Calcium in PDB 1m8v: Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer

The structure of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer, PDB code: 1m8v was solved by S.Thore, C.Mayer, C.Sauter, S.Weeks, D.Suck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.60
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	68.000, 68.000, 84.800, 105.00, 108.80, 100.00
R / Rfree (%)	21.2 / 28.2

The binding sites of Calcium atom in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer (pdb code 1m8v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer, PDB code: 1m8v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ O:Ca310 b:45.7 occ:1.00 OP2 O:U5 2.2 69.9 0.7 OP2 O:U2 2.4 93.6 0.9 OP2 O:U3 2.7 92.3 0.5 OP1 O:U6 2.7 80.9 0.6 O O:HOH313 3.4 27.9 1.0 P O:U5 3.4 64.9 1.0 P O:U2 3.5 93.5 0.7 O5' O:U2 3.5 89.0 1.0 O3' O:U4 3.6 67.2 1.0 O5' O:U3 3.8 88.0 1.0 P O:U3 3.8 91.6 1.0 O3' O:U1 3.9 86.8 1.0 O O:HOH314 4.0 43.7 1.0 C5' O:U3 4.0 93.3 1.0 P O:U6 4.1 77.5 1.0 O5' O:U5 4.2 72.2 0.1 C3' O:U2 4.3 76.6 0.5 O3' O:U2 4.5 84.4 1.0 OP2 O:U6 4.6 80.9 0.3 C6 O:U3 4.6 98.5 1.0 C3' O:U5 4.6 64.7 0.9 OP1 O:U5 4.7 57.6 1.0 OP1 O:U2 4.8 92.6 0.8 C5 O:U3 4.8 98.9 1.0 C5' O:U2 4.9 79.2 1.0 O3' O:U5 4.9 75.2 0.3 C5' O:U5 4.9 64.8 1.0 O O:HOH312 4.9 34.4 1.0 O4' O:U3 5.0 98.6 1.0 C6 O:U5 5.0 42.2 1.0 C3' O:U4 5.0 70.4 1.0

Calcium binding site 2 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ P:Ca330 b:53.9 occ:1.00 OP2 P:U2 2.1 74.0 1.0 OP1 P:U3 2.2 78.7 1.0 OP2 P:U5 2.4 61.2 0.8 OP1 P:U6 2.6 79.0 1.0 P P:U2 3.2 75.9 1.0 O5' P:U2 3.4 75.1 0.4 P P:U3 3.6 82.3 1.0 P P:U5 3.7 61.7 1.0 O5' P:U5 3.9 64.3 0.6 O3' P:U1 3.9 72.6 1.0 P P:U6 4.0 79.9 1.0 O3' P:U2 4.3 78.3 1.0 C5' P:U2 4.4 69.5 1.0 C5' P:U3 4.4 85.7 0.9 OP1 P:U2 4.4 79.0 0.8 C3' P:U2 4.5 73.3 0.0 O5' P:U3 4.5 79.2 1.0 OP2 P:U3 4.6 86.0 0.3 C3' P:U5 4.6 68.7 0.4 C6 P:U3 4.6 88.2 1.0 OP1 P:U5 4.7 49.0 1.0 O3' P:U4 4.7 64.6 0.3 C5' P:U6 4.7 85.2 1.0 OP2 P:U6 4.8 78.2 0.7 C5 P:U3 4.9 84.7 1.0 O3' P:U5 4.9 75.3 0.7 O5' P:U6 4.9 81.2 1.0 C6 P:U5 4.9 46.2 1.0 C3' P:U4 5.0 63.1 1.0 C5' P:U5 5.0 60.5 1.0

