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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 1kd1




1KD1 (3Å) -- RIBOSOME : Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
List of all 119 Mg2+ binding sites in the PDB structure 1kd1 in the full dataset (switch to benchmark dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "Site type" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
1kd1 A8118 Or 1  0.08 0  0.70no
1kd1 A8099 Or 4  0.37  0.50  0.66no
1kd1 A8053 Ob 6  0.35  0.87  0.75no
1kd1 A8114 Nb 6  0.23  0.78  0.74no
1kd1 A8102 Nb 3  0.33  0.45  0.92no
1kd1 A8113 Nb 6  0.42  0.69  0.98no
1kd1 A8112 Nb 6  0.62  0.71  0.85yes
1kd1 A8111 Nb 6  0.53  0.60  0.69yes
1kd1 A8046 Nb 4  0.60  0.38  0.59no
1kd1 A8098 Nb 6  0.48  0.77  0.94no
1kd1 A8024 Nb 4  0.15  0.45  0.53no
1kd1 A8075 2Or 6  0.65  0.55  0.78no
1kd1 A8119 2Or 2  0.10  0.39  0.67no
1kd1 A8042 2Ob 6  0.38  0.58  0.93no
1kd1 A8097 2Ob 6  0.46  0.75  0.85no
1kd1 A8011 2Nb 6 0  0.92  0.34no
1kd1 A8117 2Or·Nb 6  0.33  0.75  0.87no
1kd1 A8051 Oph·Pout 4  0.70  0.48  0.90no
1kd1 A8039 Oph·Pout 6  0.99  0.79  0.79yes
1kd1 A8104 Oph·Pout 4  0.11  0.45  0.88no

# Validation parameters Qv, Qs, Qe are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Qv measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg2+ (+2)
Qs measures the geometrical symmetry of the ligands distribution around the Mg2+ required for octahedral geometry
Qe measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg2+ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations
used for Mg2+
"Site type"
Mg2+ inner-sphere ligands Geometry for inner-sphere OP Mg2+ outer-sphere moieties
Oph phosphate oxygen (OP1/OP2)
Or ribose oxygen (O2'/O4')
     or oxygen bridging phosphate and ribose (O3'/O5')
Ob nucleobase oxygen      Nb nucleobase nitrogen
cis- two OP ligands adopt cis- isoform
trans- two OP ligands adopt trans- isoform
fac- three OP ligands adopt fac- isoform
mer- three OP ligands adopt mer- isoform
Pout phosphate moiety
Rout ribose moiety
Bout nucleobase moiety
Reference: Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].


Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>