Magnesium in PDB 5xtm: Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix

The structure of Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix, PDB code: 5xtm was solved by K.Oshima, M.Kimura, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.26 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	52.070, 71.720, 91.280, 90.00, 105.58, 90.00
R / Rfree (%)	19.7 / 22.2

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Magnesium atom in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix (pdb code 5xtm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 24 binding sites of Magnesium where determined in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix, PDB code: 5xtm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:55.4 occ:1.00 O A:HOH349 2.3 55.9 1.0 OE2 A:GLU86 2.5 44.1 1.0 O A:HOH339 3.2 46.4 1.0 CD A:GLU86 3.4 35.9 1.0 CG A:GLU86 3.6 29.6 1.0 OE1 A:GLU86 4.6 36.0 1.0 OE1 A:GLU18 4.6 50.0 1.0 CD2 A:LEU21 5.0 35.9 1.0

Magnesium binding site 2 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:37.8 occ:1.00 O B:HOH228 2.1 39.4 1.0 O B:HOH292 2.2 43.9 1.0 O6 B:G23 2.2 32.3 1.0 O B:HOH239 2.3 35.1 1.0 O B:HOH211 2.4 34.6 1.0 O B:HOH202 2.4 34.7 1.0 C6 B:G23 3.1 33.7 1.0 N7 B:G23 3.7 32.6 1.0 C5 B:G23 3.7 36.4 1.0 O B:HOH201 3.9 38.9 1.0 O B:HOH205 3.9 40.4 1.0 O6 B:G25 4.0 41.1 1.0 O6 B:G24 4.2 32.6 1.0 N4 B:C30 4.2 30.1 1.0 N1 B:G23 4.3 31.7 1.0 N7 B:G24 4.4 35.2 1.0 C8 B:G23 4.9 36.7 1.0 C6 B:G25 5.0 37.6 1.0 C6 B:G24 5.0 35.3 1.0 N7 B:A22 5.0 34.1 1.0

Magnesium binding site 3 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg102 b:67.6 occ:1.00 O3' B:C47 2.2 66.8 1.0 C3' B:C47 2.9 65.4 1.0 C5' B:C47 3.7 63.8 1.0 C4' B:C47 3.8 62.3 1.0 O5' B:C47 3.8 67.6 1.0 C2' B:C47 4.2 61.8 1.0 OP1 B:C47 4.6 86.1 1.0 P B:C47 4.8 75.7 1.0 O2' B:C47 4.8 56.8 1.0 O4' B:C47 5.0 58.7 1.0

Magnesium binding site 4 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg103 b:59.8 occ:1.00 OP1 B:G23 2.4 48.0 1.0 O B:HOH291 2.6 49.8 1.0 O B:HOH280 2.6 41.7 1.0 OP2 B:G7 3.0 38.5 1.0 O B:HOH274 3.1 46.7 1.0 O B:HOH210 3.2 40.7 1.0 OP1 B:G7 3.6 41.9 1.0 P B:G23 3.6 43.4 1.0 O3' B:A22 3.7 40.6 1.0 P B:G7 3.8 40.1 1.0 OP1 B:U35 4.0 38.5 1.0 C5' B:G23 4.1 40.1 1.0 O5' B:G23 4.3 38.3 1.0 O B:HOH209 4.4 38.6 1.0 OP1 B:G6 4.6 45.5 1.0 OP2 B:G23 4.8 40.9 1.0 O3' B:G6 4.9 36.8 1.0 O5' B:G7 5.0 33.5 1.0

Magnesium binding site 5 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg104 b:59.7 occ:1.00 O B:HOH284 2.2 41.8 1.0 O B:HOH256 2.6 34.5 1.0 O B:HOH225 2.9 38.6 1.0 O B:HOH260 2.9 45.5 1.0 O B:HOH220 4.0 40.9 1.0 N4 B:C16 4.4 26.1 1.0 OP2 B:A12 4.4 34.5 1.0

