Calcium in PDB 3foz: Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)

All present enzymatic activity of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe):
2.5.1.8;

The structure of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe), PDB code: 3foz was solved by E.Seif, B.M.Hallberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.240, 91.260, 152.360, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 26.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Calcium atom in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) (pdb code 3foz). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 22 binding sites of Calcium where determined in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe), PDB code: 3foz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca317 b:60.1 occ:1.00 O B:THR284 2.5 11.1 1.0 O B:ARG287 2.5 24.3 1.0 OP2 D:A31 3.0 22.9 1.0 C B:THR284 3.7 12.7 1.0 C B:ARG287 3.7 10.4 1.0 P D:A31 4.0 26.3 1.0 O B:TRP285 4.1 13.1 1.0 OP1 D:A31 4.1 26.5 1.0 CG2 B:THR284 4.2 2.0 1.0 CB B:ARG287 4.3 10.0 1.0 C B:TRP285 4.4 4.2 1.0 CA B:ARG287 4.4 13.6 1.0 N B:TRP285 4.6 10.9 1.0 N B:ARG287 4.6 10.9 1.0 CA B:TRP285 4.6 10.6 1.0 CA B:THR284 4.6 14.9 1.0 OP1 D:G30 4.7 6.4 1.0 N B:GLY288 4.7 15.4 1.0 O3' D:G30 4.7 15.0 1.0 CA B:GLY288 4.9 17.3 1.0

Calcium binding site 2 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca318 b:74.4 occ:1.00 CA B:GLY288 3.9 17.3 1.0 O B:GLY288 3.9 26.5 1.0 C B:GLY288 4.3 19.7 1.0 OP2 C:A73 4.4 22.1 1.0 OP1 C:A73 4.5 23.9 1.0 O B:ARG287 4.9 24.3 1.0 P C:A73 5.0 28.9 1.0

Calcium binding site 3 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca75 b:60.4 occ:1.00 OP2 C:G70 3.4 17.7 1.0 N7 C:G70 4.0 14.2 1.0 C8 C:G70 4.0 12.3 1.0 C5' C:G70 4.5 13.4 1.0 OP2 C:G71 4.6 22.1 1.0 P C:G70 4.8 27.0 1.0

Calcium binding site 4 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca76 b:47.3 occ:1.00 O2' C:A58 2.9 13.4 1.0 OP2 C:U59 2.9 25.9 1.0 C2' C:A58 3.7 11.6 1.0 O3' C:A58 4.0 13.2 1.0 P C:U59 4.0 16.6 1.0 C3' C:A58 4.1 16.1 1.0 OP2 C:U60 4.4 18.1 1.0 O6 C:G52 4.4 17.4 1.0 O6 C:G53 4.5 14.8 1.0 N7 C:G52 4.7 23.3 1.0 O4 C:U51 4.7 36.0 1.0 C5' C:U59 5.0 15.1 1.0

Calcium binding site 5 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca77 b:35.8 occ:1.00 OP2 C:G19 2.1 20.7 1.0 OP1 C:C17 2.3 13.5 1.0 P C:C17 3.4 15.1 1.0 P C:G19 3.5 14.9 1.0 O3' C:U16 3.5 17.6 1.0 O5' C:G19 4.0 11.3 1.0 OP1 C:G19 4.3 12.7 1.0 OP2 C:C17 4.4 22.7 1.0 O3' C:G18 4.5 21.4 1.0 O2' C:U16 4.6 15.6 1.0 O5' C:C17 4.6 12.9 1.0 C3' C:G18 4.8 24.3 1.0 C3' C:U16 4.9 19.7 1.0

Calcium binding site 6 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca78 b:55.0 occ:1.00 OP1 C:A7 2.3 20.8 1.0 OP2 C:A14 2.4 30.9 1.0 O4 C:U8 3.0 12.5 1.0 P C:A7 3.6 17.7 1.0 P C:A14 3.7 24.9 1.0 C4 C:U8 3.7 16.5 1.0 O5' C:A14 4.0 24.3 1.0 O3' C:G6 4.0 22.7 1.0 C5 C:U8 4.1 19.8 1.0 OP2 C:A7 4.2 15.8 1.0 OP1 C:A14 4.5 22.5 1.0 N7 C:G15 4.7 9.8 1.0 O5' C:A7 4.8 21.4 1.0 N3 C:U8 4.8 14.4 1.0 O3' C:C13 4.9 26.9 1.0 OP2 C:G15 5.0 24.8 1.0

Calcium binding site 7 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca79 b:46.4 occ:1.00 OP1 C:U60 2.2 9.7 1.0 P C:U60 3.4 12.9 1.0 O3' C:U59 3.5 7.4 1.0 C5' C:U60 4.0 11.8 1.0 O5' C:U60 4.1 20.6 1.0 O4 C:U51 4.2 36.0 1.0 O4 C:U50 4.4 14.9 1.0 N4 C:C62 4.4 2.0 1.0 OP2 C:U60 4.7 18.1 1.0 O2' C:U59 4.8 18.2 1.0 C3' C:U59 4.9 16.7 1.0

Calcium binding site 8 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca80 b:57.9 occ:1.00 OP2 C:U12 2.4 31.5 1.0 P C:U12 3.6 28.1 1.0 O3' C:C11 4.1 19.1 1.0 OP1 C:U12 4.2 34.3 1.0 OP2 C:U8 4.3 16.0 1.0 O5' C:C11 4.3 25.9 1.0 C3' C:C11 4.3 19.1 1.0 OP2 C:C11 4.3 23.3 1.0 OP1 C:A9 4.4 17.4 1.0 C5 C:U12 4.6 16.4 1.0 OP1 C:U8 4.6 12.2 1.0 P C:C11 4.7 29.9 1.0 OP2 C:A9 4.7 15.9 1.0 OP1 C:C11 4.9 29.9 1.0 O5' C:U12 4.9 24.3 1.0 P C:U8 5.0 14.3 1.0

Calcium binding site 9 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca81 b:54.3 occ:1.00 O6 C:G27 2.7 26.7 1.0 N7 C:G27 2.9 13.7 1.0 C6 C:G27 3.4 22.3 1.0 C5 C:G27 3.5 19.7 1.0 OP2 C:A26 4.0 21.3 1.0 C8 C:G27 4.1 18.6 1.0 N7 C:A26 4.2 20.7 1.0 C8 C:A26 4.6 24.1 1.0 O6 C:G28 4.6 24.6 1.0 N1 C:G27 4.7 21.4 1.0 OP2 C:G27 4.7 16.3 1.0 C4 C:G27 4.8 21.2 1.0 N7 C:G28 4.8 28.1 1.0

Calcium binding site 10 out of 22 in the Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Structure of E. Coli Isopentenyl-Trna Transferase in Complex with E. Coli Trna(Phe) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca82 b:81.6 occ:1.00 OP2 C:G10 3.8 26.4 1.0 OP1 C:A9 4.3 17.4 1.0 OP1 C:U47 4.3 23.1 1.0 OP2 C:C11 4.5 23.3 1.0 OP1 C:C11 4.9 29.9 1.0

E.Seif, B.M.Hallberg. Rna-Protein Mutually Induced Fit: Structure of Escherichia Coli Isopentenyl-Trna Transferase in Complex with Trna(Phe). J.Biol.Chem. V. 284 6600 2009.
ISSN: ISSN 0021-9258
PubMed: 19158097
DOI: 10.1074/JBC.C800235200