Calcium binding site 3 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ Q:Ca380 b:46.4 occ:1.00 OP2 Q:U5 2.2 75.5 0.9 OP2 Q:U2 2.4 88.3 0.3 OP2 Q:U3 2.5 90.1 0.5 OP1 Q:U6 2.5 81.8 1.0 O5' Q:U2 3.1 81.8 0.8 P Q:U2 3.3 81.2 1.0 P Q:U5 3.5 76.8 1.0 O5' Q:U3 3.5 86.5 1.0 P Q:U3 3.6 85.0 1.0 O5' Q:U5 3.6 74.7 0.6 P Q:U6 3.8 82.0 1.0 C5' Q:U3 4.0 93.1 0.3 O3' Q:U1 4.1 76.5 0.7 O3' Q:U4 4.1 72.9 0.8 C3' Q:U5 4.2 73.3 0.7 OP2 Q:U6 4.3 82.0 0.8 C3' Q:U2 4.3 75.0 0.0 C5' Q:U2 4.4 76.7 1.0 O3' Q:U2 4.4 80.9 1.0 O Q:HOH386 4.4 35.6 1.0 O3' Q:U5 4.5 79.3 1.0 C3' Q:U4 4.6 68.3 1.0 C5' Q:U5 4.6 71.4 1.0 OP1 Q:U2 4.6 76.3 1.0 C6 Q:U3 4.6 90.5 1.0 O Q:HOH385 4.7 29.8 1.0 C6 Q:U5 4.7 55.2 1.0 OP1 Q:U5 4.7 70.8 1.0 C5 Q:U3 4.8 88.9 1.0 OP1 Q:U3 4.8 87.0 0.4 C4' Q:U2 5.0 73.1 1.0 O5' Q:U6 5.0 86.9 0.4 C4' Q:U5 5.0 70.1 1.0

Calcium binding site 4 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ R:Ca390 b:51.4 occ:1.00 OP2 R:U2 2.0 92.0 0.4 OP2 R:U3 2.7 75.3 0.9 O5' R:U2 2.7 88.6 0.2 OP1 R:U6 2.8 67.8 0.9 P R:U2 2.9 91.5 0.9 OP2 R:U5 3.0 60.4 1.0 O5' R:U3 3.7 71.3 1.0 OP1 R:U2 3.7 81.7 1.0 P R:U3 3.8 80.1 1.0 C5' R:U5 3.8 67.8 0.3 C5' R:U2 4.1 80.2 1.0 O3' R:U1 4.1 81.1 1.0 O R:HOH213 4.1 42.3 1.0 C5' R:U3 4.2 78.4 1.0 P R:U6 4.3 66.6 1.0 P R:U5 4.3 68.1 1.0 C3' R:U2 4.4 77.0 0.7 O3' R:U2 4.5 78.9 0.9 O5' R:U5 4.6 67.2 0.8 C3' R:U4 4.8 59.4 1.0 C3' R:U5 4.9 64.7 0.9 C4' R:U2 4.9 75.9 1.0 C6 R:U3 4.9 84.0 1.0 O R:HOH27 4.9 36.7 1.0 O3' R:U4 4.9 61.5 0.8 C4' R:U5 5.0 62.2 1.0 OP2 R:U6 5.0 71.3 0.5 C5' R:U6 5.0 68.7 1.0

Calcium binding site 5 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ S:Ca340 b:51.6 occ:1.00 OP2 S:U5 2.2 98.4 0.3 OP1 S:U6 2.5 95.5 0.3 OP2 S:U2 2.6 74.4 0.5 O5' S:U5 2.9 96.2 0.8 OP2 S:U3 3.1 77.0 1.0 P S:U5 3.1 97.3 0.9 C5' S:U2 3.3 80.2 0.0 O5' S:U3 3.7 83.7 1.0 P S:U6 3.9 92.9 1.0 P S:U2 3.9 70.6 1.0 P S:U3 4.0 82.3 1.0 O5' S:U2 4.0 74.2 0.9 O3' S:U4 4.0 87.4 1.0 O S:HOH113 4.1 43.7 1.0 C5' S:U5 4.1 89.0 1.0 OP1 S:U5 4.3 91.4 1.0 C3' S:U5 4.3 83.9 1.0 C5' S:U3 4.4 92.3 0.0 C3' S:U2 4.4 78.2 0.5 C4' S:U2 4.4 74.4 1.0 OP2 S:U6 4.5 93.8 0.9 O3' S:U1 4.5 64.2 0.9 C3' S:U1 4.5 60.3 0.9 O3' S:U5 4.6 90.0 0.9 O3' S:U2 4.7 84.3 0.5 C6 S:U3 4.7 91.2 0.8 C4' S:U5 4.8 85.2 0.8 C5 S:U3 4.9 89.4 1.0 O5' S:U6 5.0 93.0 0.9 C5' S:U6 5.0 95.8 0.6

