Manganese in PDB 8qaw: Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs, PDB code: 8qaw was solved by W.Witek, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.06 / 1.55
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	137.68, 137.68, 265.907, 90, 90, 120
R / Rfree (%)	12.9 / 16.1

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Sodium	(Na)	2 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Manganese atom in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs (pdb code 8qaw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs, PDB code: 8qaw:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:20.8 occ:1.00 O E:HOH415 2.2 21.9 1.0 OE1 A:GLU145 2.2 22.8 1.0 O2 A:FMT302 2.2 23.1 1.0 NE2 E:HIS238 2.2 19.5 1.0 NE2 A:HIS141 2.2 19.5 1.0 NE2 A:HIS213 2.3 20.8 1.0 CE1 E:HIS238 3.2 17.6 1.0 C A:FMT302 3.2 23.6 1.0 CD A:GLU145 3.2 21.5 1.0 CE1 A:HIS141 3.2 19.8 1.0 CD2 A:HIS213 3.2 20.3 1.0 CD2 A:HIS141 3.2 20.8 1.0 CD2 E:HIS238 3.3 21.3 1.0 CE1 A:HIS213 3.3 19.6 1.0 OE2 A:GLU145 3.6 23.9 1.0 OD2 E:ASP176 4.0 24.5 1.0 O A:HOH465 4.2 34.5 1.0 O1 A:FMT302 4.3 23.8 1.0 ND1 E:HIS238 4.3 18.9 1.0 ND1 A:HIS141 4.3 19.2 1.0 ND1 A:HIS213 4.4 18.9 1.0 CG A:HIS213 4.4 18.3 1.0 CG A:HIS141 4.4 20.4 1.0 CG E:HIS238 4.4 18.9 1.0 C4 A:IMD301 4.4 36.8 1.0 CG A:GLU145 4.5 21.7 1.0 CB A:GLU145 4.7 21.3 1.0 O A:HOH493 4.8 23.4 1.0 CD2 E:LEU175 4.8 26.3 1.0

Manganese binding site 2 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn305 b:21.7 occ:1.00 OE1 A:GLU241 2.1 21.1 1.0 O2 B:FMT302 2.2 23.1 1.0 NE2 A:HIS115 2.3 20.7 1.0 NE2 B:HIS142 2.3 21.3 1.0 NE2 A:HIS237 2.3 20.9 1.0 O A:HOH423 2.3 23.1 1.0 CE1 B:HIS142 3.1 22.3 1.0 CD A:GLU241 3.2 21.6 1.0 CE1 A:HIS237 3.2 21.4 1.0 CE1 A:HIS115 3.2 21.9 1.0 C B:FMT302 3.3 23.5 1.0 CD2 A:HIS115 3.3 21.0 1.0 CD2 A:HIS237 3.3 20.5 1.0 CD2 B:HIS142 3.3 21.5 1.0 OE2 A:GLU241 3.5 24.5 1.0 ND1 B:HIS142 4.3 23.8 1.0 ND1 A:HIS237 4.3 21.4 1.0 ND1 A:HIS115 4.4 21.2 1.0 O1 B:FMT302 4.4 22.0 1.0 CG A:HIS237 4.4 21.8 1.0 CG A:HIS115 4.4 19.6 1.0 N3 B:IMD301 4.4 54.3 1.0 CG B:HIS142 4.4 21.2 1.0 CG A:GLU241 4.5 20.0 1.0 O B:HOH403 4.6 57.5 1.0 CB A:GLU241 4.9 19.8 1.0 O A:HOH487 4.9 39.2 1.0

