Magnesium in PDB 1xnr: Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center

The structure of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center, PDB code: 1xnr was solved by F.V.Murphy, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 3.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.122, 401.122, 175.899, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.3

The structure of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

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 - 108;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center (pdb code 1xnr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 108 binding sites of Magnesium where determined in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center, PDB code: 1xnr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:65.5 occ:1.00 OP1 A:G944 2.3 56.0 1.0 OP2 A:G945 2.4 55.7 1.0 P A:G944 3.2 41.9 1.0 OP2 A:G944 3.4 56.0 1.0 P A:G945 3.7 42.6 1.0 O5' A:G944 3.9 41.9 1.0 OP1 A:G945 4.1 55.7 1.0 N7 A:A946 4.2 44.7 1.0 C5' A:G944 4.3 41.9 1.0 O5' A:G945 4.4 42.6 1.0 O6 A:G947 4.5 56.0 1.0 O3' A:U943 4.6 44.5 1.0 OP2 A:A946 4.6 44.7 1.0 O6 A:G1233 4.6 68.1 1.0 C8 A:A946 4.8 44.7 1.0 O3' A:G944 4.8 41.9 1.0

Magnesium binding site 2 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1547 b:65.5 occ:1.00 OP1 A:G1224 1.7 88.0 1.0 P A:G1224 2.9 69.0 1.0 OP2 A:G1224 3.3 88.0 1.0 O2' A:C1223 3.5 54.8 1.0 O5' A:G1224 3.9 69.0 1.0 C2' A:C1223 3.9 54.8 1.0 O3' A:C1223 3.9 54.8 1.0 N6 A:A977 4.4 0.0 1.0 C3' A:C1223 4.4 54.8 1.0 N7 A:A977 4.5 0.0 1.0 OP2 A:U952 4.5 61.2 1.0 OP1 A:G951 4.5 61.3 1.0

Magnesium binding site 3 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:65.5 occ:1.00 O4 A:U14 2.9 53.0 1.0 OP2 A:U17 3.0 38.6 1.0 OP1 A:U17 3.8 38.6 1.0 P A:U17 3.9 35.2 1.0 C4 A:U14 3.9 53.0 1.0 N3 A:U14 4.2 53.0 1.0 O3' A:A16 4.9 45.2 1.0

Magnesium binding site 4 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1549 b:65.5 occ:1.00 O6 A:G377 3.7 64.8 1.0 N7 A:G376 4.1 67.9 1.0 N7 A:G377 4.2 64.8 1.0 O6 A:G376 4.2 67.9 1.0 C6 A:G377 4.5 64.8 1.0 C5 A:G376 4.6 67.9 1.0 C6 A:G376 4.7 67.9 1.0 C5 A:G377 4.8 64.8 1.0 C8 A:G376 4.9 67.9 1.0

Magnesium binding site 5 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1550 b:65.5 occ:1.00 OP2 A:C749 2.2 81.3 1.0 OP2 A:G750 2.3 51.6 1.0 O5' A:C749 3.3 65.8 1.0 P A:C749 3.3 65.8 1.0 P A:G750 3.7 71.6 1.0 O3' A:C748 4.3 94.8 1.0 O2' A:C748 4.4 94.8 1.0 OP1 A:C749 4.4 81.3 1.0 C3' A:C749 4.4 65.8 1.0 OP1 A:G750 4.6 51.6 1.0 O5' A:G750 4.6 71.6 1.0 O3' A:C749 4.6 65.8 1.0 C5' A:C749 4.6 65.8 1.0 N7 A:G750 4.8 51.6 1.0 C8 A:G750 5.0 51.6 1.0

