Magnesium in PDB 4ds6: Crystal Structure of A Group II Intron in the Pre-Catalytic State

The structure of Crystal Structure of A Group II Intron in the Pre-Catalytic State, PDB code: 4ds6 was solved by R.T.Chan, A.R.Robart, K.R.Rajashankar, A.M.Pyle, N.Toor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.41 / 3.64
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	89.880, 95.310, 226.173, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 24.8

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of A Group II Intron in the Pre-Catalytic State (pdb code 4ds6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 16 binding sites of Magnesium where determined in the Crystal Structure of A Group II Intron in the Pre-Catalytic State, PDB code: 4ds6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:91.6 occ:1.00 N1 A:G34 4.2 0.5 1.0 C2' A:A245 4.3 0.9 1.0 C8 A:A245 4.4 0.8 1.0 O2' A:A245 4.6 0.2 1.0 N6 A:A33 4.7 0.3 1.0 N2 A:G34 4.7 0.2 1.0 O6 A:G34 4.7 1.0 1.0 N9 A:A245 4.9 0.1 1.0 N7 A:A245 4.9 0.3 1.0 C6 A:G34 5.0 0.8 1.0

Magnesium binding site 2 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:70.8 occ:1.00 N4 A:C62 3.7 0.3 1.0 N6 A:A63 3.8 0.4 1.0 C4 A:C62 4.5 0.3 1.0 C5 A:C62 4.6 0.8 1.0 O6 A:G64 5.0 0.1 1.0

Magnesium binding site 3 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:87.5 occ:1.00 N4 A:C94 4.1 0.6 1.0 C5 A:C94 4.5 0.8 1.0 C4 A:C94 4.8 0.5 1.0

Magnesium binding site 4 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:0.5 occ:1.00 N4 A:C196 3.9 86.2 1.0 N4 A:C197 4.0 84.3 1.0 C4 A:C196 4.7 86.7 1.0 C5 A:C196 4.8 92.6 1.0

Magnesium binding site 5 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:74.9 occ:1.00 N4 A:C69 3.8 86.5 1.0 C5 A:C69 4.6 90.6 1.0 C4 A:C69 4.7 86.2 1.0

Magnesium binding site 6 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg506 b:0.3 occ:1.00 O5' A:C360 2.5 0.1 1.0 O4' A:C360 2.9 0.7 1.0 C4' A:G135 3.0 0.4 1.0 C2' A:A359 3.0 0.8 1.0 C4' A:C360 3.1 0.3 1.0 C5' A:C360 3.3 0.1 1.0 O3' A:G135 3.4 0.9 1.0 O2' A:G135 3.4 0.7 1.0 O3' A:A359 3.5 0.8 1.0 C3' A:A359 3.5 0.9 1.0 O2' A:A359 3.6 0.3 1.0 C3' A:G135 3.6 0.4 1.0 P A:C360 3.7 0.1 1.0 C5' A:G135 3.7 0.4 1.0 O4' A:G135 3.8 0.1 1.0 C1' A:C360 4.0 0.8 1.0 C2' A:G135 4.1 0.9 1.0 C8 A:A359 4.1 0.9 1.0 C1' A:A359 4.2 0.3 1.0 N9 A:A359 4.3 0.8 1.0 C1' A:G135 4.4 0.6 1.0 OP1 A:C360 4.4 0.4 1.0 C3' A:C360 4.5 0.8 1.0 O2' A:C360 4.6 0.5 1.0 P A:G136 4.7 0.5 1.0 C2' A:C360 4.7 0.1 1.0 OP2 A:C360 4.8 0.3 1.0 OP1 A:G136 4.8 0.8 1.0 N7 A:A359 4.9 0.1 1.0 C4' A:A359 5.0 0.7 1.0

Magnesium binding site 7 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg507 b:85.0 occ:1.00 O5' A:A174 2.9 0.0 1.0 C5' A:A174 3.5 0.7 1.0 OP2 A:A174 3.6 0.8 1.0 N7 A:G175 3.6 0.1 1.0 C8 A:A174 3.8 99.5 1.0 P A:A174 3.9 0.6 1.0 C2' A:G173 4.3 0.2 1.0 C8 A:G175 4.3 97.8 1.0 N7 A:A174 4.4 0.2 1.0 C4' A:A174 4.5 0.4 1.0 O4' A:A174 4.6 99.4 1.0 OP2 A:G175 4.6 0.7 1.0 C5 A:G175 4.6 99.6 1.0 O2' A:G173 4.7 0.9 1.0 O6 A:G175 4.7 0.1 1.0 O3' A:G173 4.8 0.1 1.0 C3' A:A174 4.8 98.6 1.0 C3' A:G173 4.8 0.7 1.0 N9 A:A174 4.9 0.6 1.0

Magnesium binding site 8 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 A Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg508 b:0.3 occ:1.00 OP2 A:A154 2.8 0.7 1.0 O4 A:U221 3.0 0.7 1.0 O6 A:G155 3.5 0.3 1.0 P A:A154 3.8 0.4 1.0 OP1 A:A154 3.9 0.4 1.0 O2' A:G153 4.0 0.2 1.0 C4 A:U221 4.0 0.6 1.0 C2' A:G153 4.1 0.2 1.0 O6 A:G156 4.3 0.1 1.0 N3 A:U221 4.4 0.8 1.0 N7 A:G155 4.5 0.1 1.0 C6 A:G155 4.5 0.2 1.0 C5 A:G155 4.9 0.9 1.0 O3' A:G153 4.9 0.0 1.0 O5' A:A154 5.0 0.6 1.0 C3' A:G153 5.0 0.1 1.0

Magnesium binding site 9 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 A Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg509 b:0.5 occ:1.00 N6 A:A231 4.4 0.9 1.0 N4 A:C230 4.9 0.2 1.0

Magnesium binding site 10 out of 16 in the Crystal Structure of A Group II Intron in the Pre-Catalytic State


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 A Group II Intron in the Pre-Catalytic State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg510 b:0.3 occ:1.00 N2 A:G113 4.8 0.5 1.0

R.T.Chan, A.R.Robart, K.R.Rajashankar, A.M.Pyle, N.Toor. Crystal Structure of A Group II Intron in the Pre-Catalytic State. Nat.Struct.Mol.Biol. V. 19 555 2012.
ISSN: ISSN 1545-9993
PubMed: 22484319
DOI: 10.1038/NSMB.2270