Magnesium in PDB 5aka: Em Structure of Ribosome-Srp-Ftsy Complex in Closed State

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 100; Page 11, Binding sites: 101 - 110;

Binding sites:

The binding sites of Magnesium atom in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State (pdb code 5aka). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 110 binding sites of Magnesium where determined in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State, PDB code: 5aka:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2905 b:10.4 occ:1.00 OP1 B:A802 1.8 23.9 1.0 O B:HOH3103 2.1 10.4 1.0 O B:HOH3105 2.1 10.4 1.0 O B:HOH3104 2.1 10.4 1.0 O B:HOH3101 2.1 10.4 1.0 O B:HOH3102 2.1 10.4 1.0 P B:A802 3.1 23.9 1.0 OP2 B:A802 3.7 23.9 1.0 O3' B:G801 3.9 23.7 1.0 O4 B:U803 4.1 16.1 1.0 OP2 B:G674 4.2 28.4 1.0 O5' B:A802 4.2 23.9 1.0 OP2 B:A675 4.3 12.7 1.0 N6 B:A804 4.4 27.8 1.0 C5 B:U803 4.8 16.1 1.0 C4 B:U803 4.8 16.1 1.0 C4' B:G801 4.8 23.7 1.0 C3' B:G801 5.0 23.7 1.0

Magnesium binding site 2 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2906 b:10.8 occ:1.00 O B:HOH3108 2.1 10.8 1.0 O B:HOH3106 2.1 10.8 1.0 O B:HOH3111 2.1 10.8 1.0 O B:HOH3110 2.1 10.8 1.0 O B:HOH3107 2.1 10.8 1.0 O B:HOH3109 2.1 10.8 1.0 O4 B:U2243 4.0 19.1 1.0 O4 B:U2075 4.0 20.6 1.0 N7 B:G2238 4.1 15.6 1.0 C8 B:G2238 4.2 15.6 1.0 O4 B:U2074 4.3 22.8 1.0 N6 B:A2077 4.6 7.4 1.0 O6 B:G2242 4.7 14.3 1.0 C5 B:U2074 4.7 22.8 1.0 C4 B:U2074 4.8 22.8 1.0

Magnesium binding site 3 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2907 b:13.8 occ:1.00 O E:HOH301 2.1 13.8 1.0 O E:HOH303 2.1 13.8 1.0 O E:HOH304 2.1 13.8 1.0 O B:HOH3113 2.1 13.8 1.0 O E:HOH302 2.1 13.8 1.0 O B:HOH3112 2.1 13.8 1.0 NH1 E:ARG67 4.3 0.7 1.0 O6 B:G1259 4.4 30.5 1.0 O4 B:U580 4.7 50.6 1.0 O4 B:U1258 4.8 63.9 1.0 N6 B:A1260 4.9 60.6 1.0

Magnesium binding site 4 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2908 b:21.9 occ:1.00 O B:HOH3114 2.1 21.9 1.0 O B:HOH3117 2.1 21.9 1.0 O B:HOH3119 2.1 21.9 1.0 O B:HOH3116 2.1 21.9 1.0 O B:HOH3118 2.1 21.9 1.0 O B:HOH3115 2.1 21.9 1.0 OP1 B:C560 3.6 30.1 1.0 OP1 B:A1008 3.8 63.3 1.0 OP1 B:G559 4.2 38.0 1.0 P B:C560 4.4 30.1 1.0 OP2 B:C560 4.6 30.1 1.0 O3' B:G559 4.7 38.0 1.0 OP1 B:G2038 5.0 36.0 1.0

Magnesium binding site 5 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2909 b:5.0 occ:1.00 OP1 B:A2589 1.6 35.9 1.0 O C:HOH301 2.1 5.0 1.0 O B:HOH3120 2.1 5.0 1.0 O B:HOH3121 2.1 5.0 1.0 OP2 B:A783 2.4 9.8 1.0 OP2 B:G784 2.6 20.0 1.0 P B:A2589 3.1 35.9 1.0 P B:A783 3.5 9.8 1.0 O5' B:A783 3.5 9.8 1.0 P B:G784 3.5 20.0 1.0 O3' B:G2588 3.7 5.0 1.0 O5' B:A2589 3.9 35.9 1.0 OP1 B:G784 3.9 20.0 1.0 O3' B:A783 3.9 9.8 1.0 C5' B:A2589 3.9 35.9 1.0 O C:ALA223 4.1 25.5 1.0 O3' B:A782 4.1 16.7 1.0 O B:HOH3146 4.1 7.2 1.0 OP2 B:A2589 4.2 35.9 1.0 CB C:MET224 4.4 0.8 1.0 C3' B:A783 4.5 9.8 1.0 C5' B:A783 4.5 9.8 1.0 OP1 B:A783 4.8 9.8 1.0 O5' B:G784 5.0 20.0 1.0

Magnesium binding site 6 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2910 b:10.4 occ:1.00 O B:HOH3123 2.1 10.4 1.0 O B:HOH3124 2.1 10.4 1.0 O B:HOH3126 2.1 10.4 1.0 O B:HOH3125 2.1 10.4 1.0 O B:HOH3122 2.1 10.4 1.0 OP2 B:G2588 2.2 5.0 1.0 P B:G2588 3.4 5.0 1.0 OP1 B:G2588 3.8 5.0 1.0 OP2 B:A2589 4.1 35.9 1.0 O5' B:G2588 4.2 5.0 1.0 OP1 B:A2587 4.2 22.2 1.0 N7 B:A2589 4.3 24.0 1.0 N7 B:G2588 4.5 30.4 1.0 O3' B:A2587 4.6 22.2 1.0 C8 B:G2588 4.7 30.4 1.0 O B:HOH3149 4.7 7.2 1.0 O5' B:A2587 4.8 22.2 1.0 C8 B:A2589 4.9 24.0 1.0

