Manganese in PDB 6vst: Arginase From Medicago Truncatula in Complex with Ornithine

All present enzymatic activity of Arginase From Medicago Truncatula in Complex with Ornithine:
3.5.3.1;

The structure of Arginase From Medicago Truncatula in Complex with Ornithine, PDB code: 6vst was solved by B.Sekula, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.52 / 2.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	83.672, 166.074, 150.875, 90.00, 94.50, 90.00
R / Rfree (%)	16 / 19.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Manganese atom in the Arginase From Medicago Truncatula in Complex with Ornithine (pdb code 6vst). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 24 binding sites of Manganese where determined in the Arginase From Medicago Truncatula in Complex with Ornithine, PDB code: 6vst:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:34.3 occ:1.00 OD1 A:ASP181 2.2 31.7 1.0 OD2 A:ASP268 2.3 33.4 1.0 O A:HOH502 2.4 34.3 1.0 ND1 A:HIS183 2.4 28.6 1.0 OD1 A:ASP268 2.4 32.4 1.0 OD2 A:ASP266 2.5 31.4 1.0 CG A:ASP268 2.7 31.9 1.0 MN A:MN402 3.1 28.8 1.0 CG A:ASP181 3.2 30.6 1.0 CG A:ASP266 3.2 34.4 1.0 CE1 A:HIS183 3.2 31.4 1.0 CG A:HIS183 3.5 32.2 1.0 OD2 A:ASP181 3.5 33.2 1.0 OD1 A:ASP266 3.7 35.8 1.0 CB A:HIS183 3.9 30.3 1.0 NE A:ORN403 3.9 53.2 1.0 N A:HIS183 4.0 31.5 1.0 N A:ALA182 4.2 29.6 1.0 CD A:ORN403 4.2 54.6 1.0 CB A:ASP266 4.2 30.0 1.0 CB A:ASP268 4.2 29.4 1.0 NE2 A:HIS183 4.4 30.3 1.0 CB A:ASP181 4.5 29.8 1.0 CA A:HIS183 4.5 31.5 1.0 OD1 A:ASP185 4.5 36.4 1.0 O A:HOH518 4.6 32.0 1.0 CD2 A:HIS183 4.6 31.3 1.0 OD2 A:ASP185 4.6 36.8 1.0 CB A:ALA182 4.6 28.5 1.0 CA A:ALA182 4.8 31.0 1.0 CA A:ASP181 4.8 29.2 1.0 C A:ALA182 4.8 32.6 1.0 O A:HIS183 4.8 29.6 1.0 C A:ASP181 4.9 32.5 1.0 ND1 A:HIS157 5.0 32.3 1.0 CG A:ASP185 5.0 37.3 1.0

Manganese binding site 2 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:28.8 occ:1.00 O A:HOH502 1.8 34.3 1.0 OD2 A:ASP181 1.9 33.2 1.0 OD2 A:ASP185 2.1 36.8 1.0 ND1 A:HIS157 2.1 32.3 1.0 OD2 A:ASP266 2.3 31.4 1.0 CG A:ASP181 2.8 30.6 1.0 CE1 A:HIS157 2.9 32.1 1.0 CG A:ASP185 3.1 37.3 1.0 CG A:HIS157 3.1 30.1 1.0 OD1 A:ASP181 3.1 31.7 1.0 MN A:MN401 3.1 34.3 1.0 CG A:ASP266 3.3 34.4 1.0 OD1 A:ASP185 3.4 36.4 1.0 CB A:HIS157 3.5 28.4 1.0 CB A:ASP266 3.7 30.0 1.0 NE A:ORN403 4.0 53.2 1.0 NE2 A:HIS157 4.1 30.3 1.0 CD2 A:HIS157 4.2 30.7 1.0 CB A:ASP181 4.2 29.8 1.0 NE2 A:HIS179 4.3 27.8 1.0 CB A:ASP185 4.4 34.9 1.0 OD1 A:ASP266 4.4 35.8 1.0 O A:HIS183 4.5 29.6 1.0 O A:HIS197 4.8 28.2 1.0 CG A:GLU309 4.8 29.5 1.0 OD1 A:ASP268 5.0 32.4 1.0 ND1 A:HIS183 5.0 28.6 1.0

