Manganese in PDB 4rgf: Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+

The structure of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+, PDB code: 4rgf was solved by A.Ren, K.R.Rajashankar, D.Simanshu, D.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.75 / 3.20
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.299, 64.299, 584.991, 90.00, 90.00, 120.00
R / Rfree (%)	23.1 / 27.7

The structure of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ also contains other interesting chemical elements:

Magnesium	(Mg)	1 atom
Potassium	(K)	14 atoms

Pages:

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

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ (pdb code 4rgf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+, PDB code: 4rgf:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn101 b:0.8 occ:1.00 OP2 A:A7 2.4 0.3 1.0 O4 A:U8 2.4 0.2 1.0 OP1 A:A6 2.8 0.9 1.0 O5' A:A6 3.4 0.4 1.0 C4 A:U8 3.5 0.8 1.0 P A:A6 3.8 0.3 1.0 P A:A7 3.8 0.5 1.0 C5 A:U8 4.1 0.9 1.0 N6 A:A47 4.3 0.7 1.0 O3' A:A6 4.5 0.3 1.0 C5' A:A6 4.5 0.3 1.0 C4' A:A6 4.5 0.1 1.0 OP1 A:A7 4.6 0.1 1.0 C3' A:A6 4.6 0.7 1.0 N3 A:U8 4.7 0.6 1.0 O6 A:G9 4.7 0.9 1.0 OP2 A:A6 4.8 0.1 1.0 O4 A:U45 4.8 0.9 1.0 O5' A:A7 4.8 0.4 1.0 O3' A:DU5 4.9 0.8 1.0

Manganese binding site 2 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn102 b:0.9 occ:1.00 OP2 A:G19 3.0 0.0 1.0 P A:G19 4.0 0.9 1.0 C5' A:G18 4.0 0.8 1.0 OP1 A:G19 4.3 0.7 1.0 O3' A:G18 4.3 0.8 1.0 C3' A:G18 4.8 0.9 1.0 C4' A:G18 4.8 0.4 1.0 O5' A:G18 4.9 0.3 1.0

Manganese binding site 3 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn103 b:0.7 occ:1.00 O A:HOH204 1.7 0.4 1.0 O6 A:G27 2.8 0.9 1.0 N7 A:G27 3.4 0.4 1.0 C6 A:G27 3.6 0.3 1.0 O6 A:G28 3.8 0.5 1.0 C5 A:G27 3.9 0.6 1.0 O2' A:A35 4.0 0.4 1.0 OP2 A:A26 4.2 0.2 1.0 N7 A:G28 4.4 0.6 1.0 C8 A:G27 4.6 0.9 1.0 OP1 A:C37 4.6 99.6 1.0 C6 A:G28 4.7 0.0 1.0 O6 A:G29 4.8 0.7 1.0 O3' A:G36 4.8 99.3 1.0 C5 A:G28 4.9 0.5 1.0 N1 A:G27 4.9 0.7 1.0 C5' A:G36 4.9 99.7 1.0 N4 A:C40 4.9 0.6 1.0 C2' A:A35 5.0 0.8 1.0

Manganese binding site 4 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn104 b:99.2 occ:1.00 OP2 A:A42 2.3 99.8 1.0 OP2 A:A43 2.5 99.1 1.0 P A:A42 3.6 0.1 1.0 P A:A43 3.9 99.1 1.0 O3' A:U41 4.0 0.1 1.0 N7 A:A43 4.1 98.8 1.0 OP2 A:C39 4.2 99.2 1.0 O5' A:A42 4.3 0.1 1.0 C8 A:A43 4.4 98.7 1.0 O5' A:A43 4.5 98.8 1.0 C5' A:A42 4.6 0.1 1.0 OP2 A:C40 4.7 0.4 1.0 OP1 A:C39 4.7 99.5 1.0 OP1 A:A43 4.7 99.3 1.0 C3' A:A42 4.8 99.4 1.0 OP1 A:A42 4.8 0.7 1.0 O2' A:U41 4.9 0.1 1.0 O3' A:A42 4.9 99.3 1.0 P A:C39 4.9 99.5 1.0

Manganese binding site 5 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn105 b:0.8 occ:1.00 OP1 A:A7 2.4 0.1 1.0 OP2 A:U8 2.6 0.2 1.0 P A:A7 3.8 0.5 1.0 P A:U8 4.0 0.1 1.0 OP2 A:A7 4.4 0.3 1.0 O5' A:A7 4.5 0.4 1.0 C5' A:A7 4.5 0.8 1.0 OP1 A:G36 4.6 0.1 1.0 OP1 A:U8 4.7 0.2 1.0 O3' A:A7 4.8 0.7 1.0 O3' A:A6 4.8 0.3 1.0 O5' A:U8 5.0 0.8 1.0

