Atomistry » Ytterbium » PDB 1c5k-3fty » 1z1y
Atomistry »
  Ytterbium »
    PDB 1c5k-3fty »
      1z1y »

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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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

Go back to Ytterbium Binding Sites List in 1z1y
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: Sat Oct 12 20:58:42 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy