Magnesium in PDB 4mgm: Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly

The structure of Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly, PDB code: 4mgm was solved by J.C.Grigg, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.17 / 3.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	161.233, 28.409, 132.939, 90.00, 110.69, 90.00
R / Rfree (%)	24.8 / 26.1

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly (pdb code 4mgm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly, PDB code: 4mgm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:61.5 occ:1.00 OP1 A:G58 2.3 66.3 1.0 O4 A:U59 2.6 71.2 1.0 N2 A:G58 2.8 81.8 1.0 OP1 A:U19 3.6 99.1 1.0 C2 A:G58 3.6 91.5 1.0 P A:G58 3.8 64.7 1.0 C4 A:U59 3.8 75.8 1.0 C4' A:A57 3.9 56.8 1.0 N1 A:G58 4.0 90.6 1.0 C5' A:A57 4.2 55.2 1.0 C5 A:U59 4.4 71.4 1.0 C4' A:G18 4.5 79.1 1.0 O3' A:A57 4.5 56.1 1.0 N3 A:G58 4.6 88.0 1.0 OP2 A:G58 4.6 50.6 1.0 O5' A:G58 4.7 73.2 1.0 C3' A:A57 4.7 50.9 1.0 O4' A:G18 4.8 70.2 1.0 N3 A:U59 4.9 78.0 1.0 O4' A:A57 4.9 54.9 1.0 P A:U19 4.9 1.0 1.0

Magnesium binding site 2 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:79.5 occ:1.00 OP1 A:G7 3.1 62.7 1.0 OP2 A:A14 3.1 0.0 1.0 O4 A:U8 3.7 0.3 1.0 N7 A:G15 4.3 0.3 1.0 C5' A:A14 4.3 0.1 1.0 P A:A14 4.4 0.5 1.0 C4 A:U8 4.4 0.5 1.0 P A:G7 4.4 74.9 1.0 O3' A:A6 4.7 67.7 1.0 OP2 A:G15 4.8 0.1 1.0 C5 A:U8 4.8 91.5 1.0 O5' A:A14 4.9 1.0 1.0 C8 A:G15 4.9 1.0 1.0 OP1 A:A14 4.9 0.1 1.0

Magnesium binding site 3 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:48.2 occ:1.00 O6 A:G52 3.0 37.7 1.0 N7 A:G52 3.4 37.7 1.0 O6 A:G51 3.6 36.6 1.0 N7 A:G51 3.8 38.7 1.0 C6 A:G52 3.8 36.2 1.0 C5 A:G52 3.9 34.4 1.0 C6 A:G51 4.0 35.9 1.0 C5 A:G51 4.1 38.5 1.0 O4 A:U53 4.4 33.8 1.0 C8 A:G52 4.6 42.3 1.0 C8 A:G51 4.7 35.9 1.0 O2' A:A57 4.8 59.7 1.0 N4 A:C60 4.9 34.7 1.0

Magnesium binding site 4 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg104 b:27.3 occ:1.00 O4 A:U64 2.8 43.4 1.0 O6 A:G48 3.2 32.1 1.0 O6 A:G63 3.4 38.1 1.0 O6 A:G7 3.4 31.0 1.0 C4 A:U64 3.9 36.6 1.0 N4 A:C49 4.1 37.1 1.0 C6 A:G7 4.3 34.2 1.0 C6 A:G48 4.3 31.9 1.0 N3 A:U64 4.3 35.8 1.0 C6 A:G63 4.4 33.4 1.0 N4 A:C65 4.7 38.5 1.0 N7 A:G48 4.8 33.7 1.0 C5 A:G48 5.0 31.1 1.0 C5 A:G7 5.0 30.9 1.0

Magnesium binding site 5 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg105 b:80.9 occ:1.00 OP2 A:U12 3.0 0.1 1.0 OP2 A:A9 3.2 97.5 1.0 OP2 A:U8 3.6 81.0 1.0 OP2 A:U11 3.7 0.9 1.0 OP1 A:A9 3.9 93.0 1.0 P A:A9 4.0 0.6 1.0 OP1 A:U8 4.1 76.5 1.0 C5 A:U12 4.2 0.7 1.0 O5' A:U11 4.3 0.3 1.0 P A:U8 4.3 78.5 1.0 P A:U11 4.4 0.4 1.0 P A:U12 4.5 0.2 1.0 OP1 A:U11 4.7 0.6 1.0 C6 A:U12 4.9 0.0 1.0 O5' A:A9 4.9 0.0 1.0

