Magnesium in PDB 4y1o: Oceanobacillus Iheyensis Group II Intron Domain 1

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1, PDB code: 4y1o was solved by C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.25 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.345, 132.250, 84.561, 90.00, 91.87, 90.00
R / Rfree (%)	17.9 / 22.4

The structure of Oceanobacillus Iheyensis Group II Intron Domain 1 also contains other interesting chemical elements:

Potassium

(K)

2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Magnesium atom in the Oceanobacillus Iheyensis Group II Intron Domain 1 (pdb code 4y1o). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 19 binding sites of Magnesium where determined in the Oceanobacillus Iheyensis Group II Intron Domain 1, PDB code: 4y1o:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg400 b:70.9 occ:1.00 OP2 A:G136 2.1 0.2 1.0 P A:G136 3.6 0.7 1.0 OP2 A:U225 3.8 84.0 1.0 OP2 A:G135 3.9 0.6 1.0 N3 A:A138 4.1 89.1 1.0 OP1 A:G135 4.1 0.6 1.0 O5' A:G136 4.2 0.2 1.0 P A:G135 4.3 0.9 1.0 C2 A:A138 4.3 87.2 1.0 O5' A:G135 4.4 0.2 1.0 O3' A:G135 4.5 0.7 1.0 OP1 A:G136 4.5 0.1 1.0 OP2 A:A137 4.7 0.1 1.0 C3' A:G135 4.8 0.2 1.0 N7 A:G136 4.8 98.1 1.0 C8 A:G136 4.8 99.1 1.0

Magnesium binding site 2 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:84.5 occ:1.00 O6 A:G244 4.0 75.5 1.0 N7 A:G242 4.2 74.5 1.0 O6 A:G243 4.2 93.1 1.0 O6 A:G242 4.3 71.9 1.0 C6 A:G244 4.6 65.2 1.0 N7 A:G243 4.6 58.8 1.0 C5 A:G242 4.8 68.0 1.0 C6 A:G242 4.8 70.7 1.0 N1 A:G244 5.0 50.7 1.0

Magnesium binding site 3 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:76.2 occ:1.00 OP2 A:U66 2.1 95.4 1.0 OP1 A:A67 2.7 80.9 1.0 P A:U66 3.6 99.2 1.0 P A:A67 3.9 79.8 1.0 O3' A:U66 4.0 72.2 1.0 OP1 B:C76 4.2 0.6 1.0 O5' A:U66 4.3 72.7 1.0 O3' A:U65 4.4 68.7 1.0 OP1 A:U66 4.6 0.2 1.0 C5' B:C76 4.7 0.3 1.0 OP2 A:A67 4.7 95.0 1.0

Magnesium binding site 4 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:73.0 occ:1.00 OP2 A:A67 2.2 95.0 1.0 N7 A:G68 2.3 82.0 1.0 O6 A:G68 3.2 79.2 1.0 C5 A:G68 3.2 74.1 1.0 C8 A:G68 3.4 90.8 1.0 C6 A:G68 3.5 75.7 1.0 N4 A:C116 3.6 0.9 1.0 P A:A67 3.6 79.8 1.0 N1 A:A120 4.0 49.5 1.0 OP1 A:U65 4.1 87.7 1.0 O3' A:U66 4.3 72.2 1.0 C3' A:U66 4.4 71.6 1.0 C4 A:C116 4.4 0.6 1.0 O5' A:U66 4.4 72.7 1.0 C4 A:G68 4.4 72.0 1.0 OP1 A:A67 4.4 80.9 1.0 N9 A:G68 4.5 88.8 1.0 C2 A:A120 4.6 53.8 1.0 O5' A:A67 4.7 61.7 1.0 C5' A:U66 4.9 70.5 1.0 N1 A:G68 4.9 66.3 1.0 N3 A:C116 4.9 0.6 1.0 C6 A:A120 4.9 51.5 1.0

Magnesium binding site 5 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg404 b:87.5 occ:1.00 OP1 A:A240 3.5 77.4 1.0 OP1 A:G239 3.6 72.3 1.0 OP1 A:C119 3.8 86.3 1.0 OP1 A:A174 4.2 70.8 1.0 P A:A240 4.4 73.7 1.0 OP2 A:A240 4.7 69.3 1.0 C5' A:G173 4.8 67.3 1.0 OP2 A:A120 4.8 63.7 1.0 O3' A:G239 4.8 52.0 1.0 OP1 A:G173 4.9 73.5 1.0 P A:G239 4.9 77.9 1.0

Magnesium binding site 6 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg405 b:86.8 occ:1.00 OP2 A:A154 2.5 0.1 1.0 N7 A:G155 2.5 84.7 1.0 O6 A:G155 3.0 91.7 1.0 C5 A:G155 3.2 85.5 1.0 C6 A:G155 3.4 85.0 1.0 P A:A154 3.6 0.6 1.0 C8 A:G155 3.6 88.0 1.0 O4 A:U221 3.7 0.8 1.0 OP1 A:A154 3.8 0.1 1.0 O6 A:G156 3.9 0.2 1.0 N6 A:A222 4.2 0.6 1.0 N7 A:G156 4.3 0.3 1.0 C4 A:G155 4.5 83.3 1.0 O5' A:A154 4.7 0.3 1.0 C6 A:G156 4.7 98.8 1.0 N9 A:G155 4.7 92.8 1.0 C4 A:U221 4.8 0.3 1.0 O3' A:G153 4.8 0.2 1.0 N1 A:G155 4.8 69.7 1.0 C5 A:G156 4.8 0.5 1.0

Magnesium binding site 7 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg406 b:98.9 occ:1.00 OP2 A:C145 3.0 0.7 1.0 O6 A:G136 3.6 0.2 1.0 P A:C145 4.2 0.0 1.0 OP2 A:U146 4.3 92.5 1.0 O5' A:C145 4.4 0.4 1.0 C6 A:G136 4.5 97.3 1.0 OP1 A:A134 4.6 92.8 1.0 N1 A:G136 4.7 0.4 1.0 O6 A:G135 4.8 0.9 1.0 OP2 A:A134 4.9 0.7 1.0 N2 A:G142 4.9 0.6 1.0 OP2 A:C139 4.9 0.2 1.0 OP1 A:C145 5.0 99.1 1.0

Magnesium binding site 8 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg400 b:94.2 occ:1.00 O6 B:G28 2.6 0.9 1.0 C6 B:G28 3.5 0.8 1.0 N7 B:G28 3.8 0.0 1.0 C5 B:G28 3.9 0.2 1.0 O6 B:G29 4.0 91.8 1.0 OP2 B:A27 4.1 0.1 1.0 OP1 B:U26 4.3 94.8 1.0 N4 B:C40 4.6 83.5 1.0 N1 B:G28 4.6 0.0 1.0 O5' B:A25 4.7 84.9 1.0 C3' B:A25 4.8 92.8 1.0 N7 B:G29 4.8 94.8 1.0 C6 B:G29 4.9 83.0 1.0 N2 B:G41 5.0 0.8 1.0 C8 B:G28 5.0 0.2 1.0

Magnesium binding site 9 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg401 b:80.2 occ:1.00 OP2 B:U66 2.3 96.4 1.0 OP1 B:A67 2.5 80.7 1.0 P B:A67 3.7 82.0 1.0 P B:U66 3.8 90.8 1.0 O3' B:U66 3.9 82.8 1.0 O5' B:U66 4.5 97.3 1.0 O3' B:U65 4.5 0.8 1.0 OP1 B:U66 4.6 91.6 1.0 OP2 B:A67 4.7 72.9 1.0 O5' B:A67 4.8 73.2 1.0 C5' B:A67 4.8 67.1 1.0

Magnesium binding site 10 out of 19 in the Oceanobacillus Iheyensis Group II Intron Domain 1


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Oceanobacillus Iheyensis Group II Intron Domain 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:71.4 occ:1.00 OP2 B:A67 2.3 72.9 1.0 N7 B:G68 2.6 87.9 1.0 O6 B:G68 3.2 0.5 1.0 C5 B:G68 3.4 79.0 1.0 P B:A67 3.6 82.0 1.0 C8 B:G68 3.6 84.5 1.0 C6 B:G68 3.7 86.7 1.0 OP1 B:U65 4.1 85.6 1.0 OP1 B:A67 4.2 80.7 1.0 O3' B:U66 4.3 82.8 1.0 O5' B:U66 4.4 97.3 1.0 C3' B:U66 4.4 75.4 1.0 N1 B:A120 4.6 59.4 1.0 C4 B:G68 4.7 65.8 1.0 N9 B:G68 4.8 75.1 1.0 O5' B:A67 4.8 73.2 1.0

C.Zhao, K.R.Rajashankar, M.Marcia, A.M.Pyle. Crystal Structure of Group II Intron Domain 1 Reveals A Template For Rna Assembly. Nat.Chem.Biol. V. 11 967 2015.
ISSN: ESSN 1552-4469
PubMed: 26502156
DOI: 10.1038/NCHEMBIO.1949