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Manganese in PDB 5izo: Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site

Enzymatic activity of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site

All present enzymatic activity of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site:
3.1.3.7;

Protein crystallography data

The structure of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site, PDB code: 5izo was solved by B.J.Schmier, A.Malhotra, C.M.Nelersa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.34 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.652, 119.644, 124.135, 90.00, 91.59, 90.00
R / Rfree (%) 21.2 / 26.7

Manganese Binding Sites:

The binding sites of Manganese atom in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site (pdb code 5izo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site, PDB code: 5izo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5izo

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Manganese binding site 1 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:41.4
occ:1.00
 O1 A:PO4403 2.1 48.4 1.0
OD1 A:ASP24 2.3 40.3 1.0
NE2 A:HIS20 2.3 43.7 1.0
OD2 A:ASP80 2.3 33.6 1.0
O A:HOH502 2.4 39.0 1.0
OD2 A:ASP24 2.5 37.2 1.0
CG A:ASP24 2.7 35.5 1.0
CD2 A:HIS20 3.1 40.8 1.0
CG A:ASP80 3.2 38.5 1.0
P A:PO4403 3.3 58.4 1.0
CE1 A:HIS20 3.4 39.4 1.0
OD1 A:ASP80 3.5 39.5 1.0
O3 A:PO4403 3.6 59.6 1.0
MN A:MN402 3.8 38.4 1.0
O2 A:PO4403 3.8 57.0 1.0
N A:ALA27 4.2 35.5 1.0
CB A:ASP24 4.3 35.8 1.0
CG A:HIS20 4.3 41.0 1.0
CB A:ASP26 4.4 35.8 1.0
ND1 A:HIS20 4.4 40.1 1.0
O A:ASP80 4.4 37.8 1.0
CB A:ASP80 4.5 34.1 1.0
O4 A:PO4403 4.5 54.2 1.0
CB A:ALA27 4.5 36.1 1.0
OD1 A:ASP156 4.7 39.2 1.0
N A:ASP24 4.7 34.9 1.0
CA A:ALA27 4.8 34.5 1.0
OD2 A:ASP26 4.8 34.1 1.0
O A:HOH545 4.9 30.2 1.0
O A:HOH535 4.9 41.0 1.0
C A:ASP26 5.0 36.0 1.0
CA A:ASP24 5.0 36.3 1.0

Manganese binding site 2 out of 8 in 5izo

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Manganese binding site 2 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:38.4
occ:1.00
 OD2 A:ASP26 2.0 34.1 1.0
O A:HOH551 2.0 48.0 1.0
O A:HOH545 2.2 30.2 1.0
O A:HOH502 2.3 39.0 1.0
OD1 A:ASP80 2.3 39.5 1.0
OD2 A:ASP156 2.3 45.9 1.0
CG A:ASP26 3.0 37.7 1.0
CG A:ASP80 3.0 38.5 1.0
CG A:ASP156 3.3 40.6 1.0
OD2 A:ASP80 3.3 33.6 1.0
CB A:ASP26 3.3 35.8 1.0
OD1 A:ASP156 3.5 39.2 1.0
MN A:MN401 3.8 41.4 1.0
O1 A:PO4403 4.0 48.4 1.0
O3 A:PO4403 4.1 59.6 1.0
N A:VAL123 4.1 33.4 1.0
OD1 A:ASP26 4.2 34.1 1.0
CE1 A:HIS104 4.2 41.1 1.0
CB A:ASP80 4.3 34.1 1.0
CG2 A:VAL123 4.4 32.8 1.0
CA A:SER122 4.4 33.6 1.0
NE2 A:HIS104 4.5 42.1 1.0
CB A:SER122 4.6 32.7 1.0
CB A:ASP156 4.6 38.5 1.0
P A:PO4403 4.7 58.4 1.0
CA A:ASP26 4.8 35.3 1.0
C A:SER122 4.8 33.4 1.0
CB A:VAL123 5.0 33.1 1.0
CA A:ASP80 5.0 35.1 1.0

Manganese binding site 3 out of 8 in 5izo

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Manganese binding site 3 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:38.8
occ:1.00
 OD2 B:ASP26 2.2 27.9 1.0
O B:HOH521 2.2 32.1 1.0
OD2 B:ASP156 2.2 34.7 1.0
O B:HOH606 2.2 40.6 1.0
OD1 B:ASP80 2.3 32.4 1.0
O B:HOH620 2.5 41.5 1.0
CG B:ASP80 3.0 32.5 1.0
CG B:ASP26 3.1 32.2 1.0
CG B:ASP156 3.2 36.6 1.0
OD2 B:ASP80 3.2 32.6 1.0
OD1 B:ASP156 3.4 37.7 1.0
CB B:ASP26 3.5 29.7 1.0
MN B:MN402 3.7 37.2 1.0
O B:HOH578 4.1 43.7 1.0
O3 B:PO4403 4.1 59.0 1.0
O2 B:PO4403 4.1 40.5 1.0
CE1 B:HIS104 4.2 39.1 1.0
N B:VAL123 4.3 31.7 1.0
OD1 B:ASP26 4.3 32.0 1.0
CA B:SER122 4.4 34.0 1.0
CB B:ASP80 4.4 29.0 1.0
CB B:SER122 4.6 32.0 1.0
CB B:ASP156 4.6 35.2 1.0
P B:PO4403 4.7 58.5 1.0
NE2 B:HIS104 4.7 39.0 1.0
CG2 B:VAL123 4.8 29.6 1.0
C B:SER122 4.9 33.7 1.0
CA B:ASP26 4.9 30.4 1.0
O B:HOH626 5.0 56.2 1.0