Magnesium binding site 6 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:54.3 occ:1.00 O2' B:G52 2.5 50.0 1.0 O4' B:U53 2.6 61.4 1.0 C2' B:G52 3.1 49.1 1.0 N3 B:G52 3.2 40.6 1.0 C4' B:U53 3.5 52.8 1.0 C1' B:U53 3.6 54.1 1.0 C1' B:G52 3.7 49.1 1.0 C5' B:U53 3.9 49.1 1.0 N2 B:G52 4.0 38.2 1.0 C2 B:G52 4.0 41.1 1.0 C4 B:G52 4.2 40.0 1.0 N1 B:U53 4.3 54.8 1.0 N9 B:G52 4.4 43.9 1.0 O2 B:C61 4.5 35.3 1.0 C3' B:G52 4.5 55.2 1.0 C6 B:U53 4.6 51.1 1.0 C2' B:U53 4.8 48.9 1.0 O5' B:U53 4.8 51.4 1.0 C3' B:U53 4.8 51.7 1.0 O3' B:G52 4.9 61.0 1.0 O4' B:G52 4.9 57.5 1.0 O2' B:U53 5.0 55.1 1.0

Magnesium binding site 7 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:40.2 occ:1.00 N3 B:G70 2.6 44.6 1.0 O2' B:G70 2.7 53.2 1.0 O4' B:C71 2.9 65.2 1.0 C2' B:G70 3.1 57.0 1.0 N2 B:G70 3.3 43.5 1.0 C2 B:G70 3.4 46.0 1.0 C1' B:G70 3.5 52.8 1.0 C1' B:C71 3.5 60.7 1.0 C4 B:G70 3.7 48.4 1.0 N1 B:C71 4.0 52.9 1.0 N9 B:G70 4.0 54.1 1.0 C4' B:C71 4.2 60.6 1.0 C6 B:C71 4.2 50.1 1.0 C3' B:G70 4.6 57.6 1.0 C5' B:C71 4.7 53.5 1.0 N2 B:G3 4.7 47.9 1.0 N1 B:G70 4.7 48.8 1.0 O4' B:G70 4.8 59.1 1.0 C2 B:C71 4.8 50.6 1.0 N3 B:G3 4.9 49.6 1.0 C2' B:C71 4.9 67.8 1.0 O5' B:C71 4.9 54.0 1.0 C5 B:G70 5.0 47.2 1.0

Magnesium binding site 8 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:51.7 occ:1.00 OP1 B:G58 2.9 59.1 1.0 O4 B:U59 3.2 67.2 1.0 OP1 B:U19 3.6 86.6 1.0 O5' B:U19 3.8 99.8 1.0 N7 B:G58 3.9 86.7 1.0 C4 B:U59 4.2 76.5 1.0 P B:G58 4.3 60.4 1.0 C8 B:G58 4.4 83.7 1.0 P B:U19 4.4 81.0 1.0 OP2 B:A20 4.6 0.4 1.0 O5' B:G58 4.7 68.3 1.0 C5' B:U19 4.9 0.0 1.0 C3' B:U19 4.9 0.3 1.0 C5 B:U59 5.0 73.2 1.0

Magnesium binding site 9 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:87.4 occ:1.00 OP2 B:U16 2.2 0.9 1.0 O6 B:G58 2.3 84.1 1.0 P B:U16 3.5 0.8 1.0 C6 B:G58 3.5 88.3 1.0 OP1 B:U19 3.9 86.6 1.0 C5' B:G18 4.1 72.2 1.0 OP1 B:U16 4.1 0.9 1.0 OP1 B:G18 4.1 83.2 1.0 N1 B:G58 4.4 92.0 1.0 O5' B:U16 4.4 0.8 1.0 O4 A:U16 4.5 0.7 1.0 O3' B:G15 4.5 96.2 1.0 C5 B:G58 4.5 85.9 1.0 N3 B:U59 4.6 79.5 1.0 O2' B:G15 4.7 0.9 1.0 O5' B:G18 4.8 71.6 1.0 N7 B:G58 4.8 86.7 1.0 C4' B:G18 4.9 77.1 1.0 C2' B:G15 5.0 96.8 1.0

Magnesium binding site 10 out of 14 in the Crystal Structure of the in Vitro Transcribed G. Kaustophilus Trna-Gly


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 the in Vitro Transcribed G. Kaustophilus Trna-Gly within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:69.6 occ:1.00 O2' B:U54 2.7 61.2 1.0 O6 B:G56 2.9 50.3 1.0 N4 B:C55 3.4 37.2 1.0 N7 B:G56 3.8 44.2 1.0 C6 B:G56 3.8 44.9 1.0 C5 B:C55 3.8 40.4 1.0 C4 B:C55 4.0 38.6 1.0 C2' B:U54 4.1 64.3 1.0 C5 B:G56 4.1 39.5 1.0 O3' B:U54 4.7 62.0 1.0 O6 B:G17 4.8 50.6 1.0 C1' B:U54 4.8 58.4 1.0 C3' B:U54 4.9 65.6 1.0 C6 B:C55 5.0 42.1 1.0 C8 B:G56 5.0 45.0 1.0

J.C.Grigg, A.Ke. Structural Determinants For Geometry and Information Decoding of Trna By T Box Leader Rna. Structure V. 21 2025 2013.
ISSN: ISSN 0969-2126
PubMed: 24095061
DOI: 10.1016/J.STR.2013.09.001