:ASP271 3.4 72.1 1.0
YB A:YB733 3.4 12.2 0.2
YB B:YB742 3.7 11.5 0.2
YB A:YB741 3.7 23.3 0.2
OD2 A:ASP271 4.1 72.0 1.0
CG A:ASP271 4.1 68.6 1.0

Ytterbium binding site 4 out of 8 in 1ggy

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Ytterbium binding site 4 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb741

b:23.3
occ:0.25
 YB A:YB733 3.4 12.2 0.2
YB A:YB740 3.7 22.4 0.2
YB B:YB742 3.8 11.5 0.2
OE1 B:GLU272 4.7 75.7 1.0
OD1 A:ASP270 4.8 79.3 1.0

Ytterbium binding site 5 out of 8 in 1ggy

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Ytterbium binding site 5 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb743

b:63.1
occ:0.50
 O A:ASP574 3.9 46.1 1.0
N A:ASP574 4.5 43.6 1.0
OE1 A:GLU585 4.7 57.9 1.0
C A:ASP574 4.9 42.9 1.0
CB A:ASP574 4.9 49.3 1.0

Ytterbium binding site 6 out of 8 in 1ggy

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Ytterbium binding site 6 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb732

b:39.6
occ:0.80
 YB B:YB744 1.9 22.2 0.2
OE1 B:GLU485 2.3 61.8 1.0
OE1 B:GLU490 2.4 37.8 1.0
OE2 B:GLU490 2.4 33.5 1.0
CD B:GLU490 2.7 37.3 1.0
OD1 B:ASN436 2.7 41.1 1.0
OE2 B:GLU485 2.8 65.6 1.0
CD B:GLU485 2.9 63.6 1.0
CG B:ASN436 3.7 31.7 1.0
ND2 B:ASN436 4.0 32.4 1.0
CG B:GLU490 4.1 37.4 1.0
CG B:GLU485 4.4 61.5 1.0
OD1 B:ASP438 4.4 29.4 1.0
CD1 B:LEU494 4.5 34.0 1.0
O B:ALA457 4.7 29.9 1.0
O B:ASN436 4.9 29.3 1.0
O B:GLU490 4.9 44.0 1.0

Ytterbium binding site 7 out of 8 in 1ggy

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Ytterbium binding site 7 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb742

b:11.5
occ:0.25
 CB B:ASP270 3.6 64.4 1.0
YB A:YB740 3.7 22.4 0.2
YB A:YB733 3.7 12.2 0.2
YB A:YB741 3.8 23.3 0.2
OD2 B:ASP270 3.9 73.1 1.0
CG B:ASP270 3.9 69.2 1.0
N B:ASP271 4.5 59.1 1.0
OD1 B:ASP270 4.8 70.9 1.0
O B:LYS269 4.9 60.1 1.0
CA B:ASP270 5.0 61.9 1.0

Ytterbium binding site 8 out of 8 in 1ggy

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Ytterbium binding site 8 out of 8 in the Human Factor XIII with Ytterbium Bound in the Ion Site


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Human Factor XIII with Ytterbium Bound in the Ion Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb744

b:22.2
occ:0.20
 YB B:YB732 1.9 39.6 0.8
OE2 B:GLU485 2.1 65.6 1.0
OE1 B:GLU485 2.5 61.8 1.0
CD B:GLU485 2.6 63.6 1.0
OD1 B:ASN436 2.7 41.1 1.0
O B:HOH5063 3.4 42.2 1.0
O B:ALA457 3.5 29.9 1.0
OD1 B:ASP438 3.5 29.4 1.0
OE1 B:GLU490 3.7 37.8 1.0
CG B:ASN436 3.9 31.7 1.0
CG B:GLU485 4.1 61.5 1.0
OE2 B:GLU490 4.2 33.5 1.0
C B:ASN436 4.3 27.0 1.0
CD B:GLU490 4.3 37.3 1.0
C B:ALA457 4.4 30.1 1.0
N B:SER437 4.4 26.8 1.0
O B:ASN436 4.5 29.3 1.0
CB B:ALA457 4.6 21.9 1.0
CG B:ASP438 4.6 25.7 1.0
CA B:ASN436 4.6 26.2 1.0
CA B:ALA457 4.7 27.5 1.0
ND2 B:ASN436 4.7 32.4 1.0
C B:SER437 4.7 31.1 1.0
CA B:SER437 4.9 27.1 1.0
CB B:ASN436 4.9 25.7 1.0
O B:SER437 5.0 36.0 1.0
NZ B:LYS482 5.0 30.2 1.0
N B:ASP438 5.0 28.7 1.0

Reference:

B.A.Fox, V.C.Yee, L.C.Pedersen, I.Le Trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller. Identification of the Calcium Binding Site and A Novel Ytterbium Site in Blood Coagulation Factor XIII By X-Ray Crystallography. J.Biol.Chem. V. 274 4917 1999.
ISSN: ISSN 0021-9258
PubMed: 9988734
DOI: 10.1074/JBC.274.8.4917
Page generated: Sat Oct 12 20:53:50 2024

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