Manganese binding site 3 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:36.1 occ:1.00 OD1 B:ASP181 2.2 34.4 1.0 O B:HOH501 2.3 29.9 1.0 OD2 B:ASP268 2.4 32.6 1.0 OD2 B:ASP266 2.4 34.2 1.0 OD1 B:ASP268 2.4 29.9 1.0 ND1 B:HIS183 2.6 28.1 1.0 CG B:ASP268 2.7 30.4 1.0 MN B:MN402 3.1 28.6 1.0 CG B:ASP181 3.1 31.4 1.0 CG B:ASP266 3.2 32.4 1.0 CE1 B:HIS183 3.4 29.6 1.0 OD2 B:ASP181 3.4 31.7 1.0 CG B:HIS183 3.6 29.3 1.0 OD1 B:ASP266 3.6 32.6 1.0 NE B:ORN403 3.8 58.1 1.0 CB B:HIS183 3.9 27.3 1.0 N B:HIS183 4.1 26.7 1.0 CD B:ORN403 4.1 56.9 1.0 CB B:ASP266 4.2 27.0 1.0 CB B:ASP268 4.3 29.4 1.0 N B:ALA182 4.3 27.1 1.0 CB B:ASP181 4.5 30.6 1.0 CA B:HIS183 4.6 29.8 1.0 NE2 B:HIS183 4.6 30.3 1.0 OD1 B:ASP185 4.6 38.4 1.0 OD2 B:ASP185 4.6 39.1 1.0 CD2 B:HIS183 4.7 29.0 1.0 CB B:ALA182 4.7 22.1 1.0 O B:HOH531 4.7 29.9 1.0 CA B:ASP181 4.8 30.3 1.0 CA B:ALA182 4.9 25.9 1.0 O B:HIS183 4.9 31.9 1.0 C B:ALA182 4.9 30.0 1.0 ND1 B:HIS157 5.0 35.7 1.0 CG B:ASP185 5.0 40.6 1.0

Manganese binding site 4 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:28.6 occ:1.00 OD2 B:ASP181 1.9 31.7 1.0 O B:HOH501 2.0 29.9 1.0 ND1 B:HIS157 2.1 35.7 1.0 OD2 B:ASP185 2.1 39.1 1.0 OD2 B:ASP266 2.1 34.2 1.0 CG B:ASP181 2.9 31.4 1.0 CE1 B:HIS157 3.0 33.6 1.0 MN B:MN401 3.1 36.1 1.0 CG B:ASP185 3.1 40.6 1.0 CG B:HIS157 3.1 32.3 1.0 OD1 B:ASP181 3.2 34.4 1.0 CG B:ASP266 3.2 32.4 1.0 OD1 B:ASP185 3.5 38.4 1.0 CB B:HIS157 3.5 30.4 1.0 CB B:ASP266 3.6 27.0 1.0 NE B:ORN403 4.1 58.1 1.0 NE2 B:HIS157 4.1 32.3 1.0 CD2 B:HIS157 4.2 31.1 1.0 CB B:ASP181 4.2 30.6 1.0 OD1 B:ASP266 4.3 32.6 1.0 NE2 B:HIS179 4.3 32.3 1.0 CB B:ASP185 4.4 38.1 1.0 O B:HIS183 4.6 31.9 1.0 O B:HIS197 4.8 33.2 1.0 CG B:GLU309 4.8 28.9 1.0 OD1 B:ASP268 5.0 29.9 1.0 OD2 B:ASP268 5.0 32.6 1.0

Manganese binding site 5 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:60.2 occ:1.00 O C:HOH509 2.1 49.9 1.0 OD1 C:ASP181 2.4 47.0 1.0 OD2 C:ASP266 2.4 46.9 1.0 OD1 C:ASP268 2.6 43.1 1.0 ND1 C:HIS183 2.6 45.1 1.0 OD2 C:ASP268 2.6 38.1 1.0 CG C:ASP268 2.9 40.3 1.0 MN C:MN402 3.0 42.5 1.0 CG C:ASP266 3.2 39.9 1.0 CE1 C:HIS183 3.3 46.6 1.0 O C:HOH617 3.3 55.5 1.0 CG C:ASP181 3.4 51.4 1.0 OD1 C:ASP266 3.7 42.1 1.0 OD2 C:ASP181 3.7 61.4 1.0 CG C:HIS183 3.7 51.6 1.0 CB C:HIS183 4.2 52.5 1.0 OD1 C:ASP185 4.3 52.1 1.0 N C:HIS183 4.3 40.2 1.0 CB C:ASP266 4.3 33.9 1.0 N C:ALA182 4.4 38.6 1.0 CB C:ASP268 4.5 32.4 1.0 NE2 C:HIS183 4.5 49.6 1.0 CB C:ASP181 4.7 43.4 1.0 OD2 C:ASP185 4.7 53.5 1.0 CD2 C:HIS183 4.8 49.8 1.0 CA C:HIS183 4.8 54.4 1.0 O C:HOH516 4.9 40.6 1.0 CB C:ALA182 4.9 40.1 1.0 O C:HIS183 4.9 50.1 1.0 CG C:ASP185 4.9 56.4 1.0

