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Manganese in PDB 8brp: Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.

Protein crystallography data

The structure of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp., PDB code: 8brp was solved by S.Mordhorst, T.Badmann, N.M.Boesch, B.I.Morinaka, H.Rach, J.Piel, M.Groll, A.L.Vagstadt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.29, 154.42, 174.92, 90, 90, 90
R / Rfree (%) 19.6 / 23.3

Other elements in 8brp:

The structure of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. (pdb code 8brp). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp., PDB code: 8brp:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 1 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn801

b:42.2
occ:1.00
 O A:ACT803 1.9 45.0 1.0
OD2 A:ASP167 2.0 40.9 1.0
ND1 A:HIS41 2.1 42.0 1.0
OD1 A:ASP39 2.2 37.0 1.0
OD1 A:ASP167 2.4 42.9 1.0
CG A:ASP167 2.5 41.4 1.0
CE1 A:HIS41 2.8 41.3 1.0
C A:ACT803 3.0 44.9 1.0
CG A:ASP39 3.1 38.3 1.0
OD2 A:ASP165 3.1 42.8 1.0
CG A:HIS41 3.3 40.5 1.0
OD2 A:ASP39 3.3 39.2 1.0
MN A:MN802 3.5 39.9 1.0
CG A:ASP165 3.5 41.5 1.0
N A:HIS41 3.8 38.8 1.0
CH3 A:ACT803 3.8 44.6 1.0
CB A:HIS41 3.9 39.6 1.0
OXT A:ACT803 3.9 44.7 1.0
CB A:ASP167 4.0 42.0 1.0
NE2 A:HIS41 4.0 40.3 1.0
N A:GLU40 4.1 38.9 1.0
CB A:ASP165 4.1 40.7 1.0
OD1 A:ASP165 4.1 43.0 1.0
CD2 A:HIS41 4.3 40.4 1.0
CB A:GLU40 4.4 40.4 1.0
CA A:HIS41 4.4 39.1 1.0
CB A:ASP39 4.4 37.9 1.0
CA A:GLU40 4.6 39.5 1.0
C A:GLU40 4.6 39.2 1.0
O A:HIS41 4.9 38.2 1.0
CA A:ASP39 4.9 38.0 1.0
C A:ASP39 4.9 38.3 1.0
OD2 A:ASP43 4.9 41.1 1.0
CA A:ASP167 4.9 42.3 1.0

Manganese binding site 2 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 2 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn802

b:39.9
occ:1.00
 OXT A:ACT803 2.0 44.7 1.0
OD2 A:ASP43 2.0 41.1 1.0
OD2 A:ASP39 2.1 39.2 1.0
O A:ACT803 2.1 45.0 1.0
ND1 A:HIS12 2.1 39.9 1.0
C A:ACT803 2.2 44.9 1.0
CE1 A:HIS12 2.9 40.6 1.0
OD2 A:ASP165 2.9 42.8 1.0
CG A:ASP43 3.1 38.7 1.0
CG A:ASP39 3.1 38.3 1.0
CG A:HIS12 3.3 38.2 1.0
OD1 A:ASP43 3.5 39.8 1.0
MN A:MN801 3.5 42.2 1.0
OD1 A:ASP39 3.6 37.0 1.0
CH3 A:ACT803 3.7 44.6 1.0
CB A:HIS12 3.8 37.3 1.0
CG A:ASP165 3.8 41.5 1.0
CB A:ASP165 4.0 40.7 1.0
O A:ILE73 4.0 35.2 1.0
NE2 A:HIS12 4.1 39.5 1.0
CE1 A:HIS37 4.3 36.4 1.0
CD2 A:HIS12 4.3 38.2 1.0
CB A:ASP43 4.4 37.4 1.0
CB A:ASP39 4.4 37.9 1.0
CE2 A:PHE76 4.5 33.4 1.0
O A:HIS41 4.6 38.2 1.0
CZ A:PHE76 4.6 33.2 1.0
OD2 A:ASP167 4.8 40.9 1.0
ND1 A:HIS41 4.9 42.0 1.0
NE2 A:HIS37 4.9 37.3 1.0
O A:HOH910 5.0 40.4 1.0

