Atomistry » Manganese » PDB 5hzz-5jpf » 5izo
Atomistry »
  Manganese »
    PDB 5hzz-5jpf »
      5izo »

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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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

Go back to Manganese Binding Sites List in 5izo
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: Sat Aug 16 18:14:30 2025

Last articles

Ni in 5FPZ
Ni in 5FPX
Ni in 5FM8
Ni in 5FLH
Ni in 5FLE
Ni in 5FJH
Ni in 5FJK
Ni in 5F5I
Ni in 5ERL
Ni in 5FG6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy