Magnesium in PDB 8syk: Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo State

The structure of Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo State, PDB code: 8syk was solved by J.R.Stagno, J.C.Deme, Y.-T.Lee, Y.-X.Wang, H.K.Lee, S.M.Lea, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.32 / 3.06
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.223, 81.223, 528.831, 90, 90, 90
R / Rfree (%)	22.5 / 25.7

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 - 60; Page 7, Binding sites: 61 - 61;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo State (pdb code 8syk). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 61 binding sites of Magnesium where determined in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo State, PDB code: 8syk:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:141.4 occ:1.00 O A:HOH305 2.0 118.2 1.0 OP2 A:A28 2.5 162.4 1.0 OP2 A:G29 2.7 187.3 1.0 O5' A:A28 3.4 152.8 1.0 P A:A28 3.5 164.6 1.0 N7 A:G29 4.0 165.4 1.0 P A:G29 4.1 172.6 1.0 C8 A:G29 4.5 162.1 1.0 C3' A:A28 4.5 167.4 1.0 O3' A:G27 4.5 136.9 1.0 OP1 A:A28 4.7 178.5 1.0 C5' A:A28 4.8 166.6 1.0 O3' A:A28 4.8 159.1 1.0 O5' A:G29 4.8 158.8 1.0

Magnesium binding site 2 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg204 b:145.6 occ:1.00 O3G A:GTP201 2.2 120.0 1.0 PG A:GTP201 2.9 163.8 1.0 O2G A:GTP201 3.0 164.3 1.0 O1G A:GTP201 3.3 140.5 1.0 MG A:MG221 3.6 144.4 1.0 N7 A:GTP201 4.0 106.1 1.0 O6 A:GTP201 4.2 115.3 1.0 O3B A:GTP201 4.4 133.3 1.0 C5 A:GTP201 4.8 97.6 1.0 C8 A:GTP201 5.0 106.7 1.0 C6 A:GTP201 5.0 100.1 1.0

Magnesium binding site 3 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg205 b:135.2 occ:1.00 MG A:MG221 3.9 144.4 1.0

Magnesium binding site 4 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg206 b:145.4 occ:1.00 O A:HOH304 2.2 115.4 1.0 OP2 A:G114 5.0 134.3 1.0

Magnesium binding site 5 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg207 b:126.3 occ:1.00 OP2 A:A45 2.2 150.2 1.0 P A:A45 3.5 157.6 1.0 O5' A:A45 3.9 148.0 1.0 N7 A:A46 3.9 157.9 1.0 N7 A:A45 4.2 145.9 1.0 OP1 A:A45 4.2 173.8 1.0 N6 A:A46 4.3 148.2 1.0 C8 A:A45 4.4 140.4 1.0 O3' A:A44 4.7 152.8 1.0 C5 A:A46 4.9 158.5 1.0 O5' A:A44 4.9 147.5 1.0 C3' A:A44 4.9 163.3 1.0 C8 A:A46 4.9 159.8 1.0

Magnesium binding site 6 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg208 b:120.1 occ:1.00 O11 A:TAC202 2.0 136.6 1.0 OP2 A:G66 2.2 112.6 1.0 O12 A:TAC202 2.2 155.4 1.0 C11 A:TAC202 3.1 132.4 1.0 C12 A:TAC202 3.3 146.4 1.0 P A:G66 3.5 130.1 1.0 C1B A:TAC202 3.6 127.9 1.0 O10 A:TAC202 3.8 123.2 1.0 N1 A:A59 3.9 132.0 1.0 OP1 A:G66 3.9 104.5 1.0 N2 A:G60 4.3 122.2 1.0 C1A A:TAC202 4.3 123.1 1.0 C2 A:A59 4.3 145.2 1.0 O3' A:C65 4.4 118.6 1.0 C3' A:C65 4.5 105.3 1.0 O5' A:G66 4.5 108.5 1.0 C10 A:TAC202 4.5 117.2 1.0 C1C A:TAC202 4.6 175.2 1.0 O1C A:TAC202 4.6 174.5 1.0 C2 A:G60 4.9 142.3 1.0 N3 A:G60 4.9 141.1 1.0 C6 A:A59 5.0 135.6 1.0