Manganese binding site 3 out of 8 in 8brp

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Manganese binding site 3 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn801

b:42.5
occ:1.00
 OD2 B:ASP167 1.9 39.4 1.0
OXT B:ACT803 1.9 47.0 1.0
OD1 B:ASP39 2.0 41.0 1.0
ND1 B:HIS41 2.4 38.6 1.0
CG B:ASP167 2.6 41.2 1.0
OD2 B:ASP165 2.6 44.5 1.0
OD1 B:ASP167 2.6 41.8 1.0
CG B:ASP39 2.9 40.4 1.0
CE1 B:HIS41 3.1 36.8 1.0
O B:HOH909 3.1 63.6 1.0
OD2 B:ASP39 3.1 41.9 1.0
C B:ACT803 3.1 47.8 1.0
CG B:ASP165 3.4 43.0 1.0
MN B:MN802 3.6 42.1 1.0
CG B:HIS41 3.6 39.0 1.0
O B:ACT803 3.9 47.8 1.0
N B:HIS41 3.9 39.4 1.0
N B:GLU40 4.0 39.5 1.0
CB B:ASP165 4.0 42.5 1.0
CB B:ASP167 4.0 41.9 1.0
CB B:HIS41 4.1 39.1 1.0
CH3 B:ACT803 4.1 47.8 1.0
OD1 B:ASP165 4.2 44.4 1.0
CB B:ASP39 4.3 40.2 1.0
NE2 B:HIS41 4.3 36.8 1.0
CB B:GLU40 4.4 39.4 1.0
CD2 B:HIS41 4.6 38.7 1.0
CA B:GLU40 4.6 39.3 1.0
CA B:HIS41 4.6 39.4 1.0
C B:GLU40 4.7 39.3 1.0
CA B:ASP39 4.7 40.1 1.0
C B:ASP39 4.8 40.0 1.0
O B:HIS41 4.9 41.1 1.0

Manganese binding site 4 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 4 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn802

b:42.1
occ:1.00
 OD2 B:ASP39 1.9 41.9 1.0
O B:ACT803 1.9 47.8 1.0
ND1 B:HIS12 2.0 41.9 1.0
OD2 B:ASP43 2.1 39.3 1.0
C B:ACT803 2.4 47.8 1.0
OXT B:ACT803 2.5 47.0 1.0
CE1 B:HIS12 2.7 41.0 1.0
OD2 B:ASP165 2.9 44.5 1.0
CG B:ASP39 3.1 40.4 1.0
CG B:ASP43 3.2 38.3 1.0
CG B:HIS12 3.2 40.7 1.0
MN B:MN801 3.6 42.5 1.0
OD1 B:ASP43 3.6 38.8 1.0
OD1 B:ASP39 3.6 41.0 1.0
CB B:HIS12 3.8 41.1 1.0
CH3 B:ACT803 3.8 47.8 1.0
CG B:ASP165 3.9 43.0 1.0
NE2 B:HIS12 4.0 39.3 1.0
CB B:ASP165 4.1 42.5 1.0
O B:ILE73 4.1 41.2 1.0
CD2 B:HIS12 4.2 39.9 1.0
CB B:ASP39 4.2 40.2 1.0
CE1 B:HIS37 4.3 39.5 1.0
O B:HOH909 4.4 63.6 1.0
CE2 B:PHE76 4.5 37.3 1.0
CB B:ASP43 4.5 38.4 1.0
CZ B:PHE76 4.5 37.6 1.0
O B:HIS41 4.7 41.1 1.0
O B:HOH903 4.8 38.6 1.0
OD1 B:ASP165 5.0 44.4 1.0

Manganese binding site 5 out of 8 in 8brp

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Manganese binding site 5 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn801

b:45.7
occ:1.00
 O C:ACT803 1.9 52.6 1.0
OD2 C:ASP167 1.9 45.4 1.0
OD1 C:ASP39 2.0 44.9 1.0
ND1 C:HIS41 2.2 43.8 1.0
CG C:ASP167 2.6 45.7 1.0
OD1 C:ASP167 2.6 44.0 1.0
CG C:ASP39 2.9 43.2 1.0
CE1 C:HIS41 3.0 43.9 1.0
C C:ACT803 3.1 53.1 1.0
OD2 C:ASP39 3.2 44.1 1.0
OD2 C:ASP165 3.3 52.2 1.0
CG C:HIS41 3.4 42.7 1.0
CG C:ASP165 3.5 50.7 1.0
MN C:MN802 3.6 51.0 1.0
N C:HIS41 3.8 42.3 1.0
CB C:HIS41 3.8 42.1 1.0
OD1 C:ASP165 3.9 53.2 1.0
OXT C:ACT803 3.9 51.9 1.0
CH3 C:ACT803 4.0 53.4 1.0
N C:GLU40 4.0 43.5 1.0
CB C:ASP167 4.0 46.4 1.0
CB C:ASP165 4.1 49.6 1.0
NE2 C:HIS41 4.2 43.9 1.0
CB C:ASP39 4.3 43.0 1.0
CD2 C:HIS41 4.4 43.1 1.0
CB C:GLU40 4.4 42.5 1.0
CA C:HIS41 4.4 42.2 1.0
CA C:GLU40 4.6 42.6 1.0
C C:GLU40 4.6 42.0 1.0
CA C:ASP39 4.8 42.9 1.0
C C:ASP39 4.8 43.1 1.0
O C:HIS41 4.8 42.4 1.0
OG C:SER264 4.9 54.6 1.0
OD2 C:ASP43 4.9 43.4 1.0

Manganese binding site 6 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 6 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn802

b:51.0
occ:1.00
 OD2 C:ASP39 1.9 44.1 1.0
ND1 C:HIS12 2.0 44.5 1.0
OXT C:ACT803 2.0 51.9 1.0
OD2 C:ASP43 2.2 43.4 1.0
C C:ACT803 2.4 53.1 1.0
O C:ACT803 2.4 52.6 1.0
OD2 C:ASP165 2.5 52.2 1.0
CE1 C:HIS12 2.7 43.5 1.0
CG C:ASP39 3.0 43.2 1.0
CG C:HIS12 3.1 45.8 1.0
CG C:ASP43 3.3 42.5 1.0
CG C:ASP165 3.5 50.7 1.0
MN C:MN801 3.6 45.7 1.0
OD1 C:ASP39 3.6 44.9 1.0
CB C:HIS12 3.7 47.9 1.0
CH3 C:ACT803 3.8 53.4 1.0
OD1 C:ASP43 3.8 43.0 1.0
CB C:ASP165 3.9 49.6 1.0
NE2 C:HIS12 3.9 43.5 1.0
CD2 C:HIS12 4.1 44.8 1.0
O C:ILE73 4.2 45.7 1.0
CB C:ASP39 4.2 43.0 1.0
CE1 C:HIS37 4.3 38.9 1.0
CB C:ASP43 4.6 42.2 1.0
OD1 C:ASP165 4.6 53.2 1.0
O C:HOH903 4.7 59.1 1.0
O C:HIS41 4.7 42.4 1.0
CZ C:PHE76 4.8 46.9 1.0
CE2 C:PHE76 4.8 46.9 1.0
NE2 C:HIS37 4.9 38.9 1.0
OD2 C:ASP167 4.9 45.4 1.0