Magnesium binding site 6 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1551 b:65.5 occ:1.00 OP2 A:A766 2.1 21.1 1.0 P A:A766 3.6 37.0 1.0 O2 A:C812 3.8 37.2 1.0 N4 A:C811 4.0 30.5 1.0 N3 A:C811 4.1 30.5 1.0 O4 A:U813 4.1 31.8 1.0 O5' A:A766 4.2 37.0 1.0 O3' A:G765 4.2 36.5 1.0 N3 A:C812 4.3 37.2 1.0 C3' A:G765 4.4 36.5 1.0 C2 A:C812 4.4 37.2 1.0 C4 A:C811 4.5 30.5 1.0 OP1 A:A766 4.7 21.1 1.0 N7 A:A767 4.7 39.3 1.0 C4 A:U813 4.9 31.8 1.0 N6 A:A768 4.9 35.1 1.0 C2' A:G765 4.9 36.5 1.0 N6 A:A767 5.0 39.3 1.0

Magnesium binding site 7 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1552 b:65.5 occ:1.00 OP2 A:A768 2.3 35.1 1.0 P A:A768 3.7 29.8 1.0 O5' A:A768 4.2 29.8 1.0 N7 A:A768 4.3 35.1 1.0 OP1 A:U804 4.3 50.1 1.0 OP2 A:A767 4.4 39.3 1.0 O5' A:A767 4.5 43.2 1.0 C8 A:A768 4.5 35.1 1.0 N7 A:G769 4.5 24.0 1.0 C3' A:A767 4.6 43.2 1.0 O3' A:A767 4.6 43.2 1.0 OP2 A:C805 4.7 40.4 1.0 P A:A767 4.7 43.2 1.0 OP1 A:A767 4.7 39.3 1.0 OP1 A:A768 4.8 35.1 1.0 C5' A:U804 4.9 36.8 1.0

Magnesium binding site 8 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1553 b:65.5 occ:1.00 O4 A:U772 3.8 49.5 1.0 N7 A:G771 3.9 37.1 1.0 O6 A:G771 4.1 37.1 1.0 OP1 A:G803 4.4 53.4 1.0 C5 A:G771 4.6 37.1 1.0 C5 A:C770 4.7 42.1 1.0 C6 A:G771 4.7 37.1 1.0 C4 A:U772 4.7 49.5 1.0 N4 A:C770 4.8 42.1 1.0 C4 A:C770 4.8 42.1 1.0 C8 A:G771 4.9 37.1 1.0 OP2 A:U804 5.0 50.1 1.0

Magnesium binding site 9 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1554 b:65.5 occ:1.00 OP2 A:A780 3.5 56.8 1.0 OP2 A:C779 3.6 46.7 1.0 O6 A:G800 4.0 41.8 1.0 N7 A:G800 4.0 41.8 1.0 P A:C779 4.2 33.9 1.0 O5' A:C779 4.3 33.9 1.0 OP1 A:C779 4.3 46.7 1.0 N7 A:A780 4.4 56.8 1.0 C6 A:G800 4.7 41.8 1.0 C5 A:G800 4.8 41.8 1.0 OP2 A:G799 4.8 49.5 1.0 C8 A:A780 4.8 56.8 1.0 P A:A780 4.9 30.7 1.0 OP2 A:G800 4.9 41.8 1.0

Magnesium binding site 10 out of 108 in the Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Crystal Structure of An Inosine-Cytosine Wobble Base Pair in the Context of the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1555 b:65.5 occ:1.00 OP1 A:C578 2.4 27.9 1.0 OP2 A:G576 3.2 42.9 1.0 P A:C578 3.7 37.0 1.0 O3' A:G577 3.8 41.2 1.0 OP2 A:C817 4.0 24.7 1.0 O2' A:G575 4.1 43.2 1.0 OP1 A:U820 4.2 42.3 1.0 C5' A:G821 4.5 38.2 1.0 OP2 A:C578 4.6 27.9 1.0 P A:G576 4.6 29.1 1.0 C4' A:G821 4.7 38.2 1.0 O5' A:C578 4.8 37.0 1.0 C5' A:C578 4.8 37.0 1.0

F.V.Murphy, V.Ramakrishnan. Structure of A Purine-Purine Wobble Base Pair in the Decoding Center of the Ribosome. Nat.Struct.Mol.Biol. V. 11 1251 2004.
ISSN: ISSN 1545-9993
PubMed: 15558050
DOI: 10.1038/NSMB866