Magnesium binding site 7 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg209 b:100.4 occ:1.00 OP2 A:G54 2.2 119.3 1.0 O A:HOH306 2.4 138.1 1.0 OP1 A:A53 2.8 170.1 1.0 P A:G54 3.2 131.3 1.0 MG A:MG210 3.3 105.5 1.0 O5' A:A53 3.3 116.2 1.0 OP2 A:A90 3.5 143.8 1.0 OP1 A:G54 3.5 107.0 1.0 P A:A53 3.7 147.0 1.0 O5' A:G54 4.0 124.8 1.0 C5' A:A53 4.2 133.3 1.0 OP1 A:A91 4.3 170.2 1.0 O3' A:A53 4.5 121.9 1.0 C5' A:G54 4.6 122.2 1.0 P A:A90 4.6 172.2 1.0 O3' A:G52 4.6 138.2 1.0 C3' A:A53 4.7 126.8 1.0 O5' A:A90 4.8 128.2 1.0 OP2 A:A53 4.8 132.2 1.0

Magnesium binding site 8 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg210 b:105.5 occ:1.00 OP2 A:G54 2.3 119.3 1.0 OP1 A:A91 2.4 170.2 1.0 O A:HOH306 2.9 138.1 1.0 MG A:MG209 3.3 100.4 1.0 O5' A:A53 3.4 116.2 1.0 P A:A91 3.5 167.7 1.0 C5' A:G54 3.5 122.2 1.0 P A:G54 3.5 131.3 1.0 C3' A:A53 3.6 126.8 1.0 OP2 A:A91 3.9 171.9 1.0 O3' A:A53 3.9 121.9 1.0 C5' A:A91 3.9 174.7 1.0 OP1 A:A53 3.9 170.1 1.0 C8 A:A53 3.9 124.0 1.0 O5' A:G54 4.0 124.8 1.0 O5' A:A91 4.0 179.3 1.0 P A:A53 4.1 147.0 1.0 N7 A:A92 4.2 125.9 1.0 OP2 A:A53 4.3 132.2 1.0 C2' A:A53 4.5 99.8 1.0 C5' A:A53 4.5 133.3 1.0 N7 A:A53 4.6 111.6 1.0 C4' A:A53 4.6 118.0 1.0 C8 A:A92 4.8 138.3 1.0 OP1 A:G54 4.8 107.0 1.0 N9 A:A53 4.8 122.2 1.0 O3' A:A90 4.9 166.8 1.0 C4' A:G54 4.9 138.1 1.0

Magnesium binding site 9 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg211 b:116.4 occ:1.00 O5' A:GTP201 2.4 102.8 1.0 O2A A:GTP201 2.5 126.8 1.0 PA A:GTP201 3.0 101.3 1.0 MG A:MG213 3.1 173.5 1.0 C5' A:GTP201 3.2 110.3 1.0 O2B A:GTP201 3.7 131.4 1.0 O3A A:GTP201 4.0 136.7 1.0 O1A A:GTP201 4.1 107.4 1.0 C4' A:GTP201 4.4 103.5 1.0 PB A:GTP201 4.5 140.2 1.0 O4' A:GTP201 4.8 105.0 1.0

Magnesium binding site 10 out of 61 in the Crystal Structure of Rna Device 43 Truncation Mutant 3 (U100C), Holo 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 Rna Device 43 Truncation Mutant 3 (U100C), Holo State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg212 b:120.0 occ:1.00 O1B A:GTP201 2.3 123.4 1.0 O2B A:GTP201 2.6 131.4 1.0 PB A:GTP201 3.0 140.2 1.0 MG A:MG219 3.0 117.8 1.0 MG A:MG213 3.3 173.5 1.0 O3B A:GTP201 3.9 133.3 1.0 O3A A:GTP201 4.3 136.7 1.0 O1G A:GTP201 4.5 140.5 1.0 PG A:GTP201 4.9 163.8 1.0

J.R.Stagno, J.C.Deme, Y.-T.Lee, Y.-X.Wang, H.K.Lee, S.M.Lea. Crystal Structure of Rna Device 43 Truncation Mutant, Holo State To Be Published.