Manganese binding site 3 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:20.5 occ:1.00 O A:HOH417 2.2 21.3 1.0 O1 B:FMT302 2.2 22.0 1.0 NE2 B:HIS141 2.2 20.7 1.0 OE1 B:GLU145 2.2 21.3 1.0 NE2 A:HIS238 2.3 20.1 1.0 NE2 B:HIS213 2.3 21.2 1.0 C B:FMT302 3.1 23.5 1.0 CE1 B:HIS141 3.2 21.4 1.0 CE1 A:HIS238 3.2 19.2 1.0 CD B:GLU145 3.2 21.8 1.0 CE1 B:HIS213 3.2 21.1 1.0 CD2 B:HIS213 3.2 21.1 1.0 CD2 B:HIS141 3.3 20.6 1.0 CD2 A:HIS238 3.3 20.4 1.0 OE2 B:GLU145 3.6 23.1 1.0 OD2 A:ASP176 4.0 26.1 1.0 O B:HOH422 4.1 34.8 1.0 O2 B:FMT302 4.2 23.1 1.0 ND1 B:HIS141 4.3 20.4 1.0 ND1 B:HIS213 4.3 20.2 1.0 ND1 A:HIS238 4.3 18.8 1.0 CG B:HIS213 4.4 19.0 1.0 CG B:HIS141 4.4 19.8 1.0 CG A:HIS238 4.4 18.8 1.0 C4 B:IMD301 4.4 52.1 1.0 CG B:GLU145 4.5 22.1 1.0 CB B:GLU145 4.7 21.5 1.0 CD2 A:LEU175 4.7 26.4 1.0 O B:HOH502 4.9 22.5 1.0

Manganese binding site 4 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn305 b:24.7 occ:1.00 OE1 B:GLU241 2.2 24.4 1.0 O2 G:FMT302 2.2 26.4 1.0 NE2 G:HIS142 2.3 23.3 1.0 NE2 B:HIS115 2.3 23.4 1.0 O B:HOH430 2.3 26.1 1.0 NE2 B:HIS237 2.3 23.9 1.0 CE1 G:HIS142 3.1 24.9 1.0 CD B:GLU241 3.1 24.3 1.0 CE1 B:HIS115 3.2 23.8 1.0 CE1 B:HIS237 3.2 23.4 1.0 C G:FMT302 3.3 27.4 1.0 CD2 B:HIS115 3.3 23.6 1.0 CD2 B:HIS237 3.3 23.2 1.0 CD2 G:HIS142 3.3 23.6 1.0 OE2 B:GLU241 3.5 28.1 1.0 N3 G:IMD301 4.2 61.2 1.0 ND1 G:HIS142 4.3 25.0 1.0 ND1 B:HIS237 4.3 23.1 1.0 ND1 B:HIS115 4.3 25.4 1.0 O1 G:FMT302 4.4 25.8 1.0 CG B:HIS115 4.4 24.1 1.0 CG B:HIS237 4.4 23.4 1.0 CG G:HIS142 4.4 23.4 1.0 CG B:GLU241 4.5 22.6 1.0 O G:HOH401 4.7 56.0 1.0 CB B:GLU241 4.9 21.7 1.0 C2 G:IMD301 4.9 60.4 1.0 CE B:MET116 5.0 24.4 1.0

Manganese binding site 5 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn304 b:23.8 occ:1.00 OE1 C:GLU241 2.1 24.3 1.0 O1 F:FMT302 2.2 25.8 1.0 NE2 C:HIS237 2.3 24.0 1.0 NE2 C:HIS115 2.3 23.1 1.0 NE2 F:HIS142 2.3 23.7 1.0 O C:HOH426 2.3 26.1 1.0 CE1 F:HIS142 3.1 23.7 1.0 CE1 C:HIS237 3.1 22.3 1.0 CD C:GLU241 3.1 23.5 1.0 CE1 C:HIS115 3.2 24.2 1.0 C F:FMT302 3.3 27.4 1.0 CD2 C:HIS115 3.3 22.7 1.0 CD2 C:HIS237 3.3 22.5 1.0 CD2 F:HIS142 3.4 25.4 1.0 OE2 C:GLU241 3.5 27.7 1.0 N1 F:IMD301 4.2 57.6 1.0 ND1 C:HIS237 4.3 22.9 1.0 ND1 F:HIS142 4.3 24.8 1.0 ND1 C:HIS115 4.4 23.1 1.0 O2 F:FMT302 4.4 25.5 1.0 CG C:HIS237 4.4 22.6 1.0 CG C:HIS115 4.4 22.6 1.0 CG F:HIS142 4.5 24.1 1.0 CG C:GLU241 4.5 21.7 1.0 O F:HOH404 4.6 57.5 1.0 CB C:GLU241 4.9 21.4 1.0 C2 F:IMD301 5.0 56.6 1.0

