Magnesium in PDB 5fj1: Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group

The structure of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group, PDB code: 5fj1 was solved by L.Huang, D.M.J.Lilley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.720 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.052, 84.360, 174.499, 90.00, 90.00, 90.00
R / Rfree (%)	16.68 / 18.3

The structure of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group (pdb code 5fj1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group, PDB code: 5fj1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1025 b:92.5 occ:1.00 O6 A:G5 2.7 63.5 1.0 O6 A:G4 3.0 77.0 1.0 O A:HOH2001 3.1 69.3 1.0 OP2 A:G3 3.4 58.6 1.0 N7 A:G4 3.6 67.1 1.0 MG A:MG1026 3.7 97.6 1.0 C6 A:G5 3.8 51.1 1.0 C6 A:G4 3.8 58.9 1.0 C5 A:G4 4.1 56.3 1.0 N1 A:G5 4.3 50.5 1.0 P A:G3 4.7 53.4 1.0 C8 A:G4 4.8 67.4 1.0 O2' A:G20 4.8 57.8 1.0 C5 A:G5 4.9 51.5 1.0

Magnesium binding site 2 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1026 b:97.6 occ:1.00 O6 A:G4 2.6 77.0 1.0 N7 A:G3 3.2 50.1 1.0 C6 A:G4 3.4 58.9 1.0 N7 A:G2 3.5 58.2 1.0 MG A:MG1025 3.7 92.5 1.0 C5 A:G2 3.9 42.9 1.0 O6 A:G3 4.0 61.4 1.0 C8 A:G3 4.1 50.1 1.0 C8 A:G2 4.1 41.7 1.0 C5 A:G4 4.1 56.3 1.0 C5 A:G3 4.1 53.4 1.0 O6 A:G2 4.2 61.0 1.0 N1 A:G4 4.2 53.3 1.0 C6 A:G2 4.2 51.5 1.0 N7 A:G4 4.4 67.1 1.0 C6 A:G3 4.5 57.5 1.0 C4 A:G2 4.8 43.5 1.0 OP2 A:G3 4.9 58.6 1.0 N9 A:G2 4.9 45.4 1.0 O2' A:G20 4.9 57.8 1.0 OP2 A:G2 4.9 54.3 1.0

Magnesium binding site 3 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1027 b:79.0 occ:1.00 N1 A:G20 3.4 60.7 1.0 O2' A:G5 3.6 65.5 1.0 N2 A:G20 3.9 51.2 1.0 C8 A:G5 3.9 54.6 1.0 C2 A:G20 4.1 59.4 1.0 N7 A:G5 4.2 58.5 1.0 O6 A:G20 4.2 73.8 1.0 C2' A:G5 4.3 57.0 1.0 C6 A:G20 4.3 67.1 1.0 N9 A:G5 4.5 53.9 1.0 C5 A:G5 4.9 51.5 1.0 C1' A:G5 5.0 53.3 1.0

Magnesium binding site 4 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1028 b:85.7 occ:1.00 O6 A:G10 3.2 84.6 1.0 O A:HOH2003 3.6 66.6 1.0 C6 A:G10 3.7 69.2 1.0 N7 A:G10 3.7 65.9 1.0 C5 A:G10 3.9 66.7 1.0 OP2 A:A12 4.3 79.3 1.0 OP1 A:A12 4.3 97.2 1.0 O A:HOH2002 4.5 71.6 1.0 C8 A:G10 4.7 70.1 1.0 N1 A:G10 4.8 65.3 1.0 P A:A12 4.9 84.0 1.0