Manganese binding site 6 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:42.5 occ:1.00 OD2 C:ASP181 2.0 61.4 1.0 O C:HOH509 2.0 49.9 1.0 ND1 C:HIS157 2.1 56.4 1.0 OD2 C:ASP266 2.2 46.9 1.0 OD2 C:ASP185 2.3 53.5 1.0 CG C:ASP181 2.8 51.4 1.0 MN C:MN401 3.0 60.2 1.0 OD1 C:ASP181 3.0 47.0 1.0 CE1 C:HIS157 3.1 50.4 1.0 CG C:ASP266 3.1 39.9 1.0 CG C:ASP185 3.2 56.4 1.0 CG C:HIS157 3.2 50.9 1.0 OD1 C:ASP185 3.4 52.1 1.0 CB C:ASP266 3.5 33.9 1.0 CB C:HIS157 3.5 44.0 1.0 NE2 C:HIS157 4.2 50.0 1.0 O C:HOH617 4.2 55.5 1.0 CB C:ASP181 4.3 43.4 1.0 OD1 C:ASP266 4.3 42.1 1.0 CD2 C:HIS157 4.3 51.7 1.0 NE2 C:HIS179 4.3 37.8 1.0 CB C:ASP185 4.5 57.4 1.0 O C:HIS183 4.7 50.1 1.0 CG C:GLU309 4.7 28.4 1.0 O C:HIS197 4.8 48.4 1.0 CA C:ASP266 4.9 30.5 1.0 OD1 C:ASP268 4.9 43.1 1.0 CE1 C:HIS179 5.0 38.4 1.0

Manganese binding site 7 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:55.5 occ:1.00 OD1 D:ASP181 2.2 66.5 1.0 OD1 D:ASP268 2.4 45.4 1.0 OD2 D:ASP268 2.5 46.3 1.0 OD2 D:ASP266 2.5 50.9 1.0 ND1 D:HIS183 2.6 45.8 1.0 CG D:ASP268 2.8 45.3 1.0 O D:HOH552 2.9 43.6 1.0 MN D:MN402 3.1 39.0 1.0 CG D:ASP181 3.2 56.6 1.0 CG D:ASP266 3.2 46.7 1.0 CE1 D:HIS183 3.4 45.6 1.0 OD2 D:ASP181 3.5 58.6 1.0 OD1 D:ASP266 3.6 49.6 1.0 CG D:HIS183 3.7 48.2 1.0 N D:HIS183 4.0 39.9 1.0 CB D:HIS183 4.1 45.0 1.0 N D:ALA182 4.1 40.2 1.0 CB D:ASP266 4.2 41.8 1.0 CB D:ASP268 4.3 39.4 1.0 CB D:ASP181 4.5 51.8 1.0 OD1 D:ASP185 4.6 55.2 1.0 CB D:ALA182 4.6 40.6 1.0 NE2 D:HIS183 4.6 46.0 1.0 CA D:HIS183 4.6 45.1 1.0 O D:HOH594 4.7 61.8 1.0 CA D:ALA182 4.7 42.6 1.0 CD2 D:HIS183 4.8 46.0 1.0 C D:ALA182 4.8 42.8 1.0 OD2 D:ASP185 4.8 60.4 1.0 CA D:ASP181 4.8 44.4 1.0 O D:HOH539 4.8 44.6 1.0 O D:HIS183 4.9 45.7 1.0 ND1 D:HIS157 5.0 49.2 1.0 C D:ASP181 5.0 42.5 1.0

Manganese binding site 8 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:39.0 occ:1.00 OD2 D:ASP181 1.9 58.6 1.0 ND1 D:HIS157 2.0 49.2 1.0 OD2 D:ASP185 2.1 60.4 1.0 OD2 D:ASP266 2.2 50.9 1.0 O D:HOH552 2.3 43.6 1.0 CG D:ASP181 2.8 56.6 1.0 CE1 D:HIS157 2.9 46.6 1.0 CG D:ASP185 3.1 54.9 1.0 OD1 D:ASP181 3.1 66.5 1.0 CG D:HIS157 3.1 46.0 1.0 MN D:MN401 3.1 55.5 1.0 CG D:ASP266 3.3 46.7 1.0 OD1 D:ASP185 3.3 55.2 1.0 CB D:HIS157 3.6 40.5 1.0 CB D:ASP266 3.6 41.8 1.0 NE2 D:HIS157 4.0 46.4 1.0 CD2 D:HIS157 4.2 46.8 1.0 CB D:ASP181 4.2 51.8 1.0 NE2 D:HIS179 4.3 46.2 1.0 OD1 D:ASP266 4.4 49.6 1.0 CB D:ASP185 4.4 50.9 1.0 O D:HIS183 4.6 45.7 1.0 O D:HIS197 4.7 43.5 1.0 CG D:GLU309 4.8 40.1 1.0 OD1 D:ASP268 4.9 45.4 1.0

