Magnesium in PDB 3g78: Insight Into Group II Intron Catalysis From Revised Crystal Structure

The structure of Insight Into Group II Intron Catalysis From Revised Crystal Structure, PDB code: 3g78 was solved by J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.29 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.109, 94.970, 225.998, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.7

The structure of Insight Into Group II Intron Catalysis From Revised Crystal Structure also contains other interesting chemical elements:

Potassium

(K)

26 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 - 51;

Binding sites:

The binding sites of Magnesium atom in the Insight Into Group II Intron Catalysis From Revised Crystal Structure (pdb code 3g78). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 51 binding sites of Magnesium where determined in the Insight Into Group II Intron Catalysis From Revised Crystal Structure, PDB code: 3g78:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg10 b:10.3 occ:1.00 OP2 A:C377 1.8 2.0 1.0 OP1 A:U375 2.0 3.1 1.0 O A:HOH588 2.2 2.0 1.0 O3' Z:U6 2.3 41.1 1.0 OP1 Z:U7 2.9 41.7 1.0 P A:C377 3.1 2.0 1.0 P Z:U7 3.2 42.5 1.0 P A:U375 3.2 3.3 1.0 O2' Z:U6 3.3 37.7 1.0 C3' Z:U6 3.4 38.6 1.0 C4' Z:U6 3.7 37.3 1.0 OP1 A:C377 3.7 2.0 1.0 OP2 A:U375 3.7 3.8 1.0 MG Z:MG11 3.8 2.0 1.0 O5' A:C377 3.8 2.0 1.0 C2' Z:U6 3.9 37.8 1.0 O3' A:G374 3.9 4.2 1.0 OP1 A:G359 4.0 2.2 1.0 OP2 Z:U7 4.2 42.8 1.0 OP2 A:G359 4.3 2.8 1.0 O3' A:A376 4.3 2.0 1.0 O5' Z:U7 4.4 43.9 1.0 C5' A:C377 4.4 2.0 1.0 O5' A:U375 4.5 2.5 1.0 C5' Z:U7 4.6 45.8 1.0 C3' A:A376 4.6 2.0 1.0 C5' Z:U6 4.6 36.4 1.0 P A:G359 4.6 2.0 1.0 O4' Z:U6 4.7 36.6 1.0 C5' A:A376 4.7 2.0 1.0 C4' A:A376 4.8 2.0 1.0 C1' Z:U6 5.0 37.1 1.0

Magnesium binding site 2 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg11 b:2.0 occ:1.00 OP1 Z:U7 1.6 41.7 1.0 OP1 A:C358 2.1 4.4 1.0 OP1 A:C377 2.3 2.0 1.0 OP2 A:G359 2.4 2.8 1.0 P Z:U7 2.6 42.5 1.0 OP2 Z:U7 2.9 42.8 1.0 P A:C377 3.4 2.0 1.0 P A:C358 3.5 4.8 1.0 OP2 A:C377 3.7 2.0 1.0 O5' Z:U7 3.7 43.9 1.0 O3' Z:U6 3.8 41.1 1.0 P A:G359 3.8 2.0 1.0 MG Z:MG10 3.8 10.3 1.0 O A:HOH675 3.8 6.8 1.0 O A:HOH588 4.1 2.0 1.0 O5' A:C358 4.1 5.0 1.0 O Z:HOH790 4.2 25.1 1.0 C5' A:C358 4.2 4.3 1.0 O A:HOH487 4.3 2.0 1.0 C5' Z:U7 4.3 45.8 1.0 OP1 A:G359 4.4 2.2 1.0 OP2 A:C358 4.4 5.0 1.0 O5' A:C377 4.5 2.0 1.0 K A:K480 4.5 4.5 1.0 O3' A:C357 4.5 5.2 1.0 O3' A:A376 4.6 2.0 1.0 O5' A:G359 4.7 2.0 1.0 O3' A:C358 4.7 2.6 1.0

Magnesium binding site 3 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ Z:Mg12 b:43.6 occ:1.00 OP2 Z:U7 2.4 42.8 1.0 P Z:U7 3.5 42.5 1.0 O3' Z:U6 3.5 41.1 1.0 C3' Z:U6 3.6 38.6 1.0 C5' Z:U6 3.6 36.4 1.0 C5 Z:U7 3.6 45.9 1.0 O Z:HOH790 4.0 25.1 1.0 O5' Z:U7 4.0 43.9 1.0 C4' Z:U6 4.1 37.3 1.0 O A:HOH588 4.2 2.0 1.0 C6 Z:U7 4.2 46.0 1.0 C4 Z:U7 4.6 45.8 1.0 OP2 Z:U6 4.7 32.5 1.0 O5' Z:U6 4.7 34.5 1.0 O4 Z:U7 4.8 46.0 1.0 OP1 Z:U7 4.8 41.7 1.0 C2' Z:U6 4.9 37.8 1.0 P Z:U6 5.0 32.9 1.0

Magnesium binding site 4 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg413 b:30.4 occ:1.00 OP1 A:A380 2.7 7.5 1.0 O A:HOH739 3.0 2.8 1.0 C5' A:A287 3.3 30.0 1.0 O A:HOH723 3.4 14.5 1.0 O5' A:A287 3.5 28.4 1.0 O2' A:G5 3.7 2.3 1.0 P A:A380 3.7 7.0 1.0 O3' A:U379 3.8 6.3 1.0 C4' A:A287 3.8 31.4 1.0 OP2 A:A380 4.3 7.7 1.0 N6 A:A376 4.6 3.8 1.0 C5' A:C6 4.7 2.1 1.0 O4' A:A287 4.7 32.4 1.0 O3' A:A287 4.7 29.0 1.0 O2' A:C286 4.9 18.0 1.0 C3' A:A287 5.0 31.3 1.0