Magnesium binding site 5 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1025 b:91.6 occ:1.00 O6 B:G2 3.0 55.9 1.0 O6 B:G3 3.0 58.6 1.0 O B:HOH2001 3.0 63.5 1.0 C6 B:G2 3.8 50.0 1.0 O6 B:G4 3.9 75.0 1.0 C6 B:G3 3.9 61.2 1.0 N7 B:G2 4.0 56.5 1.0 N1 B:G4 4.1 62.7 1.0 N7 B:G3 4.1 48.5 1.0 C6 B:G4 4.1 69.4 1.0 C5 B:G2 4.3 42.8 1.0 C5 B:G3 4.3 51.0 1.0 OP2 B:A21 4.3 60.1 1.0 N4 B:C24 4.4 56.5 1.0 N4 B:C23 4.6 50.1 1.0 O4 A:U1 4.6 67.2 1.0 C2 B:G4 4.9 61.6 1.0

Magnesium binding site 6 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1026 b:76.1 occ:1.00 O6 B:G4 3.0 75.0 1.0 O6 B:G5 3.0 71.3 1.0 O B:HOH2001 3.2 63.5 1.0 MG B:MG1027 3.4 92.4 1.0 OP2 B:G3 3.4 45.9 1.0 N7 B:G4 3.8 59.1 1.0 C6 B:G4 3.9 69.4 1.0 C6 B:G5 4.0 55.8 1.0 C5 B:G4 4.2 59.3 1.0 N1 B:G5 4.5 52.5 1.0 P B:G3 4.8 60.9 1.0 O2' B:G20 4.8 67.8 1.0 O B:HOH2002 4.8 68.6 1.0 N7 B:G3 5.0 48.5 1.0 OP2 B:G2 5.0 51.3 1.0

Magnesium binding site 7 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1027 b:92.4 occ:1.00 O B:HOH2002 2.5 68.6 1.0 O6 B:G5 2.7 71.3 1.0 MG B:MG1026 3.4 76.1 1.0 C6 B:G5 3.8 55.8 1.0 N7 B:G5 4.3 55.1 1.0 C5 B:G5 4.4 45.3 1.0 OP2 B:G3 4.8 45.9 1.0 OP2 B:G4 4.8 49.7 1.0 O6 B:G20 4.8 82.7 1.0 N7 B:G4 4.9 59.1 1.0

Magnesium binding site 8 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1028 b:75.7 occ:1.00 O2' B:G5 3.5 72.8 1.0 N1 B:G20 3.9 58.5 1.0 C8 B:G5 4.1 53.5 1.0 N2 B:G20 4.2 54.2 1.0 C2' B:G5 4.2 54.1 1.0 N7 B:G5 4.5 55.1 1.0 C2 B:G20 4.6 62.2 1.0 N9 B:G5 4.6 56.9 1.0 O6 B:G20 4.7 82.7 1.0 C6 B:G20 4.8 60.8 1.0

Magnesium binding site 9 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1029 b:86.8 occ:1.00 O6 B:G10 3.3 86.8 1.0 C6 B:G10 3.7 69.2 1.0 N7 B:G10 3.9 63.7 1.0 C5 B:G10 3.9 59.0 1.0 OP2 B:A12 4.1 62.8 1.0 OP1 B:A12 4.2 82.2 1.0 P B:A12 4.6 74.0 1.0 N1 B:G10 4.7 66.9 1.0 C8 B:G10 4.8 66.1 1.0

Magnesium binding site 10 out of 21 in the Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of the Standard Kink Turn Hmkt-7 As Stem Loop in P212121 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1025 b:81.3 occ:1.00 N1 C:G20 3.4 69.1 1.0 O2' C:G5 3.7 76.0 1.0 N2 C:G20 3.9 61.6 1.0 C8 C:G5 4.1 77.3 1.0 O6 C:G20 4.1 81.8 1.0 C2 C:G20 4.2 68.6 1.0 C6 C:G20 4.3 70.6 1.0 N7 C:G5 4.3 79.8 1.0 C2' C:G5 4.4 73.8 1.0 N9 C:G5 4.6 74.5 1.0 C5 C:G5 4.9 70.4 1.0

L.Huang, J.Wang, D.M.J.Lilley. A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function. Nucleic Acids Res. V. 44 5390 2016.
ISSN: ISSN 0305-1048
PubMed: 27016741
DOI: 10.1093/NAR/GKW201