Manganese binding site 7 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 7 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn801

b:47.9
occ:1.00
 OD2 D:ASP167 1.9 50.8 1.0
OXT D:ACT803 2.0 52.2 1.0
OD1 D:ASP39 2.0 45.1 1.0
ND1 D:HIS41 2.3 48.3 1.0
OD2 D:ASP165 2.5 44.6 1.0
CG D:ASP167 2.8 53.1 1.0
C D:ACT803 2.9 51.6 1.0
CG D:ASP39 2.9 46.1 1.0
CE1 D:HIS41 3.0 47.9 1.0
OD1 D:ASP167 3.1 55.4 1.0
OD2 D:ASP39 3.2 46.5 1.0
CG D:ASP165 3.3 48.0 1.0
MN D:MN802 3.4 48.9 1.0
CG D:HIS41 3.4 48.5 1.0
O D:ACT803 3.7 51.1 1.0
CH3 D:ACT803 3.8 51.4 1.0
CB D:HIS41 3.9 48.1 1.0
N D:HIS41 4.0 47.6 1.0
OD1 D:ASP165 4.0 50.6 1.0
CB D:ASP165 4.2 47.1 1.0
N D:GLU40 4.2 49.2 1.0
CB D:ASP167 4.2 54.0 1.0
NE2 D:HIS41 4.2 48.6 1.0
CB D:ASP39 4.3 45.8 1.0
CD2 D:HIS41 4.4 48.0 1.0
CA D:HIS41 4.6 48.1 1.0
CB D:GLU40 4.6 51.5 1.0
OD2 D:ASP43 4.8 46.2 1.0
CA D:GLU40 4.8 49.9 1.0
C D:GLU40 4.8 49.0 1.0
O D:HIS41 4.8 46.7 1.0
OG D:SER264 4.8 47.6 1.0
CA D:ASP39 4.8 46.8 1.0
C D:ASP39 4.9 48.0 1.0
ND1 D:HIS12 5.0 45.8 1.0

Manganese binding site 8 out of 8 in 8brp

Go back to Manganese Binding Sites List in 8brp
Manganese binding site 8 out of 8 in the Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Peptide Arginase Ospr From the Cyanobacterium Kamptonema Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn802

b:48.9
occ:1.00
 ND1 D:HIS12 1.9 45.8 1.0
O D:ACT803 2.0 51.1 1.0
OD2 D:ASP43 2.0 46.2 1.0
OD2 D:ASP39 2.2 46.5 1.0
OXT D:ACT803 2.2 52.2 1.0
C D:ACT803 2.3 51.6 1.0
OD2 D:ASP165 2.7 44.6 1.0
CE1 D:HIS12 2.8 45.0 1.0
CG D:HIS12 3.1 45.1 1.0
CG D:ASP43 3.1 44.5 1.0
CG D:ASP39 3.3 46.1 1.0
MN D:MN801 3.4 47.9 1.0
OD1 D:ASP43 3.5 46.0 1.0
CB D:HIS12 3.6 44.4 1.0
OD1 D:ASP39 3.7 45.1 1.0
CG D:ASP165 3.8 48.0 1.0
CH3 D:ACT803 3.8 51.4 1.0
NE2 D:HIS12 3.9 43.4 1.0
O D:ILE73 4.1 42.9 1.0
CD2 D:HIS12 4.1 44.5 1.0
CB D:ASP165 4.1 47.1 1.0
CE1 D:HIS37 4.2 42.0 1.0
CB D:ASP43 4.4 43.6 1.0
CB D:ASP39 4.5 45.8 1.0
CZ D:PHE76 4.6 36.6 1.0
CE2 D:PHE76 4.6 36.8 1.0
O D:HIS41 4.6 46.7 1.0
NE2 D:HIS37 4.7 42.8 1.0
OD1 D:ASP165 4.8 50.6 1.0
OD2 D:ASP167 5.0 50.8 1.0

Reference:

S.Mordhorst, T.Badmann, N.M.Bosch, B.I.Morinaka, H.Rauch, J.Piel, M.Groll, A.L.Vagstad. Structural and Biochemical Insights Into Post-Translational Arginine-to-Ornithine Peptide Modifications By An Atypical Arginase. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 36791048
DOI: 10.1021/ACSCHEMBIO.2C00879
Page generated: Sun Oct 6 11:27:09 2024

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