Magnesium binding site 5 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg414 b:48.7 occ:1.00 O A:HOH670 2.0 4.5 1.0 OP2 A:U4 2.3 7.6 1.0 OP1 A:G3 3.0 26.8 1.0 O5' A:G3 3.7 23.5 1.0 P A:U4 3.7 7.1 1.0 O A:HOH842 3.9 6.4 1.0 P A:G3 4.0 27.1 1.0 O3' A:G3 4.2 8.2 1.0 OP1 A:U4 4.3 7.6 1.0 O A:HOH611 4.4 20.6 1.0 C5' A:G3 4.4 16.8 1.0 O4' A:U2 4.4 33.9 1.0 C3' A:G3 4.6 10.4 1.0 O5' A:U4 4.8 6.3 1.0 O3' A:U2 4.9 29.3 1.0

Magnesium binding site 6 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg415 b:42.5 occ:1.00 O6 A:G15 3.0 17.5 1.0 O6 A:G14 3.4 8.6 1.0 O4 A:U256 3.4 27.8 1.0 O4 A:U255 4.1 33.7 1.0 C6 A:G15 4.1 17.7 1.0 C6 A:G14 4.2 8.5 1.0 C4 A:U256 4.3 27.5 1.0 N3 A:U256 4.5 27.5 1.0 N7 A:G15 4.5 17.8 1.0 C5 A:G15 4.7 17.7 1.0 N4 A:C257 4.7 22.7 1.0 O6 A:G16 4.8 22.2 1.0 C5 A:G14 4.8 8.7 1.0 N7 A:G14 4.9 9.0 1.0 C2' A:A12 4.9 10.0 1.0

Magnesium binding site 7 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:18.1 occ:1.00 O6 A:G242 3.9 3.9 1.0 N7 A:G242 3.9 3.8 1.0 O6 A:G244 4.0 2.0 1.0 O6 A:G243 4.0 2.0 1.0 O A:HOH568 4.1 2.0 1.0 N7 A:G243 4.2 2.0 1.0 C6 A:G242 4.4 3.6 1.0 C5 A:G242 4.5 3.4 1.0 O A:HOH752 4.5 14.8 1.0 O A:HOH871 4.6 15.4 1.0 C6 A:G244 4.7 2.0 1.0 C6 A:G243 4.8 2.0 1.0 C5 A:G243 4.9 2.0 1.0 C8 A:G242 4.9 3.6 1.0

Magnesium binding site 8 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:64.1 occ:1.00 O A:HOH752 2.4 14.8 1.0 OP2 A:G243 4.2 5.1 1.0 OP1 A:C39 4.3 9.1 1.0 O6 A:G244 4.6 2.0 1.0 O3' A:C38 4.6 6.3 1.0 N7 A:G244 4.7 2.0 1.0 OP1 A:C38 4.9 2.0 1.0 P A:C39 5.0 8.6 1.0

Magnesium binding site 9 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg418 b:36.6 occ:1.00 O6 A:G385 2.3 10.5 1.0 O A:HOH704 2.6 6.9 1.0 O6 A:G386 3.3 11.7 1.0 C6 A:G385 3.3 10.7 1.0 O A:HOH508 3.4 2.0 1.0 O2 A:C289 3.7 5.5 1.0 N4 A:C358 3.8 3.2 1.0 N7 A:G385 3.8 11.2 1.0 C5 A:G385 3.9 11.0 1.0 C6 A:G386 4.2 11.7 1.0 MG A:MG420 4.3 62.1 1.0 O6 A:G359 4.3 6.6 1.0 O A:HOH889 4.4 9.0 1.0 N1 A:G385 4.5 10.4 1.0 O4 A:U384 4.6 18.0 1.0 N3 A:U384 4.6 17.3 1.0 N7 A:G386 4.7 12.1 1.0 C5 A:G386 4.7 12.1 1.0 N2 A:G288 4.8 10.9 1.0 C2 A:C289 4.8 5.3 1.0 C1' A:C289 5.0 6.1 1.0

Magnesium binding site 10 out of 51 in the Insight Into Group II Intron Catalysis From Revised Crystal Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Insight Into Group II Intron Catalysis From Revised Crystal Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg419 b:30.4 occ:1.00 O A:HOH549 2.0 2.0 1.0 O A:HOH564 2.5 2.0 1.0 OP1 A:G373 3.9 2.0 1.0 OP1 A:G135 4.0 8.2 1.0 OP1 A:U132 4.4 2.0 1.0 O3' A:A134 4.5 7.0 1.0 OP1 A:G133 4.5 2.0 1.0 OP1 A:C361 4.5 3.3 1.0 OP2 A:G373 4.8 2.0 1.0 P A:G373 4.8 2.0 1.0 O2' A:A134 4.9 6.8 1.0 P A:G135 4.9 8.0 1.0

J.Wang, J.Wang. N/A N/A.
ISSN: ISSN 0907-4449
PubMed: 20823550
DOI: 10.1107/S0907444910029938