Manganese binding site 9 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn401 b:43.9 occ:1.00 OD1 E:ASP181 2.3 34.4 1.0 OD2 E:ASP266 2.4 40.0 1.0 OD2 E:ASP268 2.4 37.8 1.0 O D:HOH502 2.4 40.5 1.0 ND1 E:HIS183 2.4 34.1 1.0 OD1 E:ASP268 2.5 39.0 1.0 CG E:ASP268 2.8 38.5 1.0 MN E:MN402 3.1 34.5 1.0 CG E:ASP266 3.1 37.2 1.0 CE1 E:HIS183 3.2 35.6 1.0 CG E:ASP181 3.3 33.7 1.0 CG E:HIS183 3.4 38.4 1.0 OD2 E:ASP181 3.6 40.8 1.0 OD1 E:ASP266 3.6 40.9 1.0 CB E:HIS183 3.8 35.2 1.0 N E:HIS183 4.0 35.6 1.0 NE D:ORN403 4.0 62.1 1.0 CB E:ASP266 4.2 31.8 1.0 N E:ALA182 4.3 29.1 1.0 CB E:ASP268 4.3 30.9 1.0 CD D:ORN403 4.3 63.9 1.0 NE2 E:HIS183 4.4 36.8 1.0 CD2 E:HIS183 4.5 35.5 1.0 CA E:HIS183 4.5 35.0 1.0 CB E:ASP181 4.6 30.3 1.0 OD2 E:ASP185 4.6 47.2 1.0 OD1 E:ASP185 4.6 42.5 1.0 CB E:ALA182 4.7 28.5 1.0 CA E:ALA182 4.8 32.5 1.0 CA E:ASP181 4.8 31.3 1.0 O E:HOH571 4.8 37.9 1.0 C E:ALA182 4.9 33.9 1.0 O E:HIS183 4.9 34.6 1.0 ND1 E:HIS157 4.9 40.7 1.0

Manganese binding site 10 out of 24 in the Arginase From Medicago Truncatula in Complex with Ornithine


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Arginase From Medicago Truncatula in Complex with Ornithine within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn402 b:34.5 occ:1.00 ND1 E:HIS157 2.0 40.7 1.0 OD2 E:ASP181 2.0 40.8 1.0 OD2 E:ASP185 2.1 47.2 1.0 O D:HOH502 2.2 40.5 1.0 OD2 E:ASP266 2.2 40.0 1.0 CE1 E:HIS157 2.8 39.2 1.0 CG E:ASP181 2.9 33.7 1.0 CG E:HIS157 3.0 39.3 1.0 OD1 E:ASP181 3.1 34.4 1.0 MN E:MN401 3.1 43.9 1.0 CG E:ASP185 3.2 45.5 1.0 CG E:ASP266 3.2 37.2 1.0 CB E:HIS157 3.5 35.3 1.0 CB E:ASP266 3.6 31.8 1.0 OD1 E:ASP185 3.6 42.5 1.0 NE2 E:HIS157 4.0 40.4 1.0 CD2 E:HIS157 4.1 39.2 1.0 NE2 E:HIS179 4.2 38.4 1.0 NE D:ORN403 4.3 62.1 1.0 CB E:ASP181 4.3 30.3 1.0 OD1 E:ASP266 4.4 40.9 1.0 CB E:ASP185 4.5 43.2 1.0 O E:HIS183 4.6 34.6 1.0 O E:HIS197 4.8 39.0 1.0 CG E:GLU309 4.8 37.5 1.0 CE1 E:HIS179 5.0 36.9 1.0 CA E:ASP266 5.0 33.7 1.0 CA E:HIS157 5.0 33.8 1.0

B.Sekula, B.Sekula. N/A N/A.
ISSN: ESSN 1664-462X
PubMed: 32754173
DOI: 10.3389/FPLS.2020.00987