Magnesium binding site 6 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg105 b:59.8 occ:1.00 N7 B:G45 2.2 55.5 1.0 O6 B:G45 2.4 51.7 1.0 O2' B:A43 2.7 55.0 1.0 C5 B:G45 2.8 50.1 1.0 C6 B:G45 2.9 52.2 1.0 N4 B:C46 3.0 51.6 1.0 O3' B:A43 3.2 52.7 1.0 C8 B:G45 3.5 55.5 1.0 N7 B:A44 3.5 46.7 1.0 C2' B:A43 3.6 49.4 1.0 C4 B:C46 3.7 53.4 1.0 C1' B:A43 3.8 47.0 1.0 C8 B:A44 4.0 45.3 1.0 C3' B:A43 4.0 48.8 1.0 C4 B:G45 4.1 52.5 1.0 C5 B:C46 4.2 55.3 1.0 O6 B:G2 4.2 46.7 1.0 OP2 B:A44 4.2 67.7 1.0 P B:A44 4.2 53.2 1.0 C5 B:A44 4.3 48.0 1.0 N1 B:G45 4.3 51.6 1.0 O5' B:A44 4.3 51.8 1.0 N3 B:A43 4.3 50.4 1.0 N3 B:C46 4.4 55.3 1.0 N9 B:G45 4.4 55.8 1.0 N3 B:U3 4.4 49.5 1.0 N9 B:A43 4.6 45.8 1.0 O4 B:U3 4.7 50.6 1.0 N6 B:A44 4.7 47.8 1.0 C4 B:A43 4.8 45.2 1.0 C6 B:A44 4.8 45.3 1.0 O4' B:A43 4.9 44.9 1.0 N9 B:A44 4.9 48.5 1.0 OP2 B:G45 5.0 61.3 1.0 C4' B:A43 5.0 47.4 1.0

Magnesium binding site 7 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg106 b:48.6 occ:1.00 O B:HOH250 2.1 46.1 1.0 OP2 B:A13 2.2 36.4 1.0 O B:HOH272 2.2 52.1 1.0 O B:HOH283 2.4 42.7 1.0 P B:A13 3.6 41.4 1.0 O B:HOH295 4.1 43.3 1.0 OP1 B:A13 4.2 38.4 1.0 O B:HOH215 4.4 41.2 1.0 O3' B:A12 4.4 40.1 1.0 C3' B:A12 4.4 35.9 1.0 C5' B:A13 4.5 35.1 1.0 O5' B:A13 4.6 37.9 1.0 C4' B:A12 5.0 39.5 1.0

Magnesium binding site 8 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg107 b:53.0 occ:1.00 OP2 B:G8 2.3 36.5 1.0 O B:HOH236 2.8 43.0 1.0 O B:HOH263 2.9 39.6 1.0 O B:HOH262 3.2 40.2 1.0 O B:HOH241 3.8 47.5 1.0 P B:G8 3.8 32.1 1.0 OP1 B:U35 4.0 38.5 1.0 OP2 B:U35 4.1 30.9 1.0 C3' B:G7 4.3 32.0 1.0 O B:HOH210 4.4 40.7 1.0 O3' B:G7 4.5 33.4 1.0 C5' B:G7 4.5 31.8 1.0 P B:U35 4.6 35.4 1.0 O5' B:G8 4.6 31.0 1.0 OP1 B:G8 4.7 41.6 1.0

Magnesium binding site 9 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg108 b:50.2 occ:1.00 OP1 B:A14 2.1 38.0 1.0 P B:A14 3.6 35.8 1.0 OP1 B:G15 4.2 45.9 1.0 OP2 B:G15 4.3 32.9 1.0 O3' B:A13 4.3 41.1 1.0 OP2 B:A14 4.4 38.8 1.0 O5' B:A14 4.5 29.6 1.0 P B:G15 4.6 37.8 1.0 O B:HOH253 4.6 33.0 1.0 C5' B:A14 4.7 33.4 1.0 O3' B:A14 4.8 35.3 1.0

Magnesium binding site 10 out of 24 in the Crystal Structure of PHORPP38 Bound to A K-Turn in P12.2 Helix


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 PHORPP38 Bound to A K-Turn in P12.2 Helix within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg109 b:81.1 occ:1.00 O3G B:GTP1 2.0 85.9 1.0 OP2 B:G2 2.1 62.6 1.0 PG B:GTP1 2.6 0.4 1.0 O1G B:GTP1 2.6 93.6 1.0 O2G B:GTP1 2.9 0.7 1.0 P B:G2 3.6 63.7 1.0 O2A B:GTP1 4.0 81.2 1.0 O3B B:GTP1 4.1 95.1 1.0 MG B:MG110 4.1 63.4 1.0 O3A B:GTP1 4.1 83.0 1.0 OP1 B:G2 4.2 67.4 1.0 O5' B:G2 4.4 63.1 1.0 C3' B:GTP1 4.5 62.5 1.0 O3' B:GTP1 4.6 68.0 1.0 PA B:GTP1 4.7 73.9 1.0 MG B:MG112 4.7 78.3 1.0 PB B:GTP1 4.8 0.1 1.0 O4 B:U3 4.9 50.6 1.0 C5' B:GTP1 5.0 67.4 1.0

K.Oshima, X.Gao, S.Hayashi, T.Ueda, T.Nakashima, M.Kimura. Crystal Structures of the Archaeal Rnase P Protein RPP38 in Complex with Rna Fragments Containing A K-Turn Motif. Acta Crystallogr F Struct V. 74 57 2018BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 29372908
DOI: 10.1107/S2053230X17018039