Calcium in PDB 6y3g: Crystal Structure of Phenylalanine Trna From Escherichia Coli

The structure of Crystal Structure of Phenylalanine Trna From Escherichia Coli, PDB code: 6y3g was solved by G.Bourgeois, Y.Mechulam, E.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.98 / 3.10
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	109.618, 109.618, 138.518, 90, 90, 120
R / Rfree (%)	21.5 / 23.6

The binding sites of Calcium atom in the Crystal Structure of Phenylalanine Trna From Escherichia Coli (pdb code 6y3g). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Phenylalanine Trna From Escherichia Coli, PDB code: 6y3g:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca105 b:103.1 occ:1.00 OP1 F:U50 2.4 99.0 1.0 OP1 F:C48 2.5 73.6 1.0 OP2 F:3AU47 2.8 92.6 1.0 O5' F:3AU47 3.2 176.5 1.0 P F:3AU47 3.6 89.7 1.0 P F:U50 3.8 108.5 1.0 P F:C48 3.9 115.1 1.0 C5' F:C48 4.2 69.4 1.0 O5' F:U50 4.3 117.2 1.0 O3' F:3AU47 4.3 88.0 1.0 C3' F:3AU47 4.5 111.4 1.0 C5' F:3AU47 4.5 154.4 1.0 O3' F:G46 4.5 74.3 1.0 O5' F:C48 4.6 87.4 1.0 OP2 F:U50 4.7 136.2 1.0 OP1 F:3AU47 4.8 113.2 1.0 O3' F:C49 4.8 94.5 1.0 C5' F:U50 4.9 74.7 1.0 OP2 F:U51 4.9 116.6 1.0

Calcium binding site 2 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca106 b:161.1 occ:1.00 OP1 F:A9 2.6 116.8 1.0 O F:HOH201 3.5 76.2 1.0 OP1 F:4SU8 3.5 126.3 1.0 OP2 F:C11 3.8 94.7 1.0 P F:A9 4.0 105.4 1.0 OP1 F:C11 4.6 103.1 1.0 OP2 F:A9 4.7 105.3 1.0 O3' F:4SU8 4.7 99.6 1.0 P F:C11 4.7 118.5 1.0 OP2 F:G10 4.9 98.5 1.0 P F:4SU8 5.0 119.2 1.0

Calcium binding site 3 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca107 b:120.2 occ:1.00 OP1 F:U59 2.3 104.3 1.0 OP2 F:A21 2.4 172.7 1.0 O3' F:H2U20 2.8 165.9 1.0 P F:A21 3.1 159.0 1.0 P F:U59 3.6 93.8 1.0 O3' F:A58 3.7 74.6 1.0 O5' F:A21 3.9 146.4 1.0 C4' F:A58 3.9 90.1 1.0 C3' F:A58 4.1 84.5 1.0 C3' F:H2U20 4.1 131.1 1.0 C5' F:A58 4.4 79.5 1.0 OP1 F:A21 4.5 113.8 1.0 C4' F:H2U20 4.6 97.1 1.0 O5' F:U59 4.6 74.4 1.0 OP2 F:U59 4.6 109.8 1.0 N4 F:C48 4.9 76.2 1.0 O4 F:U60 4.9 133.0 1.0 O2' F:3AU47 5.0 101.0 1.0

Calcium binding site 4 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca108 b:167.1 occ:1.00 N6 F:A64 4.3 117.2 1.0 OP2 F:G63 4.4 123.2 1.0 N7 F:A64 4.6 128.4 1.0

Calcium binding site 5 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca109 b:176.7 occ:1.00 OP2 F:U33 4.0 169.0 1.0 OP1 F:A35 4.2 121.2 1.0 C5 F:U33 4.7 173.8 1.0

Calcium binding site 6 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca110 b:147.9 occ:1.00 O2 F:PSU32 3.2 140.2 1.0 O3 F:GOL112 3.7 166.5 1.0 OP2 F:A31 4.0 121.6 1.0 N7 F:A31 4.1 119.2 1.0 C2 F:PSU32 4.2 135.7 1.0 N7 F:G30 4.3 118.3 1.0 C8 F:G30 4.5 120.0 1.0 C8 F:A31 4.9 118.6 1.0 N1 F:PSU32 4.9 146.1 1.0 C5 F:G30 4.9 105.9 1.0 C3 F:GOL112 5.0 166.1 1.0 OP2 F:G30 5.0 99.9 1.0

Calcium binding site 7 out of 7 in the Crystal Structure of Phenylalanine Trna From Escherichia Coli


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Phenylalanine Trna From Escherichia Coli within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca111 b:165.9 occ:1.00 O6 F:G6 3.5 125.9 1.0 O6 F:G5 3.9 164.4 1.0 N7 F:G5 4.2 153.9 1.0 N7 F:G6 4.4 125.9 1.0 C6 F:G6 4.5 130.7 1.0 C6 F:G5 4.5 164.6 1.0 C5 F:G5 4.6 165.2 1.0 N4 F:C67 4.8 122.3 1.0 C5 F:G6 4.9 129.6 1.0 N6 F:A7 5.0 146.9 1.0

G.Bourgeois, J.Seguin, M.Babin, M.Gondry, Y.Mechulam, E.Schmitt. Structural Basis of the Interaction Between Cyclodipeptide Synthases and Aminoacylated Trna Substrates. Rna V. 26 1589 2020.
ISSN: ESSN 1469-9001
PubMed: 32680846
DOI: 10.1261/RNA.075184.120