Manganese binding site 6 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn305 b:20.9 occ:1.00 O2 C:FMT302 2.2 23.6 1.0 O D:HOH407 2.2 22.1 1.0 NE2 C:HIS141 2.2 20.4 1.0 OE1 C:GLU145 2.2 22.1 1.0 NE2 D:HIS238 2.3 19.9 1.0 NE2 C:HIS213 2.3 20.5 1.0 CE1 C:HIS141 3.2 20.4 1.0 C C:FMT302 3.2 24.1 1.0 CD C:GLU145 3.2 22.1 1.0 CE1 D:HIS238 3.2 19.2 1.0 CD2 C:HIS141 3.2 20.8 1.0 CD2 C:HIS213 3.2 20.5 1.0 CE1 C:HIS213 3.3 20.5 1.0 CD2 D:HIS238 3.3 20.6 1.0 OE2 C:GLU145 3.6 23.8 1.0 OD2 D:ASP176 4.0 25.4 1.0 O C:HOH439 4.1 35.2 1.0 O1 C:FMT302 4.3 23.2 1.0 ND1 C:HIS141 4.3 20.7 1.0 ND1 D:HIS238 4.3 20.3 1.0 ND1 C:HIS213 4.4 20.7 1.0 CG C:HIS141 4.4 20.6 1.0 CG C:HIS213 4.4 19.5 1.0 CG D:HIS238 4.4 20.0 1.0 C5 C:IMD301 4.4 49.0 1.0 CG C:GLU145 4.5 21.4 1.0 CB C:GLU145 4.7 21.2 1.0 CD2 D:LEU175 4.8 29.1 1.0 O C:HOH488 4.8 22.7 1.0

Manganese binding site 7 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn305 b:22.1 occ:1.00 OE1 D:GLU241 2.1 23.4 1.0 NE2 D:HIS115 2.3 22.4 1.0 NE2 C:HIS142 2.3 22.1 1.0 NE2 D:HIS237 2.3 22.2 1.0 O1 C:FMT302 2.3 23.2 1.0 O D:HOH441 2.3 24.1 1.0 CE1 C:HIS142 3.1 23.4 1.0 CD D:GLU241 3.1 24.5 1.0 CE1 D:HIS237 3.2 21.8 1.0 CE1 D:HIS115 3.2 23.9 1.0 CD2 D:HIS115 3.3 22.6 1.0 CD2 D:HIS237 3.3 21.9 1.0 C C:FMT302 3.3 24.1 1.0 CD2 C:HIS142 3.3 21.7 1.0 OE2 D:GLU241 3.5 27.6 1.0 N1 C:IMD301 4.2 49.7 1.0 ND1 D:HIS237 4.3 22.1 1.0 ND1 C:HIS142 4.3 23.3 1.0 ND1 D:HIS115 4.3 23.5 1.0 CG D:HIS237 4.4 23.4 1.0 CG D:HIS115 4.4 22.4 1.0 CG C:HIS142 4.4 21.6 1.0 O2 C:FMT302 4.4 23.6 1.0 CG D:GLU241 4.5 22.9 1.0 O C:HOH402 4.6 58.3 1.0 CB D:GLU241 4.9 21.6 1.0 C2 C:IMD301 4.9 49.8 1.0 CE D:MET116 5.0 23.6 1.0 C5 C:IMD301 5.0 49.0 1.0

Manganese binding site 8 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn306 b:21.7 occ:1.00 O1 D:FMT303 2.2 24.2 1.0 O H:HOH420 2.2 22.8 1.0 OE1 D:GLU145 2.2 23.4 1.0 NE2 D:HIS141 2.2 21.1 1.0 NE2 H:HIS238 2.3 20.2 1.0 NE2 D:HIS213 2.3 20.3 1.0 C D:FMT303 3.1 25.5 1.0 CD D:GLU145 3.2 22.4 1.0 CE1 D:HIS141 3.2 21.5 1.0 CE1 H:HIS238 3.2 18.8 1.0 CD2 D:HIS213 3.2 20.9 1.0 CD2 D:HIS141 3.2 21.2 1.0 CD2 H:HIS238 3.3 20.4 1.0 CE1 D:HIS213 3.3 21.9 1.0 OE2 D:GLU145 3.6 23.9 1.0 OD2 H:ASP176 4.0 25.0 1.0 O D:HOH435 4.1 37.2 1.0 O2 D:FMT303 4.3 24.2 1.0 ND1 D:HIS141 4.3 20.9 1.0 ND1 H:HIS238 4.3 19.9 1.0 ND1 D:HIS213 4.4 20.9 1.0 CG D:HIS213 4.4 19.9 1.0 CG D:HIS141 4.4 20.4 1.0 CG H:HIS238 4.4 18.9 1.0 C4 D:IMD302 4.4 56.0 1.0 CG D:GLU145 4.4 21.5 1.0 CB D:GLU145 4.7 21.5 1.0 CD2 H:LEU175 4.8 27.2 1.0 O D:HOH499 4.9 23.3 1.0

