Magnesium in PDB 2r8s: High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain

The structure of High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain, PDB code: 2r8s was solved by J.D.Ye, V.Tereshko, S.S.Sidhu, S.Koide, A.A.Kossiakoff, J.A.Piccirilli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	133.085, 53.230, 160.555, 90.00, 108.42, 90.00
R / Rfree (%)	19.5 / 22.6

The binding sites of Magnesium atom in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain (pdb code 2r8s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain, PDB code: 2r8s:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1001 b:32.3 occ:1.00 O R:HOH1007 1.9 33.8 1.0 O R:HOH1006 2.0 32.5 1.0 O R:HOH1005 2.0 36.4 1.0 OP2 R:A186 2.1 31.5 1.0 OP2 R:A184 2.1 33.2 1.0 OP1 R:A183 2.2 30.1 1.0 P R:A183 3.3 29.2 1.0 P R:A184 3.5 32.9 1.0 P R:A186 3.6 31.6 1.0 OP2 R:A183 3.8 28.3 1.0 O R:HOH1008 4.0 31.1 1.0 O R:HOH1067 4.1 37.9 1.0 O5' R:A183 4.2 28.9 1.0 O R:HOH1178 4.2 49.4 1.0 O R:HOH1060 4.2 37.6 1.0 OP1 R:A184 4.2 31.8 1.0 N7 R:A184 4.2 33.5 1.0 O3' R:U185 4.2 34.0 1.0 N7 R:A186 4.3 28.5 1.0 C8 R:A186 4.3 30.4 1.0 C3' R:A183 4.3 31.3 1.0 OP1 R:A186 4.4 31.6 1.0 O3' R:A183 4.4 32.3 1.0 C3' R:U185 4.4 39.2 1.0 C8 R:A184 4.4 33.3 1.0 O5' R:A184 4.4 34.7 1.0 O5' R:A186 4.5 30.9 1.0 O3' R:U182 4.5 32.6 1.0 O R:HOH1033 4.7 32.6 1.0 O R:HOH1098 4.8 39.1 1.0 N3 R:A139 4.8 33.2 1.0 C5' R:A183 4.9 31.2 1.0 MG R:MG1002 5.0 36.1 1.0 O R:HOH1151 5.0 48.8 1.0

Magnesium binding site 2 out of 4 in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1002 b:36.1 occ:1.00 O R:HOH1009 2.1 32.6 1.0 O R:HOH1008 2.1 31.1 1.0 OP1 R:A184 2.1 31.8 1.0 OP2 R:A187 2.1 35.6 1.0 OP1 R:A186 2.1 31.6 1.0 OP2 R:G188 2.1 44.8 1.0 P R:A186 3.4 31.6 1.0 P R:G188 3.4 47.3 1.0 P R:A184 3.4 32.9 1.0 P R:A187 3.6 39.4 1.0 O R:HOH1194 3.8 52.0 1.0 OP1 R:G188 3.8 50.6 1.0 OP2 R:A186 3.8 31.5 1.0 O R:HOH1139 4.0 44.0 1.0 OP2 R:A184 4.1 33.2 1.0 O3' R:A183 4.1 32.3 1.0 C3' R:A186 4.1 36.6 1.0 O5' R:A186 4.2 30.9 1.0 C5' R:A187 4.3 44.3 1.0 O5' R:G188 4.3 43.0 1.0 O3' R:A186 4.3 41.7 1.0 O5' R:A187 4.4 46.1 1.0 OP1 R:A183 4.4 30.1 1.0 O3' R:A187 4.4 43.6 1.0 O5' R:A184 4.5 34.7 1.0 O3' R:U185 4.5 34.0 1.0 C5' R:A186 4.5 36.0 1.0 OP1 R:A187 4.6 45.5 1.0 C4' R:U185 4.6 39.5 1.0 C4' R:A187 4.8 41.9 1.0 C5' R:U185 4.9 38.5 1.0 C3' R:U185 4.9 39.2 1.0 MG R:MG1001 5.0 32.3 1.0 C5' R:A184 5.0 34.4 1.0 C4' R:A186 5.0 34.1 1.0

Magnesium binding site 3 out of 4 in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1003 b:33.2 occ:1.00 O R:HOH1014 1.9 34.9 1.0 O R:HOH1010 2.1 32.2 1.0 O R:HOH1013 2.1 27.7 1.0 O R:HOH1011 2.1 34.0 1.0 O R:HOH1012 2.2 32.8 1.0 O6 R:G188 2.2 33.1 1.0 C6 R:G188 3.2 30.2 1.0 N7 R:G188 3.7 30.8 1.0 C5 R:G188 3.8 29.5 1.0 OP1 R:U168 4.0 30.2 1.0 OP1 R:C165 4.0 28.6 1.0 OP2 R:U168 4.1 31.5 1.0 OP1 R:C166 4.1 27.4 1.0 O R:HOH1173 4.1 47.8 1.0 N7 R:A183 4.2 34.0 1.0 OP2 R:C166 4.2 28.1 1.0 C8 R:A183 4.3 32.0 1.0 O R:HOH1151 4.3 48.8 1.0 N1 R:G188 4.4 31.8 1.0 OP1 R:U182 4.4 34.8 1.0 C5 R:U168 4.5 32.6 1.0 P R:C166 4.6 28.1 1.0 P R:U168 4.6 30.3 1.0 OP2 R:A183 4.6 28.3 1.0 O R:HOH1079 4.7 38.8 1.0 C5' R:C165 4.9 30.3 1.0 O3' R:C165 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in the High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of High Resolution Structure of A Specific Synthetic Fab Bound to P4-P6 Rna Ribozyme Domain within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg1004 b:35.0 occ:1.00 O4 R:U258 2.2 35.3 1.0 O6 R:G257 2.2 33.7 1.0 O R:HOH1017 2.3 39.0 1.0 O R:HOH1016 2.4 36.2 1.0 O R:HOH1015 2.4 33.6 1.0 O R:HOH1018 2.5 35.1 1.0 C6 R:G257 3.2 32.5 1.0 C4 R:U258 3.3 35.1 1.0 N7 R:G257 3.7 34.5 1.0 C5 R:G257 3.8 32.8 1.0 N3 R:U258 3.9 32.7 1.0 N4 R:C216 4.0 37.4 1.0 O6 R:G215 4.0 37.5 1.0 O R:HOH1030 4.0 23.2 0.5 OP2 R:A256 4.3 40.7 1.0 N1 R:G257 4.4 32.7 1.0 C5 R:U258 4.5 37.2 1.0 O R:HOH1100 4.6 40.0 1.0 O R:HOH1030 4.7 13.6 0.5 OP2 R:C255 4.8 43.1 1.0 O R:HOH1128 4.9 41.8 1.0 C5' R:C255 4.9 50.0 1.0 C8 R:G257 5.0 31.6 1.0

J.D.Ye, V.Tereshko, J.K.Frederiksen, A.Koide, F.A.Fellouse, S.S.Sidhu, S.Koide, A.A.Kossiakoff, J.A.Piccirilli. Synthetic Antibodies For Specific Recognition and Crystallization of Structured Rna Proc.Natl.Acad.Sci.Usa V. 105 82 2008.
ISSN: ISSN 0027-8424
PubMed: 18162543
DOI: 10.1073/PNAS.0709082105