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Manganese in PDB 6tfh: Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+)

Protein crystallography data

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh 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) 48.49 / 2.95
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 56.935, 58.360, 193.968, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 26.6

Other elements in 6tfh:

The structure of Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) also contains other interesting chemical elements:

Bromine (Br) 1 atom
Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) (pdb code 6tfh). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 9 binding sites of Manganese where determined in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+), PDB code: 6tfh:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Manganese binding site 1 out of 9 in 6tfh

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Manganese binding site 1 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn101

b:0.5
occ:1.00
 OP2 A:A11 2.2 86.8 1.0
P A:A11 3.7 71.8 1.0
OP1 A:A10 3.9 78.8 1.0
C3' A:A10 3.9 84.9 1.0
O5' A:A11 4.2 85.2 1.0
C5' A:A11 4.2 0.9 1.0
O3' A:A10 4.3 85.4 1.0
C4' A:A10 4.6 91.7 1.0
O4' A:A11 4.7 0.4 1.0
C5' A:A10 4.7 85.1 1.0
OP1 A:A11 4.7 63.9 1.0
O5' A:A10 4.9 89.0 1.0
C5 A:A11 4.9 0.6 1.0
P A:A10 4.9 93.8 1.0
C4 A:A11 5.0 0.6 1.0
N7 A:A11 5.0 0.5 1.0

Manganese binding site 2 out of 9 in 6tfh

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Manganese binding site 2 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn102

b:0.7
occ:1.00
 N7 A:G23 2.4 83.4 1.0
O6 A:G23 3.4 85.7 1.0
C8 A:G23 3.4 82.0 1.0
C5 A:G23 3.4 74.4 1.0
C6 A:G23 3.8 75.0 1.0
OP2 A:G23 4.2 0.2 1.0
C5 A:U22 4.2 94.5 1.0
N9 A:G23 4.6 84.2 1.0
C4 A:G23 4.6 74.1 1.0
OP2 A:U22 4.6 92.9 1.0
C6 A:U22 4.6 81.2 1.0
C4 A:U22 4.7 90.6 1.0
N7 A:G24 4.7 91.8 1.0
O4 A:U22 4.9 78.5 1.0

Manganese binding site 3 out of 9 in 6tfh

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Manganese binding site 3 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn103

b:0.6
occ:1.00
 OP1 A:A8 2.3 0.1 1.0
O1N A:NAD110 2.5 0.4 1.0
O2A A:NAD110 2.5 83.7 1.0
H52N A:NAD110 3.2 0.1 1.0
P A:A8 3.3 0.0 1.0
OP2 A:A8 3.5 85.5 1.0
OP2 A:C15 3.8 93.8 1.0
PN A:NAD110 3.8 0.2 1.0
PA A:NAD110 3.9 0.5 1.0
C5D A:NAD110 4.1 0.4 1.0
C5' A:A7 4.1 0.5 1.0
OP1 A:C14 4.1 0.8 1.0
OP1 A:C15 4.3 88.9 1.0
O5D A:NAD110 4.3 0.8 1.0
C3' A:A7 4.4 0.0 1.0
O3' A:A7 4.4 88.6 1.0
O3 A:NAD110 4.4 0.7 1.0
C4' A:A7 4.4 0.9 1.0
O5' A:A8 4.5 0.6 1.0
C5' A:A8 4.5 0.9 1.0
P A:C15 4.6 82.4 1.0
H51N A:NAD110 4.7 0.1 1.0
OP1 A:A7 4.8 96.1 1.0
O5B A:NAD110 4.8 0.1 1.0
C4D A:NAD110 4.8 0.1 1.0
O1A A:NAD110 4.9 0.8 1.0
O2N A:NAD110 5.0 0.5 1.0

Manganese binding site 4 out of 9 in 6tfh

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Manganese binding site 4 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn104

b:0.6
occ:1.00
 OP2 A:A8 2.2 85.5 1.0
OP2 A:C9 2.2 90.0 1.0
N7 A:A10 2.3 88.4 1.0
N6 A:A10 2.9 0.9 1.0
C5 A:A10 3.1 93.9 1.0
C6 A:A10 3.3 0.1 1.0
C8 A:A10 3.4 98.7 1.0
P A:A8 3.6 0.0 1.0
P A:C9 3.6 92.4 1.0
OP2 A:C14 3.7 79.3 1.0
O5' A:A8 4.0 0.6 1.0
OP1 A:C9 4.2 0.6 1.0
C5' A:A8 4.3 0.9 1.0
C4 A:A10 4.3 95.0 1.0
OP2 A:C15 4.3 93.8 1.0
O3' A:A7 4.5 88.6 1.0
N9 A:A10 4.5 97.9 1.0
O5' A:C9 4.5 85.5 1.0
O3' A:A8 4.5 75.9 1.0
OP1 A:A8 4.6 0.1 1.0
P A:C14 4.7 91.5 1.0
N1 A:A10 4.7 94.6 1.0
OP1 A:C14 4.7 0.8 1.0
C5 A:C9 4.8 0.4 1.0
C3' A:A8 4.8 77.1 1.0

