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Manganese in PDB 4y1i: Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+

Protein crystallography data

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+, PDB code: 4y1i was solved by I.R.Price, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.90 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 67.285, 127.881, 115.324, 90.00, 93.37, 90.00
R / Rfree (%) 19.3 / 22.4

Other elements in 4y1i:

The structure of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ also contains other interesting chemical elements:

Magnesium (Mg) 25 atoms
Barium (Ba) 19 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ (pdb code 4y1i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+, PDB code: 4y1i:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 4y1i

Go back to Manganese Binding Sites List in 4y1i
Manganese binding site 1 out of 3 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn224

b:67.8
occ:1.00
OP1 A:G9 2.2 43.5 1.0
OP1 A:U44 2.2 64.2 1.0
N7 A:A41 2.3 46.2 1.0
OP2 A:C45 2.3 40.6 1.0
OP2 A:U39 2.3 65.3 1.0
OP2 A:C40 2.3 43.9 1.0
C8 A:A41 3.1 52.1 1.0
C5 A:A41 3.3 39.7 1.0
P A:U44 3.5 53.7 1.0
P A:C45 3.6 55.2 1.0
N6 A:A41 3.6 54.5 1.0
C5' A:U39 3.7 62.8 1.0
P A:U39 3.7 49.4 1.0
P A:G9 3.7 50.7 1.0
P A:C40 3.8 58.3 1.0
C6 A:A41 3.9 48.2 1.0
O5' A:U39 4.0 43.6 1.0
OP2 A:U44 4.0 43.8 1.0
OP1 A:C45 4.1 38.7 1.0
O5' A:U44 4.1 35.5 1.0
O5' A:G9 4.3 56.3 1.0
N9 A:A41 4.3 46.6 1.0
C4 A:A41 4.4 38.7 1.0
C5' A:U44 4.4 47.8 1.0
O3' A:G8 4.4 58.8 1.0
C5 A:C40 4.5 46.5 1.0
O5' A:C40 4.5 60.1 1.0
OP1 A:U39 4.6 57.0 1.0
O3' A:U44 4.6 46.3 1.0
O5' A:C45 4.6 43.4 1.0
OP1 A:C40 4.6 81.6 1.0
OP2 A:G9 4.7 50.8 1.0
O3' A:U43 4.7 64.5 1.0
O3' A:G38 4.7 41.4 1.0
O3' A:U39 4.8 61.7 1.0
C4' A:U39 4.8 52.6 1.0
C3' A:U44 4.9 45.8 1.0
C6 A:C40 5.0 50.9 1.0
C3' A:U39 5.0 60.7 1.0

Manganese binding site 2 out of 3 in 4y1i

Go back to Manganese Binding Sites List in 4y1i
Manganese binding site 2 out of 3 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn225

b:0.4
occ:1.00
N7 A:G81 2.3 64.8 1.0
O A:HOH314 3.0 52.1 1.0
O6 A:G81 3.1 60.2 1.0
C5 A:G81 3.2 56.0 1.0
C8 A:G81 3.4 66.9 1.0
C6 A:G81 3.5 60.9 1.0
C4 A:G81 4.4 57.5 1.0
OP2 A:A80 4.4 64.6 1.0
N9 A:G81 4.5 66.4 1.0
O4 A:U82 4.5 60.3 1.0
N1 A:G77 4.6 58.7 1.0
N2 A:G77 4.8 59.5 1.0
N1 A:G81 4.9 58.2 1.0

Manganese binding site 3 out of 3 in 4y1i

Go back to Manganese Binding Sites List in 4y1i
Manganese binding site 3 out of 3 in the Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Lactococcus Lactis Yybp-Ykoy Mn Riboswitch Bound to MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn223

b:89.5
occ:1.00
OP2 B:C40 2.1 57.5 1.0
OP2 B:C45 2.2 69.8 1.0
OP1 B:U44 2.2 83.8 1.0
OP2 B:U39 2.3 72.1 1.0
N7 B:A41 2.4 74.5 1.0
OP1 B:G9 2.4 63.5 1.0
C8 B:A41 3.3 79.6 1.0
P B:C45 3.4 72.0 1.0
P B:U39 3.4 65.7 1.0
C5 B:A41 3.5 74.1 1.0
P B:G9 3.5 59.6 1.0
P B:C40 3.6 60.0 1.0
P B:U44 3.7 74.4 1.0
N6 B:A41 3.7 67.2 1.0
OP1 B:C45 3.8 79.9 1.0
O B:HOH328 3.8 66.8 1.0
OP1 B:U39 3.9 56.1 1.0
OP2 B:G9 3.9 52.0 1.0
C6 B:A41 4.0 67.5 1.0
C5' B:U39 4.1 56.3 1.0
O3' B:G8 4.1 68.0 1.0
O5' B:U39 4.1 63.9 1.0
O3' B:U39 4.3 51.1 1.0
O3' B:U44 4.3 74.8 1.0
OP1 B:C40 4.3 69.7 1.0
OP2 B:U44 4.4 67.5 1.0
O5' B:U44 4.5 76.9 1.0
N9 B:A41 4.5 79.7 1.0
O5' B:C45 4.5 73.1 1.0
O5' B:C40 4.5 59.8 1.0
MG B:MG206 4.6 50.0 1.0
C3' B:U39 4.6 66.9 1.0
O3' B:U43 4.6 80.0 1.0
C4 B:A41 4.6 75.3 1.0
C5' B:U44 4.6 79.3 1.0
C5 B:C40 4.7 70.2 1.0
O3' B:G38 4.7 55.3 1.0
C4' B:U39 4.9 62.1 1.0
C3' B:U44 4.9 80.4 1.0
O5' B:G9 4.9 58.5 1.0

Reference:

I.R.Price, A.Gaballa, F.Ding, J.D.Helmann, A.Ke. Mn(2+)-Sensing Mechanisms of Yybp-Ykoy Orphan Riboswitches. Mol.Cell V. 57 1110 2015.
ISSN: ISSN 1097-2765
PubMed: 25794619
DOI: 10.1016/J.MOLCEL.2015.02.016
Page generated: Tue Dec 15 04:33:32 2020

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