Magnesium binding site 7 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2911 b:28.9 occ:1.00 O B:HOH3131 2.1 28.9 1.0 O B:HOH3130 2.1 28.9 1.0 O B:HOH3127 2.1 28.9 1.0 O B:HOH3129 2.1 28.9 1.0 O B:HOH3128 2.1 28.9 1.0 OP2 B:U1647 2.2 37.0 1.0 P B:U1647 3.4 37.0 1.0 O3' B:C1646 3.5 42.0 1.0 O2' B:A1616 3.9 60.1 1.0 O5' B:U1647 4.1 37.0 1.0 O2' B:C1646 4.3 42.0 1.0 O B:HOH3287 4.6 21.6 1.0 N3 B:A1616 4.6 65.6 1.0 OP1 B:U1647 4.7 37.0 1.0 OP1 B:U1325 4.7 44.5 1.0 C3' B:C1646 4.8 42.0 1.0 O3' B:A1616 4.8 60.1 1.0 OP2 B:A1272 4.9 37.5 1.0

Magnesium binding site 8 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2912 b:58.0 occ:1.00 O B:HOH3135 2.1 58.0 1.0 O B:HOH3136 2.1 58.0 1.0 O B:HOH3133 2.1 58.0 1.0 O B:HOH3132 2.1 58.0 1.0 O B:HOH3134 2.1 58.0 1.0 OP2 B:A2518 2.2 50.2 1.0 P B:A2518 3.3 50.2 1.0 O5' B:A2518 3.6 50.2 1.0 OP2 B:A2541 3.7 10.0 1.0 N7 B:A2541 3.9 31.2 1.0 OP1 B:A2518 3.9 50.2 1.0 OP2 B:C2540 4.0 26.9 1.0 OP2 B:U2519 4.2 41.5 1.0 O2' B:C2517 4.4 35.0 1.0 C8 B:A2541 4.5 31.2 1.0 O3' B:C2517 4.6 35.0 1.0 O5' B:C2540 4.7 26.9 1.0 P B:C2540 4.9 26.9 1.0 C5' B:A2518 5.0 50.2 1.0

Magnesium binding site 9 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2913 b:35.6 occ:1.00 O B:HOH3138 2.1 35.6 1.0 O B:HOH3141 2.1 35.6 1.0 O B:HOH3137 2.1 35.6 1.0 O B:HOH3139 2.1 35.6 1.0 O B:HOH3140 2.1 35.6 1.0 OP1 B:G338 2.2 60.2 1.0 P B:G338 3.3 60.2 1.0 OP2 B:U296 3.5 43.0 1.0 O5' B:G338 3.7 60.2 1.0 O6 B:G298 3.8 60.0 1.0 OP2 B:G338 3.9 60.2 1.0 OP2 B:G297 4.0 54.9 1.0 C5' B:G338 4.3 60.2 1.0 O3' B:C337 4.7 54.4 1.0 P B:U296 4.9 43.0 1.0 C6 B:G298 4.9 60.0 1.0

Magnesium binding site 10 out of 110 in the Em Structure of Ribosome-Srp-Ftsy Complex in Closed State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Em Structure of Ribosome-Srp-Ftsy Complex in Closed State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg2914 b:39.4 occ:1.00 OP2 B:C1153 1.9 29.2 1.0 O B:HOH3142 2.1 39.4 1.0 O B:HOH3144 2.1 39.4 1.0 O B:HOH3145 2.1 39.4 1.0 O B:HOH3143 2.1 39.4 1.0 OP2 B:U999 2.8 33.5 1.0 P B:C1153 3.1 29.2 1.0 OP1 B:C1153 3.7 29.2 1.0 O3' B:C1152 3.8 44.8 1.0 P B:U999 3.9 33.5 1.0 C3' B:C1152 3.9 44.8 1.0 OP1 B:U999 4.2 33.5 1.0 O5' B:C1152 4.2 44.8 1.0 O5' B:C1153 4.3 29.2 1.0 OP1 B:C1152 4.4 44.8 1.0 OP1 B:C998 4.4 63.9 1.0 OP2 B:C1152 4.4 44.8 1.0 P B:C1152 4.5 44.8 1.0 C5' B:C1152 4.5 44.8 1.0 O3' B:C998 4.6 63.9 1.0 O6 B:G1154 4.8 68.8 1.0 C4' B:C1152 4.8 44.8 1.0 O5' B:C998 5.0 63.9 1.0

O.Von Loeffelholz, Q.Jiang, A.Ariosa, M.Karuppasamy, K.Huard, I.Berger, S.Shan, C.Schaffitzel. Ribosome-Srp-Ftsy Cotranslational Targeting Complex in the Closed State. Proc.Natl.Acad.Sci.Usa 2015.
ISSN: ESSN 1091-6490
PubMed: 25775537
DOI: 10.1073/PNAS.1424453112