Manganese binding site 4 out of 8 in 5izo

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Manganese binding site 4 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:37.2
occ:1.00
 OD2 B:ASP80 2.1 32.6 1.0
O2 B:PO4403 2.1 40.5 1.0
O B:HOH521 2.2 32.1 1.0
OD2 B:ASP24 2.2 37.3 1.0
NE2 B:HIS20 2.3 30.9 1.0
OD1 B:ASP24 2.5 36.3 1.0
CG B:ASP24 2.7 32.4 1.0
CG B:ASP80 3.1 32.5 1.0
CD2 B:HIS20 3.2 30.6 1.0
CE1 B:HIS20 3.2 29.1 1.0
P B:PO4403 3.3 58.5 1.0
OD1 B:ASP80 3.5 32.4 1.0
O3 B:PO4403 3.6 59.0 1.0
MN B:MN401 3.7 38.8 1.0
O1 B:PO4403 3.9 57.1 1.0
CB B:ASP24 4.2 33.9 1.0
N B:ALA27 4.2 29.4 1.0
ND1 B:HIS20 4.3 32.3 1.0
CG B:HIS20 4.3 31.6 1.0
O B:ASP80 4.4 31.1 1.0
CB B:ASP26 4.4 29.7 1.0
CB B:ALA27 4.4 27.6 1.0
CB B:ASP80 4.4 29.0 1.0
O4 B:PO4403 4.5 54.8 1.0
O B:HOH560 4.6 59.2 1.0
OD1 B:ASP156 4.6 37.7 1.0
N B:ASP24 4.6 34.2 1.0
OD2 B:ASP26 4.7 27.9 1.0
CA B:ALA27 4.7 27.7 1.0
O B:HOH606 4.7 40.6 1.0
C B:ASP26 4.8 29.8 1.0
CA B:ASP24 5.0 33.0 1.0

Manganese binding site 5 out of 8 in 5izo

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Manganese binding site 5 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:39.9
occ:1.00
 O C:HOH504 2.1 31.1 1.0
OD1 C:ASP80 2.2 33.8 1.0
OD2 C:ASP26 2.2 34.6 1.0
O C:HOH614 2.3 38.0 1.0
O C:HOH601 2.3 30.0 1.0
OD2 C:ASP156 2.5 38.4 1.0
CG C:ASP80 3.0 33.6 1.0
CG C:ASP26 3.1 37.2 1.0
OD2 C:ASP80 3.2 29.9 1.0
CB C:ASP26 3.4 32.8 1.0
CG C:ASP156 3.4 36.3 1.0
OD1 C:ASP156 3.6 41.8 1.0
MN C:MN402 3.8 35.8 1.0
O4 C:PO4403 3.9 54.0 1.0
N C:VAL123 4.2 28.7 1.0
CE1 C:HIS104 4.3 35.8 1.0
OD1 C:ASP26 4.3 36.0 1.0
CG2 C:VAL123 4.4 32.0 1.0
CB C:ASP80 4.4 31.4 1.0
CA C:SER122 4.5 31.8 1.0
NE2 C:HIS104 4.7 38.0 1.0
CB C:ASP156 4.8 36.6 1.0
CA C:ASP26 4.8 32.8 1.0
C C:SER122 4.9 31.4 1.0
O3 C:PO4403 4.9 58.0 1.0
CB C:VAL123 4.9 29.6 1.0
CB C:SER122 4.9 31.7 1.0
P C:PO4403 4.9 61.2 1.0

