Magnesium in PDB 1l9a: Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna

The structure of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna, PDB code: 1l9a was solved by C.Oubridge, A.Kuglstatter, L.Jovine, K.Nagai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.84 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.765, 223.875, 43.024, 90.00, 90.00, 90.00
R / Rfree (%)	26.4 / 29.6

The structure of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna also contains other interesting chemical elements:

Mercury

(Hg)

1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna (pdb code 1l9a). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna, PDB code: 1l9a:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:87.1 occ:1.00 OP2 B:A205 2.9 60.4 1.0 O B:HOH7 3.4 71.2 1.0 N7 B:A205 4.1 62.5 1.0 P B:A205 4.3 60.2 1.0 C3' B:G204 4.6 59.6 1.0 C8 B:A205 4.6 62.2 1.0 OP2 B:G204 4.7 69.1 1.0 O5' B:A205 4.8 60.4 1.0 N7 B:G206 4.9 58.6 1.0 O3' B:G204 4.9 59.1 1.0 O5' B:G204 5.0 68.5 1.0

Magnesium binding site 2 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:91.2 occ:1.00 OP1 B:U218 2.3 82.1 1.0 P B:U218 3.8 82.0 1.0 O5' B:U218 4.5 84.0 1.0 OP2 B:U218 4.6 80.1 1.0 O3' B:C217 4.7 80.3 1.0 C5' B:U218 4.8 87.7 1.0 MG B:MG106 4.9 92.5 1.0

Magnesium binding site 3 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:62.8 occ:1.00 OP2 B:G193 2.3 70.8 1.0 P B:G193 3.6 70.0 1.0 N7 B:G194 3.7 57.6 1.0 O5' B:G193 3.8 67.5 1.0 N7 B:G193 3.9 55.3 1.0 C8 B:G193 4.0 56.6 1.0 O4 B:U195 4.1 68.1 1.0 C3' B:A192 4.4 74.7 1.0 O6 B:G194 4.5 61.0 1.0 O3' B:A192 4.5 72.2 1.0 OP1 B:G193 4.6 69.2 1.0 C8 B:G194 4.6 59.3 1.0 C5 B:G194 4.7 58.1 1.0 C5' B:A192 4.8 81.8 1.0 OP2 B:G194 5.0 61.1 1.0

Magnesium binding site 4 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:74.3 occ:1.00 OP1 B:G187 2.4 0.6 1.0 P B:G187 3.7 0.7 1.0 OP2 B:G187 4.3 0.5 1.0 O5' B:G187 4.4 0.0 1.0 C5' B:G187 4.6 98.5 1.0 OP2 B:G188 4.9 97.5 1.0 O3' B:C186 4.9 0.8 1.0

Magnesium binding site 5 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:83.0 occ:1.00 OP1 B:A215 2.5 96.4 1.0 P B:A215 3.8 95.5 1.0 OP1 B:C161 4.1 71.3 1.0 O5' B:A215 4.3 93.9 1.0 OP2 B:C162 4.6 79.4 1.0 OP2 B:A215 4.7 95.8 1.0 OP1 B:C162 4.8 80.0 1.0 O3' B:A214 4.9 95.9 1.0 O5' B:C161 4.9 71.5 1.0

Magnesium binding site 6 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:92.5 occ:1.00 OP2 B:C219 2.9 96.6 1.0 OP1 B:C219 3.4 97.5 1.0 P B:C219 3.6 97.7 1.0 C5' B:U218 4.3 87.7 1.0 O3' B:U218 4.5 95.0 1.0 MG B:MG102 4.9 91.2 1.0 O5' B:C219 5.0 98.7 1.0 OP1 B:U218 5.0 82.1 1.0 C3' B:U218 5.0 91.8 1.0 OP2 B:U218 5.0 80.1 1.0

Magnesium binding site 7 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:86.1 occ:1.00 OP1 B:G210 2.7 84.3 1.0 OP2 B:G210 2.7 84.5 1.0 P B:G210 3.1 84.0 1.0 OP1 B:G209 3.6 84.7 1.0 O3' B:G209 4.0 82.5 1.0 O5' B:G210 4.5 83.2 1.0 P B:G209 4.5 84.1 1.0 C5' B:G209 4.5 79.2 1.0 O5' B:G209 4.5 81.3 1.0 C3' B:G209 4.7 79.3 1.0 OP2 B:G209 4.8 82.8 1.0

Magnesium binding site 8 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg109 b:95.3 occ:1.00 OP1 B:U211 4.0 93.8 1.0 OP2 B:U211 4.2 92.7 1.0 P B:U211 4.5 93.0 1.0 OP2 B:G182 4.6 0.8 1.0 OP1 B:G182 4.8 0.2 1.0

Magnesium binding site 9 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg110 b:85.6 occ:1.00 OP2 B:G165 2.4 0.8 1.0 OP1 B:G165 2.7 0.4 1.0 P B:G165 2.8 0.8 1.0 O3' B:G164 3.2 0.5 1.0 C3' B:G164 3.5 0.8 1.0 C5' B:G164 3.5 0.5 1.0 O5' B:G164 3.8 0.3 1.0 C4' B:G164 4.0 0.1 1.0 OP1 B:G164 4.1 0.7 1.0 O5' B:G165 4.3 0.9 1.0 P B:G164 4.6 0.7 1.0 N3 B:G175 4.8 0.5 1.0 C2' B:G164 4.9 0.3 1.0 O2' B:G175 5.0 0.4 1.0

Magnesium binding site 10 out of 24 in the Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of SRP19 in Complex with the S Domain of Signal Recognition Particle Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg111 b:93.7 occ:1.00 O B:HOH20 2.7 89.3 1.0 OP2 B:G227 3.4 0.8 1.0 C5' B:U226 3.4 0.8 1.0 O3' B:U226 3.5 0.6 1.0 OP1 B:U226 3.5 0.7 1.0 P B:G227 3.7 0.5 1.0 O5' B:U226 3.7 0.6 1.0 OP1 B:G227 3.9 0.2 1.0 C3' B:U226 3.9 0.8 1.0 C4' B:U226 4.1 0.7 1.0 P B:U226 4.2 0.6 1.0 O B:HOH21 4.8 62.6 1.0 OP2 B:U226 4.9 0.3 1.0

C.Oubridge, A.Kuglstatter, L.Jovine, K.Nagai. Crystal Structure of SRP19 in Complex with the S Domain of Srp Rna and Its Implication For the Assembly of the Signal Recognition Particle. Mol.Cell V. 9 1251 2002.
ISSN: ISSN 1097-2765
PubMed: 12086622
DOI: 10.1016/S1097-2765(02)00530-0