Manganese binding site 6 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn101 b:0.9 occ:1.00 O4 B:U8 2.3 0.3 1.0 OP1 B:A6 2.3 0.5 1.0 OP2 B:A7 2.4 0.8 1.0 C4 B:U8 3.3 0.4 1.0 P B:A6 3.6 0.6 1.0 C5 B:U8 3.7 1.0 1.0 O5' B:A6 3.7 0.8 1.0 P B:A7 3.7 0.3 1.0 OP1 B:A7 4.3 0.5 1.0 O3' B:A6 4.4 1.0 1.0 N6 B:A47 4.5 0.7 1.0 C4' B:A6 4.5 0.0 1.0 OP2 B:A6 4.5 0.6 1.0 N3 B:U8 4.6 0.1 1.0 C5' B:A6 4.6 0.1 1.0 C3' B:A6 4.6 1.0 1.0 O6 B:G9 4.7 0.7 1.0 O3' B:DU5 4.7 0.5 1.0 O5' B:A7 4.9 0.9 1.0

Manganese binding site 7 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn102 b:0.6 occ:1.00 OP2 B:A42 1.8 0.5 1.0 OP2 B:A43 2.2 0.5 1.0 P B:A42 3.2 0.9 1.0 P B:A43 3.7 0.6 1.0 O3' B:U41 3.7 0.0 1.0 O5' B:A42 4.0 0.6 1.0 N7 B:A43 4.2 0.2 1.0 C5' B:A42 4.2 0.3 1.0 C8 B:A43 4.3 0.7 1.0 OP1 B:A42 4.3 1.0 1.0 C3' B:A42 4.4 0.2 1.0 O5' B:A43 4.4 0.4 1.0 OP2 B:C39 4.4 0.5 1.0 OP1 B:A43 4.6 0.5 1.0 O3' B:A42 4.6 0.1 1.0 OP2 B:C40 4.7 0.5 1.0 C3' B:U41 4.8 1.0 1.0 O2' B:U41 4.8 0.3 1.0 C4' B:A42 4.9 0.8 1.0

Manganese binding site 8 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn102 b:0.2 occ:1.00 OP2 C:U41 2.5 0.9 1.0 OP2 B:C31 2.8 0.1 1.0 C5' C:U41 3.3 0.8 1.0 O3' B:U30 3.8 0.3 1.0 P C:U41 3.9 0.8 1.0 P B:C31 3.9 0.5 1.0 O5' C:U41 4.1 0.7 1.0 C4' C:U41 4.3 0.8 1.0 OP1 B:C31 4.8 0.2 1.0 OP1 C:U41 4.9 0.5 1.0 O3' C:C40 4.9 0.5 1.0

Manganese binding site 9 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn103 b:0.2 occ:1.00 OP1 C:C31 2.2 0.2 1.0 N1 C:A6 3.1 0.6 1.0 P C:C31 3.2 0.3 1.0 C2 C:A6 3.4 0.0 1.0 OP2 C:C31 3.5 0.6 1.0 O3' C:U30 3.9 0.1 1.0 OP2 C:U4 4.2 0.8 1.0 C6 C:A6 4.2 0.2 1.0 C2' C:U30 4.4 0.1 1.0 OP1 C:U4 4.4 0.5 1.0 O5' C:C31 4.5 0.1 1.0 C3' C:U30 4.5 0.6 1.0 N6 C:A6 4.6 0.8 1.0 N3 C:A6 4.7 0.9 1.0 O2' C:U30 4.8 0.3 1.0 P C:U4 4.9 0.2 1.0 C5' C:C31 4.9 0.9 1.0

Manganese binding site 10 out of 11 in the Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of the in-Line Aligned ENV22 Twister Ribozyme Soaked with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn104 b:0.2 occ:1.00 OP2 C:A42 2.2 0.5 1.0 OP2 C:A43 2.4 0.2 1.0 P C:A42 3.5 0.9 1.0 O5' C:A42 3.6 0.6 1.0 OP2 C:C39 3.8 0.2 1.0 P C:A43 3.8 0.6 1.0 OP2 C:C40 4.3 0.5 1.0 N7 C:A43 4.4 0.1 1.0 O3' C:U41 4.4 0.6 1.0 OP1 C:A43 4.5 0.8 1.0 O5' C:A43 4.6 0.5 1.0 O2' C:U41 4.6 0.8 1.0 OP1 C:A42 4.6 0.0 1.0 C8 C:A43 4.7 0.6 1.0 P C:C39 4.8 0.5 1.0 OP1 C:C39 4.8 0.5 1.0 O3' C:A42 4.9 0.1 1.0 C5' C:A42 4.9 0.8 1.0 C3' C:A42 4.9 0.6 1.0

A.Ren, M.Kosutic, K.R.Rajashankar, M.Frener, T.Santner, E.Westhof, R.Micura, D.J.Patel. In-Line Alignment and Mg(2+) Coordination at the Cleavage Site of the ENV22 Twister Ribozyme. Nat Commun V. 5 5534 2014.
ISSN: ESSN 2041-1723
PubMed: 25410397
DOI: 10.1038/NCOMMS6534