Manganese binding site 6 out of 8 in 5izo

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Manganese binding site 6 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:35.8
occ:1.00
 OD2 C:ASP80 2.1 29.9 1.0
O4 C:PO4403 2.2 54.0 1.0
O C:HOH504 2.2 31.1 1.0
OD2 C:ASP24 2.3 39.8 1.0
NE2 C:HIS20 2.4 27.9 1.0
OD1 C:ASP24 2.6 35.7 1.0
CG C:ASP24 2.8 40.8 1.0
CG C:ASP80 3.2 33.6 1.0
CD2 C:HIS20 3.2 30.2 1.0
CE1 C:HIS20 3.4 23.8 1.0
P C:PO4403 3.5 61.2 1.0
OD1 C:ASP80 3.6 33.8 1.0
MN C:MN401 3.8 39.9 1.0
O1 C:PO4403 4.0 57.5 1.0
O2 C:PO4403 4.2 58.3 1.0
N C:ALA27 4.2 33.0 1.0
CB C:ASP24 4.3 36.0 1.0
CB C:ASP80 4.4 31.4 1.0
CG C:HIS20 4.4 31.1 1.0
CB C:ASP26 4.4 32.8 1.0
ND1 C:HIS20 4.4 28.1 1.0
O C:ASP80 4.5 36.8 1.0
CB C:ALA27 4.5 31.0 1.0
O3 C:PO4403 4.6 58.0 1.0
CA C:ALA27 4.7 33.4 1.0
N C:ASP24 4.8 35.2 1.0
C C:ASP26 4.9 33.2 1.0
OD1 C:ASP156 4.9 41.8 1.0
OD2 C:ASP26 4.9 34.6 1.0
CE1 C:HIS104 5.0 35.8 1.0

Manganese binding site 7 out of 8 in 5izo

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Manganese binding site 7 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:42.9
occ:1.00
 OD1 D:ASP80 2.0 37.6 1.0
O D:HOH505 2.1 34.3 1.0
O D:HOH566 2.3 43.3 1.0
O D:HOH573 2.3 38.8 1.0
OD2 D:ASP26 2.3 43.5 1.0
OD2 D:ASP156 2.3 42.6 1.0
CG D:ASP80 3.1 35.3 1.0
CG D:ASP26 3.1 41.9 1.0
CG D:ASP156 3.1 38.8 1.0
OD1 D:ASP156 3.3 45.5 1.0
CB D:ASP26 3.4 41.3 1.0
OD2 D:ASP80 3.4 30.4 1.0
O2 D:PO4403 3.9 53.7 1.0
MN D:MN402 3.9 44.1 1.0
N D:VAL123 4.1 39.4 1.0
OD1 D:ASP26 4.2 41.0 1.0
CA D:SER122 4.2 39.8 1.0
CE1 D:HIS104 4.3 51.8 1.0
CB D:ASP80 4.3 38.4 1.0
CB D:SER122 4.4 39.2 1.0
O3 D:PO4403 4.4 54.5 1.0
CG2 D:VAL123 4.4 38.4 1.0
CB D:ASP156 4.5 36.3 1.0
NE2 D:HIS104 4.6 53.1 1.0
C D:SER122 4.7 39.5 1.0
P D:PO4403 4.7 58.3 1.0
CA D:ASP26 4.8 39.0 1.0
CB D:VAL123 5.0 38.9 1.0
C D:ASP26 5.0 39.4 1.0

Manganese binding site 8 out of 8 in 5izo

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Manganese binding site 8 out of 8 in the Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Bacillus Nanornase A (H103A) + 2 Divalent Cations + PO4 at the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:44.1
occ:1.00
 OD2 D:ASP80 2.1 30.4 1.0
O2 D:PO4403 2.1 53.7 1.0
O D:HOH505 2.1 34.3 1.0
NE2 D:HIS20 2.2 43.5 1.0
OD1 D:ASP24 2.3 45.5 1.0
OD2 D:ASP24 2.3 44.6 1.0
CG D:ASP24 2.6 43.9 1.0
CD2 D:HIS20 3.1 42.5 1.0
CG D:ASP80 3.2 35.3 1.0
CE1 D:HIS20 3.3 46.6 1.0
P D:PO4403 3.3 58.3 1.0
OD1 D:ASP80 3.6 37.6 1.0
O1 D:PO4403 3.7 60.7 1.0
O3 D:PO4403 3.8 54.5 1.0
MN D:MN401 3.9 42.9 1.0
CB D:ASP24 4.1 42.5 1.0
CB D:ALA27 4.1 38.1 1.0
N D:ALA27 4.1 38.4 1.0
O D:HOH511 4.2 50.4 1.0
CG D:HIS20 4.3 44.0 1.0
ND1 D:HIS20 4.3 45.1 1.0
CB D:ASP80 4.4 38.4 1.0
O D:ASP80 4.5 40.1 1.0
CA D:ALA27 4.5 38.7 1.0
CB D:ASP26 4.6 41.3 1.0
O4 D:PO4403 4.6 57.7 1.0
OD1 D:ASP156 4.6 45.5 1.0
N D:ASP24 4.6 42.5 1.0
O D:HOH566 4.7 43.3 1.0
OD2 D:ASP26 4.8 43.5 1.0
C D:ASP26 4.8 39.4 1.0
CA D:ASP24 4.9 42.5 1.0
O D:HOH527 4.9 42.1 1.0

Reference:

B.J.Schmier, C.M.Nelersa, A.Malhotra. Structural Basis For the Bidirectional Activity of Bacillus Nanornase Nrna. Sci Rep V. 7 11085 2017.
ISSN: ESSN 2045-2322
PubMed: 28894100
DOI: 10.1038/S41598-017-09403-X
Page generated: Tue Dec 15 04:42:10 2020

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