Magnesium in PDB 1xmo: Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center

The structure of Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center, PDB code: 1xmo was solved by F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, P.F.Agris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	99.00 / 3.25
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	400.811, 400.811, 176.125, 90.00, 90.00, 90.00
R / Rfree (%)	23.1 / 28.4

The structure of Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 - 107;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center (pdb code 1xmo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 107 binding sites of Magnesium where determined in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center, PDB code: 1xmo:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1546 b:23.7 occ:0.90 OP2 A:G945 2.4 63.8 1.0 OP1 A:G944 2.4 57.5 1.0 P A:G944 3.3 57.5 1.0 P A:G945 3.5 39.0 1.0 OP2 A:G944 3.5 57.5 1.0 OP1 A:G945 3.7 63.8 1.0 OP2 A:A946 3.9 37.2 1.0 O5' A:G944 4.0 57.5 1.0 N7 A:A946 4.1 37.2 1.0 O5' A:G945 4.3 39.0 1.0 O6 A:G947 4.6 59.7 1.0 C8 A:A946 4.6 37.2 1.0 C5' A:G944 4.6 57.5 1.0 O3' A:U943 4.7 42.5 1.0 O3' A:G944 4.7 57.5 1.0 O6 A:G1233 4.8 70.1 1.0

Magnesium binding site 2 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1547 b:23.7 occ:1.00 OP1 A:G1224 1.8 82.5 1.0 P A:G1224 3.0 72.0 1.0 OP2 A:G1224 3.4 82.5 1.0 O2' A:C1223 3.8 61.7 1.0 O5' A:G1224 4.0 72.0 1.0 O3' A:C1223 4.0 61.7 1.0 C2' A:C1223 4.2 61.7 1.0 N7 A:A977 4.3 0.2 1.0 OP1 A:G951 4.4 67.8 1.0 N6 A:A977 4.4 0.2 1.0 OP2 A:U952 4.6 58.8 1.0 C3' A:C1223 4.6 61.7 1.0

Magnesium binding site 3 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1548 b:23.7 occ:0.55 OP2 A:U17 2.9 45.2 1.0 O4 A:U14 3.4 59.6 1.0 OP1 A:U17 3.6 45.2 1.0 P A:U17 3.7 38.4 1.0 C4 A:U14 4.4 59.6 1.0 N3 A:U14 4.7 59.6 1.0 O5' A:U17 4.8 38.4 1.0 O3' A:A16 4.9 47.0 1.0

Magnesium binding site 4 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1549 b:23.7 occ:0.86 O6 A:G377 3.5 63.5 1.0 N7 A:G376 4.0 57.0 1.0 O6 A:G376 4.0 57.0 1.0 N7 A:G377 4.3 63.5 1.0 C6 A:G377 4.4 63.5 1.0 C5 A:G376 4.5 57.0 1.0 C6 A:G376 4.5 57.0 1.0 C5 A:G377 4.8 63.5 1.0 C8 A:G376 4.9 57.0 1.0

Magnesium binding site 5 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1550 b:23.7 occ:0.72 OP2 A:G750 2.1 63.9 1.0 OP2 A:C749 2.3 83.0 1.0 P A:C749 3.1 67.2 1.0 O5' A:C749 3.3 67.2 1.0 OP1 A:C749 3.5 83.0 1.0 P A:G750 3.6 66.3 1.0 C3' A:C749 4.3 67.2 1.0 OP1 A:G750 4.3 63.9 1.0 O3' A:C749 4.4 67.2 1.0 O5' A:G750 4.5 66.3 1.0 C5' A:C749 4.5 67.2 1.0 O3' A:C748 4.6 0.7 1.0 O2' A:C748 4.7 0.7 1.0 N7 A:G750 4.7 63.9 1.0 C2' A:C748 4.9 0.7 1.0 C8 A:G750 5.0 63.9 1.0