Manganese binding site 9 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn304 b:22.7 occ:1.00 OE1 E:GLU241 2.2 23.7 1.0 O1 A:FMT302 2.2 23.8 1.0 NE2 E:HIS115 2.3 21.0 1.0 NE2 A:HIS142 2.3 22.7 1.0 NE2 E:HIS237 2.3 21.3 1.0 O E:HOH438 2.3 24.1 1.0 CE1 A:HIS142 3.2 24.2 1.0 CD E:GLU241 3.2 23.4 1.0 CE1 E:HIS115 3.2 22.8 1.0 CE1 E:HIS237 3.2 21.1 1.0 C A:FMT302 3.3 23.6 1.0 CD2 E:HIS115 3.3 22.7 1.0 CD2 E:HIS237 3.3 21.6 1.0 CD2 A:HIS142 3.3 22.6 1.0 OE2 E:GLU241 3.5 27.9 1.0 N3 A:IMD301 4.2 40.1 1.0 ND1 A:HIS142 4.3 23.0 1.0 ND1 E:HIS237 4.3 21.0 1.0 ND1 E:HIS115 4.3 23.7 1.0 O2 A:FMT302 4.4 23.1 1.0 CG E:HIS115 4.4 23.3 1.0 CG E:HIS237 4.4 20.8 1.0 CG A:HIS142 4.4 22.2 1.0 CG E:GLU241 4.5 22.4 1.0 O A:HOH406 4.6 48.9 1.0 C2 A:IMD301 4.7 39.8 1.0 CB E:GLU241 4.9 22.2 1.0 O E:HOH475 5.0 39.0 1.0 CE E:MET116 5.0 24.8 1.0

Manganese binding site 10 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Imd, Edo, Fmt, Gol and Trs within 5.0Å range: probe atom residue distance (Å) B Occ E:Mn305 b:22.7 occ:1.00 O E:HOH431 2.2 23.1 1.0 O2 E:FMT302 2.2 25.1 1.0 OE1 E:GLU145 2.2 22.8 1.0 NE2 E:HIS141 2.2 22.4 1.0 NE2 G:HIS238 2.3 21.5 1.0 NE2 E:HIS213 2.3 21.4 1.0 C E:FMT302 3.1 26.4 1.0 CE1 E:HIS141 3.2 24.1 1.0 CD E:GLU145 3.2 23.6 1.0 CE1 G:HIS238 3.2 21.6 1.0 CD2 E:HIS213 3.2 22.0 1.0 CE1 E:HIS213 3.3 22.2 1.0 CD2 G:HIS238 3.3 22.8 1.0 CD2 E:HIS141 3.3 23.0 1.0 OE2 E:GLU145 3.5 26.0 1.0 OD2 G:ASP176 4.1 26.2 1.0 O E:HOH447 4.1 37.5 1.0 O1 E:FMT302 4.3 26.0 1.0 ND1 E:HIS141 4.3 22.5 1.0 ND1 G:HIS238 4.3 20.8 1.0 ND1 E:HIS213 4.4 21.6 1.0 CG E:HIS213 4.4 21.4 1.0 C4 E:IMD301 4.4 56.7 1.0 CG E:HIS141 4.4 22.0 1.0 CG G:HIS238 4.4 20.1 1.0 CG E:GLU145 4.5 23.9 1.0 CB E:GLU145 4.7 24.2 1.0 O E:HOH504 4.9 24.4 1.0 CD2 G:LEU175 4.9 30.7 1.0

W.Witek, J.Sliwiak, M.Rawski, M.Ruszkowski. Targeting Imidazole-Glycerol Phosphate Dehydratase in Plants: Novel Approach For Structural and Functional Studies, and Inhibitor Blueprinting. Front Plant Sci V. 15 43980 2024.
ISSN: ESSN 1664-462X
PubMed: 38559763
DOI: 10.3389/FPLS.2024.1343980