Calcium binding site 6 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ T:Ca320 b:48.3 occ:1.00 OP2 T:U5 2.3 93.7 0.3 OP2 T:U2 2.9 83.5 0.8 OP2 T:U3 3.0 95.8 1.0 O5' T:U3 3.2 95.0 1.0 C5' T:U2 3.4 75.4 1.0 P T:U5 3.4 89.4 1.0 O5' T:U5 3.4 87.1 0.3 P T:U3 3.7 94.9 1.0 C5' T:U3 3.8 98.6 0.5 O3' T:U4 3.8 87.5 0.8 P T:U2 4.1 81.4 1.0 O5' T:U2 4.2 78.5 1.0 C3' T:U2 4.4 74.8 1.0 C6 T:U3 4.5 0.8 0.7 C4' T:U2 4.5 72.2 1.0 O3' T:U2 4.6 87.2 1.0 O3' T:U1 4.6 80.1 0.5 C5 T:U3 4.7 99.7 0.9 C3' T:U5 4.7 73.9 0.3 OP1 T:U5 4.7 87.8 1.0 O3' T:U5 4.8 74.1 1.0 C3' T:U1 4.8 71.9 1.0 C5' T:U5 4.8 77.8 1.0 O4' T:U3 4.8 100.0 1.0 O T:HOH324 4.9 22.1 1.0 C4' T:U3 4.9 98.2 1.0 OP1 T:U3 4.9 99.8 0.2 C6 T:U2 5.0 56.2 1.0

Calcium binding site 7 out of 7 in the Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of Pyrococcus Abyssii Sm Protein in Complex with A Uridine Heptamer within 5.0Å range: probe atom residue distance (Å) B Occ U:Ca370 b:45.0 occ:1.00 OP2 U:U3 2.4 83.8 0.5 OP2 U:U2 2.4 73.0 1.0 OP2 U:U5 2.5 73.3 0.9 OP1 U:U6 2.7 83.3 1.0 P U:U3 3.6 82.0 1.0 O5' U:U3 3.7 81.7 1.0 P U:U2 3.7 75.5 1.0 P U:U5 3.8 72.3 1.0 O5' U:U2 3.9 75.3 0.2 O5' U:U5 4.0 74.9 0.7 O U:HOH205 4.0 32.1 1.0 C3' U:U2 4.1 68.3 0.8 P U:U6 4.1 82.1 1.0 O3' U:U2 4.2 75.4 0.9 C5' U:U3 4.3 89.4 0.0 O3' U:U1 4.5 73.7 1.0 C6 U:U3 4.5 93.7 0.9 O3' U:U4 4.6 70.5 0.8 C3' U:U5 4.6 69.8 0.9 OP2 U:U6 4.7 81.2 1.0 C6 U:U2 4.7 49.9 0.9 C5 U:U3 4.7 95.1 0.4 C3' U:U1 4.8 72.9 0.7 C5' U:U2 4.8 69.6 1.0 OP1 U:U3 4.8 80.4 0.6 OP1 U:U2 4.9 76.7 1.0 OP1 U:U5 4.9 69.0 1.0 O3' U:U5 4.9 79.9 0.5 C3' U:U4 5.0 64.7 1.0

S.Thore, C.Mayer, C.Sauter, S.Weeks, D.Suck. Crystal Structure of Pyrococcus Abyssii Sm Core and Its Complex with Rna: Common Features of Rna-Binding in Archaea and Eukarya J.Biol.Chem. V. 278 1239 2003.
ISSN: ISSN 0021-9258
PubMed: 12409299
DOI: 10.1074/JBC.M207685200