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Ytterbium in PDB 1z1y: Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax

Protein crystallography data

The structure of Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax, PDB code: 1z1y was solved by A.K.Saxena, K.Singh, H.P.Su, M.M.Klein, A.W.Stowers, A.J.Saul, C.A.Long, D.N.Garboczi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.60 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.164, 43.700, 65.650, 90.00, 103.15, 90.00
R / Rfree (%) 24.4 / 27.6

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax (pdb code 1z1y). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 9 binding sites of Ytterbium where determined in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax, PDB code: 1z1y:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Ytterbium binding site 1 out of 9 in 1z1y

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Ytterbium binding site 1 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb182

b:21.0
occ:1.00
 OE1 A:GLU124 4.1 19.1 1.0
OD1 A:ASN122 4.4 16.5 1.0
CD A:GLU124 4.4 19.6 1.0
OE2 A:GLU124 4.6 2.0 1.0
CB A:GLU124 4.6 21.7 1.0
ND2 A:ASN122 4.8 16.1 1.0

Ytterbium binding site 2 out of 9 in 1z1y

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Ytterbium binding site 2 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb183

b:24.4
occ:1.00
 OE1 A:GLU126 2.4 21.8 1.0
O A:HOH199 2.4 35.7 1.0
OD1 A:ASP125 2.6 22.6 1.0
OE2 A:GLU126 3.0 12.6 1.0
CD A:GLU126 3.1 18.9 1.0
CG A:ASP125 3.5 21.2 1.0
CA A:ASP125 4.2 20.9 1.0
CH2 A:MLY128 4.2 27.0 1.0
OD2 A:ASP125 4.2 22.1 1.0
O A:HOH220 4.3 27.1 1.0
CB A:ASP125 4.4 20.9 1.0
C A:ASP125 4.4 21.3 1.0
CG A:GLU126 4.5 21.0 1.0
CE A:MLY128 4.7 24.8 1.0
O A:ASP125 4.7 20.9 1.0
NZ A:MLY128 4.8 27.2 1.0
CH1 A:MLY128 4.8 26.8 1.0
N A:GLU126 4.9 22.0 1.0
CD A:MLY128 5.0 22.3 1.0

Ytterbium binding site 3 out of 9 in 1z1y

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Ytterbium binding site 3 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb184

b:53.3
occ:1.00
 YB A:YB185 3.5 61.9 1.0
YB A:YB186 3.5 65.6 1.0
YB A:YB187 3.6 62.9 1.0

Ytterbium binding site 4 out of 9 in 1z1y

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Ytterbium binding site 4 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb185

b:61.9
occ:1.00
 YB A:YB187 3.4 62.9 1.0
YB A:YB186 3.5 65.6 1.0
YB A:YB184 3.5 53.3 1.0

Ytterbium binding site 5 out of 9 in 1z1y

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Ytterbium binding site 5 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb186

b:65.6
occ:1.00
 YB A:YB185 3.5 61.9 1.0
YB A:YB184 3.5 53.3 1.0
YB A:YB187 3.6 62.9 1.0

Ytterbium binding site 6 out of 9 in 1z1y

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Ytterbium binding site 6 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb187

b:62.9
occ:1.00
 OE1 A:GLU107 2.6 53.1 1.0
YB A:YB185 3.4 61.9 1.0
CD A:GLU107 3.5 52.3 1.0
YB A:YB186 3.6 65.6 1.0
YB A:YB184 3.6 53.3 1.0
OE2 A:GLU107 3.7 51.5 1.0
CG A:GLU107 4.7 51.6 1.0

Ytterbium binding site 7 out of 9 in 1z1y

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Ytterbium binding site 7 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb188

b:50.6
occ:1.00
 OD2 A:ASP62 2.3 41.9 1.0
OD1 A:ASP62 2.8 41.5 1.0
CG A:ASP62 2.9 40.9 1.0
CB A:ASP62 4.3 39.9 1.0
NE2 A:GLN65 4.4 43.2 1.0
CB A:ALA64 4.6 39.8 1.0

Ytterbium binding site 8 out of 9 in 1z1y

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Ytterbium binding site 8 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb182

b:30.9
occ:1.00
 OD1 B:ASP82 2.3 37.3 1.0
OD2 B:ASP82 2.5 37.2 1.0
O B:HOH208 2.6 22.5 1.0
CG B:ASP82 2.7 37.5 1.0
CB B:ASP82 4.3 36.7 1.0
CA B:ASP82 5.0 36.6 1.0

Ytterbium binding site 9 out of 9 in 1z1y

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Ytterbium binding site 9 out of 9 in the Crystal Structure of Methylated PVS25, An Ookinete Protein From Plasmodium Vivax


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 Methylated PVS25, An Ookinete Protein From Plasmodium Vivax within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Yb183

b:75.3
occ:1.00
 OD2 B:ASP87 2.5 34.9 1.0
CG B:ASP87 3.5 31.6 1.0
CB B:ASP87 3.8 28.1 1.0
O A:HOH197 4.4 33.0 1.0
OD1 B:ASP87 4.5 35.6 1.0
O A:HOH241 4.6 37.7 1.0
OE1 A:GLU134 4.7 39.3 1.0
OE1 B:GLN109 4.7 46.2 1.0
OH A:TYR155 4.7 23.8 1.0
O A:THR135 4.8 27.0 1.0
CA B:GLY76 4.8 25.3 1.0
CD A:GLU134 4.9 38.0 1.0
O B:HOH203 5.0 24.6 1.0

Reference:

A.K.Saxena, K.Singh, H.P.Su, M.M.Klein, A.W.Stowers, A.J.Saul, C.A.Long, D.N.Garboczi. The Essential Mosquito-Stage P25 and P28 Proteins From Plasmodium Form Tile-Like Triangular Prisms Nat.Struct.Mol.Biol. V. 13 90 2006.
ISSN: ISSN 1545-9993
PubMed: 16327807
DOI: 10.1038/NSMB1024
Page generated: Tue Aug 19 18:47:55 2025

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