Magnesium in PDB 3bwp: Crystal Structure of A Self-Spliced Group II Intron

The structure of Crystal Structure of A Self-Spliced Group II Intron, PDB code: 3bwp was solved by N.Toor, K.S.Keating, S.D.Taylor, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.854, 94.958, 225.910, 90.00, 90.00, 90.00
R / Rfree (%)	27.6 / 31

The structure of Crystal Structure of A Self-Spliced Group II Intron also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of A Self-Spliced Group II Intron (pdb code 3bwp). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Crystal Structure of A Self-Spliced Group II Intron, PDB code: 3bwp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:59.1 occ:1.00 OP1 A:U375 2.2 50.6 1.0 OP2 A:C377 2.5 55.7 1.0 P A:C377 3.5 54.9 1.0 P A:U375 3.6 50.5 1.0 OP1 A:C377 3.6 53.8 1.0 MG A:MG414 3.9 46.9 1.0 O3' A:G374 4.1 51.7 1.0 OP2 A:G359 4.4 64.6 1.0 OP2 A:U375 4.5 51.3 1.0 O3' A:A376 4.6 52.8 1.0 O5' A:U375 4.6 50.7 1.0 O5' A:C377 4.7 56.0 1.0 OP1 A:G359 4.8 63.4 1.0 C3' A:A376 4.8 51.4 1.0 C5' A:A376 4.9 49.0 1.0 C4' A:A376 4.9 50.4 1.0

Magnesium binding site 2 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:46.9 occ:1.00 OP2 A:G359 2.2 64.6 1.0 OP1 A:C377 2.5 53.8 1.0 OP1 A:C358 2.5 71.7 1.0 O5' A:C358 3.5 68.8 1.0 P A:G359 3.6 62.0 1.0 P A:C358 3.6 69.7 1.0 C5' A:C358 3.7 67.1 1.0 P A:C377 3.8 54.9 1.0 MG A:MG413 3.9 59.1 1.0 O3' A:C358 4.1 64.2 1.0 OP1 A:G359 4.3 63.4 1.0 OP2 A:C377 4.3 55.7 1.0 O3' A:C357 4.6 70.4 1.0 O5' A:G359 4.6 62.8 1.0 C4' A:C358 4.7 66.6 1.0 O5' A:C377 4.7 56.0 1.0 OP2 A:C358 4.7 70.2 1.0 C3' A:C358 4.7 65.9 1.0 O3' A:A376 4.9 52.8 1.0

Magnesium binding site 3 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:37.0 occ:1.00 OP1 A:G107 2.5 43.0 1.0 P A:G107 3.9 43.3 1.0 O3' A:A106 4.2 43.3 1.0 OP1 A:G108 4.4 43.3 1.0 OP2 A:A105 4.5 54.2 1.0 N7 A:A105 4.5 53.4 1.0 C5' A:G107 4.6 44.9 1.0 O5' A:G107 4.6 42.5 1.0 C8 A:A105 4.7 52.8 1.0 OP2 A:A106 4.7 51.8 1.0 OP2 A:G107 5.0 42.2 1.0

Magnesium binding site 4 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:58.6 occ:1.00 OP1 A:G111 2.4 58.3 1.0 P A:G111 3.8 55.5 1.0 OP1 A:C112 3.9 60.5 1.0 C3' A:A110 4.1 54.1 1.0 O5' A:G111 4.3 56.6 1.0 O3' A:A110 4.3 54.1 1.0 O2' A:U13 4.5 77.9 1.0 O3' A:U13 4.6 76.7 1.0 O2 A:U13 4.6 79.4 1.0 OP2 A:C112 4.7 59.7 1.0 OP1 A:G14 4.8 74.7 1.0 P A:C112 4.8 61.1 1.0 C5' A:G14 4.9 72.0 1.0 C5' A:A110 4.9 54.4 1.0 OP2 A:G111 4.9 52.4 1.0

Magnesium binding site 5 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:63.5 occ:1.00 OP2 A:C372 2.5 61.8 1.0 P A:C372 3.6 58.8 1.0 OP1 A:A371 4.0 60.8 1.0 O6 A:G373 4.0 53.4 1.0 OP1 A:C372 4.0 59.4 1.0 O5' A:A371 4.1 60.5 1.0 O3' A:A371 4.3 57.4 1.0 P A:A371 4.3 60.5 1.0 OP2 A:A371 4.4 62.4 1.0 N7 A:G373 4.5 55.1 1.0 C3' A:A371 4.5 58.2 1.0 C5' A:A371 4.8 60.1 1.0 O5' A:C372 4.9 56.8 1.0 C6 A:G373 4.9 53.5 1.0 C5 A:C372 5.0 53.0 1.0

Magnesium binding site 6 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg418 b:84.8 occ:1.00 O4 A:U363 4.2 72.4 1.0 N7 A:G362 4.3 75.5 1.0 OP1 A:G378 4.5 54.6 1.0 O4 A:U379 4.5 61.2 1.0 N4 A:C361 4.6 74.7 1.0 O6 A:G362 4.6 77.7 1.0 C4 A:C361 4.7 72.7 1.0

Magnesium binding site 7 out of 7 in the Crystal Structure of A Self-Spliced Group II Intron


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 A Self-Spliced Group II Intron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg419 b:81.7 occ:1.00 OP2 A:U96 4.1 44.9 1.0 OP1 A:A95 4.3 48.9 1.0 OP1 A:U96 4.4 45.1 1.0 OP1 A:G284 4.4 62.2 1.0 P A:U96 4.6 44.5 1.0

N.Toor, K.S.Keating, S.D.Taylor, A.M.Pyle. Crystal Structure of A Self-Spliced Group II Intron Science V. 320 77 2008.
ISSN: ISSN 0036-8075
PubMed: 18388288
DOI: 10.1126/SCIENCE.1153803