Manganese binding site 5 out of 9 in 6tfh

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Manganese binding site 5 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn105

b:0.0
occ:1.00
 N7 A:G32 2.3 0.8 1.0
C8 A:G32 3.2 0.5 1.0
C5 A:G32 3.4 0.6 1.0
O6 A:G32 3.8 0.8 1.0
OP2 A:A31 3.9 0.7 1.0
C6 A:G32 3.9 0.1 1.0
N9 A:G32 4.4 0.1 1.0
C4 A:G32 4.5 0.3 1.0
OP2 A:G32 4.6 0.7 1.0
P A:A31 4.9 0.6 1.0
OP1 A:A31 5.0 0.5 1.0

Manganese binding site 6 out of 9 in 6tfh

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Manganese binding site 6 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn106

b:0.3
occ:1.00
 N7 A:G19 2.1 0.9 1.0
C5 A:G19 2.9 0.8 1.0
O6 A:G19 2.9 0.7 1.0
C6 A:G19 3.2 0.1 1.0
C8 A:G19 3.2 0.4 1.0
C4 A:G19 4.1 0.1 1.0
N9 A:G19 4.3 0.8 1.0
N1 A:G19 4.5 0.1 1.0
N7 A:A18 4.7 90.4 1.0
OP2 A:G19 4.7 94.7 1.0
C5 A:A18 5.0 89.4 1.0

Manganese binding site 7 out of 9 in 6tfh

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Manganese binding site 7 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn107

b:0.6
occ:1.00
 OP2 A:A7 2.4 0.9 1.0
OP1 A:G16 3.6 0.7 1.0
P A:A7 3.7 89.7 1.0
O5' A:A7 3.8 93.6 1.0
OP2 A:G16 4.0 87.0 1.0
C8 A:A7 4.2 98.3 1.0
P A:G16 4.3 84.4 1.0
OP1 A:C15 4.4 88.9 1.0
N7 A:A7 4.5 0.2 1.0
C2' A:A7 4.6 0.4 1.0
OP1 A:A7 4.6 96.1 1.0
O3' A:C6 4.9 92.4 1.0

Manganese binding site 8 out of 9 in 6tfh

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Manganese binding site 8 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn108

b:0.6
occ:1.00
 N7 A:G38 3.4 88.4 1.0
O6 A:G38 4.0 69.2 1.0
C5 A:G38 4.2 80.4 1.0
C8 A:G38 4.3 76.4 1.0
O2' A:G36 4.4 0.2 1.0
C6 A:G38 4.5 68.8 1.0
C4 A:G36 4.7 91.9 1.0
C2' A:G36 4.8 0.3 1.0
N3 A:G36 4.8 76.7 1.0
C5 A:G36 4.8 91.9 1.0
N9 A:G36 5.0 98.7 1.0

Manganese binding site 9 out of 9 in 6tfh

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Manganese binding site 9 out of 9 in the Crystal Structure of the Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (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 Adp-Binding Domain of the Nad+ Riboswitch with Nicotinamide Adenine Dinucleotide, Reduced (Nadh); Soaking with Manganese(II) (MN2+) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn109

b:0.4
occ:1.00
 N7 A:G47 2.5 0.1 1.0
C5 A:G47 3.2 1.0 1.0
O6 A:G47 3.3 0.6 1.0
C8 A:G47 3.5 0.9 1.0
C6 A:G47 3.5 0.8 1.0
OP2 A:U46 4.2 0.6 1.0
C5 A:U46 4.2 0.9 1.0
OP2 A:G47 4.4 0.3 1.0
C4 A:G47 4.4 0.3 1.0
C4 A:U46 4.4 0.5 1.0
N9 A:G47 4.5 0.2 1.0
O4 A:U46 4.5 0.5 1.0
N7 A:G48 4.5 0.2 1.0
C6 A:U46 4.7 0.5 1.0
N1 A:G47 4.8 0.1 1.0

Reference:

L.Huang, J.Wang, D.M.J.Lilley. Structure and Ligand Binding of the Adp-Binding Domain of the Nad+ Riboswitch. Rna V. 26 878 2020.
ISSN: ESSN 1469-9001
PubMed: 32295864
DOI: 10.1261/RNA.074898.120
Page generated: Sun Oct 6 07:12:03 2024

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