Magnesium binding site 6 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1551 b:23.7 occ:1.00 OP2 A:A766 2.0 28.1 1.0 N4 A:C811 3.4 37.0 1.0 P A:A766 3.5 43.1 1.0 O2 A:C812 3.9 37.5 1.0 N3 A:C811 3.9 37.0 1.0 C4 A:C811 4.1 37.0 1.0 N3 A:C812 4.2 37.5 1.0 O5' A:A766 4.3 43.1 1.0 O3' A:G765 4.3 37.6 1.0 C3' A:G765 4.4 37.6 1.0 C2 A:C812 4.4 37.5 1.0 OP1 A:A766 4.5 28.1 1.0 O4 A:U813 4.6 38.3 1.0 C2' A:G765 4.8 37.6 1.0 N7 A:A767 4.8 41.7 1.0 N6 A:A768 4.9 51.9 1.0

Magnesium binding site 7 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1552 b:23.7 occ:0.99 OP2 A:A768 2.2 51.9 1.0 P A:A768 3.6 34.2 1.0 O5' A:A768 4.2 34.2 1.0 O5' A:A767 4.2 51.1 1.0 OP1 A:U804 4.4 58.9 1.0 OP2 A:C805 4.5 49.9 1.0 N7 A:A768 4.5 51.9 1.0 OP1 A:A768 4.5 51.9 1.0 OP2 A:A767 4.6 41.7 1.0 O3' A:A767 4.6 51.1 1.0 OP1 A:A767 4.6 41.7 1.0 C3' A:A767 4.6 51.1 1.0 P A:A767 4.7 51.1 1.0 C8 A:A768 4.7 51.9 1.0 N7 A:G769 4.9 29.3 1.0 C5' A:U804 4.9 38.6 1.0

Magnesium binding site 8 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1553 b:23.7 occ:1.00 O6 A:G771 3.7 49.1 1.0 O4 A:U772 3.8 56.8 1.0 N7 A:G771 3.9 49.1 1.0 OP1 A:G803 4.4 47.9 1.0 C6 A:G771 4.4 49.1 1.0 C5 A:G771 4.5 49.1 1.0 C5 A:C770 4.5 41.6 1.0 N4 A:C770 4.6 41.6 1.0 C4 A:C770 4.7 41.6 1.0 C4 A:U772 4.8 56.8 1.0 C8 A:G771 5.0 49.1 1.0

Magnesium binding site 9 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1554 b:23.7 occ:0.81 OP2 A:A780 3.2 50.6 1.0 OP2 A:C779 3.6 53.4 1.0 OP1 A:C779 3.7 53.4 1.0 P A:C779 3.9 41.3 1.0 O5' A:C779 4.0 41.3 1.0 O6 A:G800 4.4 48.7 1.0 N7 A:A780 4.6 50.6 1.0 N7 A:G800 4.6 48.7 1.0 CE K:LYS122 4.7 55.7 1.0 NZ K:LYS122 4.7 55.7 1.0 P A:A780 4.7 31.9 1.0 C8 A:A780 4.8 50.6 1.0 C3' A:C779 4.9 41.3 1.0 OP2 A:G799 5.0 67.1 1.0

Magnesium binding site 10 out of 107 in the Crystal Structure of MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in 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 MNM5U34T6A37-Trnalysuuu Complexed with Aag-Mrna in the Decoding Center within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1555 b:23.7 occ:1.00 OP1 A:C578 2.4 35.8 1.0 OP2 A:G576 3.5 53.5 1.0 P A:C578 3.7 33.3 1.0 O3' A:G577 3.8 52.9 1.0 OP2 A:C817 3.8 35.1 1.0 OP1 A:U820 4.3 52.4 1.0 C5' A:C578 4.5 33.3 1.0 O2' A:G575 4.5 45.9 1.0 O5' A:C578 4.6 33.3 1.0 C5' A:G821 4.7 32.9 1.0 OP2 A:C578 4.8 35.8 1.0 C4' A:G821 4.9 32.9 1.0 P A:G576 4.9 46.3 1.0 P A:C817 5.0 44.7 1.0

F.V.Murphy, V.Ramakrishnan, A.Malkiewicz, P.F.Agris. The Role of Modifications in Codon Discrimination By Trna(Lys)(Uuu). Nat.Struct.Mol.Biol. V. 11 1186 2004.
ISSN: ISSN 1545-9993
PubMed: 15558052
DOI: 10.1038/NSMB861