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Manganese in PDB 8qay: Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4

Enzymatic activity of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4

All present enzymatic activity of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4:
4.2.1.19;

Protein crystallography data

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4, PDB code: 8qay 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) 36.40 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 137.6, 137.6, 265.65, 90, 90, 120
R / Rfree (%) 18.9 / 23.1

Other elements in 8qay:

The structure of Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4 also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

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, Fmt, Act, Cit, Edo, SO4 (pdb code 8qay). 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, Fmt, Act, Cit, Edo, SO4, PDB code: 8qay:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 8qay

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Manganese binding site 1 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn303

b:32.4
occ:1.00
 OE1 A:GLU145 2.2 32.9 1.0
O2 A:FMT301 2.2 35.3 1.0
NE2 A:HIS141 2.3 34.4 1.0
O E:HOH421 2.3 30.4 1.0
NE2 A:HIS213 2.3 28.5 1.0
NE2 E:HIS238 2.4 31.0 1.0
CD A:GLU145 3.1 34.8 1.0
CE1 A:HIS141 3.2 29.9 1.0
CD2 A:HIS141 3.3 29.5 1.0
CD2 A:HIS213 3.3 31.9 1.0
C A:FMT301 3.3 33.8 1.0
CE1 A:HIS213 3.3 31.1 1.0
CE1 E:HIS238 3.3 30.8 1.0
CD2 E:HIS238 3.4 29.4 1.0
OE2 A:GLU145 3.5 33.6 1.0
O A:HOH428 3.9 35.9 1.0
OD2 E:ASP176 4.1 37.1 1.0
ND1 A:HIS141 4.4 27.8 1.0
ND1 A:HIS213 4.4 31.7 1.0
O1 A:FMT301 4.4 34.0 1.0
CG A:HIS141 4.4 30.8 1.0
CG A:GLU145 4.4 31.6 1.0
CG A:HIS213 4.4 29.4 1.0
ND1 E:HIS238 4.5 29.1 1.0
CG E:HIS238 4.5 28.2 1.0
CB A:GLU145 4.6 30.7 1.0
CD2 E:LEU175 4.8 29.4 1.0
O A:HOH465 4.9 33.2 1.0

Manganese binding site 2 out of 16 in 8qay

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Manganese binding site 2 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn304

b:34.3
occ:1.00
 OE1 A:GLU241 2.1 33.8 1.0
O2 B:FMT301 2.1 33.3 1.0
NE2 B:HIS142 2.3 37.6 1.0
O B:HOH419 2.3 36.3 1.0
NE2 A:HIS115 2.4 35.0 1.0
NE2 A:HIS237 2.4 31.2 1.0
C B:FMT301 3.0 33.6 1.0
CE1 B:HIS142 3.1 33.4 1.0
CD A:GLU241 3.2 35.4 1.0
CE1 A:HIS237 3.3 26.6 1.0
CD2 A:HIS115 3.3 34.8 1.0
CE1 A:HIS115 3.3 34.1 1.0
CD2 B:HIS142 3.4 32.0 1.0
CD2 A:HIS237 3.4 28.8 1.0
OE2 A:GLU241 3.6 33.1 1.0
O1 B:FMT301 4.2 30.5 1.0
ND1 B:HIS142 4.3 36.6 1.0
ND1 A:HIS237 4.4 29.4 1.0
ND1 A:HIS115 4.5 34.5 1.0
CG B:HIS142 4.5 34.6 1.0
CG A:HIS115 4.5 33.0 1.0
CG A:GLU241 4.5 34.5 1.0
CG A:HIS237 4.5 28.3 1.0
CB A:GLU241 4.9 30.4 1.0

Manganese binding site 3 out of 16 in 8qay

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Manganese binding site 3 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:31.7
occ:1.00
 OE1 B:GLU241 2.1 30.7 1.0
NE2 B:HIS115 2.2 31.4 1.0
O B:HOH446 2.3 36.7 1.0
NE2 F:HIS142 2.3 29.1 1.0
NE2 B:HIS237 2.3 30.2 1.0
O2 F:FMT301 2.3 31.2 1.0
CE1 F:HIS142 3.1 26.4 1.0
CE1 B:HIS237 3.2 27.9 1.0
CE1 B:HIS115 3.2 31.0 1.0
CD B:GLU241 3.2 29.8 1.0
CD2 B:HIS115 3.3 31.4 1.0
C F:FMT301 3.3 30.9 1.0
CD2 B:HIS237 3.4 30.4 1.0
CD2 F:HIS142 3.4 27.4 1.0
OE2 B:GLU241 3.7 39.1 1.0
ND1 F:HIS142 4.3 29.5 1.0
ND1 B:HIS237 4.3 32.6 1.0
ND1 B:HIS115 4.3 32.2 1.0
CG B:HIS115 4.4 31.3 1.0
CG B:HIS237 4.4 32.0 1.0
O1 F:FMT301 4.5 29.6 1.0
CG B:GLU241 4.5 32.1 1.0
CG F:HIS142 4.5 29.9 1.0
O B:HOH414 4.8 37.9 1.0
CB B:GLU241 4.9 26.4 1.0

Manganese binding site 4 out of 16 in 8qay

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Manganese binding site 4 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:29.9
occ:1.00
 O A:HOH416 2.1 28.5 1.0
OE1 B:GLU145 2.2 36.5 1.0
NE2 B:HIS141 2.3 27.4 1.0
NE2 A:HIS238 2.3 28.1 1.0
NE2 B:HIS213 2.3 29.8 1.0
O1 B:FMT301 2.4 30.5 1.0
CD B:GLU145 3.1 38.0 1.0
CE1 B:HIS141 3.2 29.7 1.0
CE1 A:HIS238 3.2 25.3 1.0
CE1 B:HIS213 3.3 28.5 1.0
CD2 B:HIS141 3.3 29.2 1.0
CD2 B:HIS213 3.3 29.1 1.0
CD2 A:HIS238 3.4 26.7 1.0
OE2 B:GLU145 3.4 36.6 1.0
C B:FMT301 3.5 33.6 1.0
OD2 A:ASP176 4.1 31.6 1.0
ND1 B:HIS141 4.4 31.3 1.0
ND1 B:HIS213 4.4 29.4 1.0
ND1 A:HIS238 4.4 24.7 1.0
CG B:GLU145 4.4 29.1 1.0
CG B:HIS141 4.4 29.4 1.0
CG B:HIS213 4.4 27.7 1.0
CG A:HIS238 4.5 28.2 1.0
O2 B:FMT301 4.6 33.3 1.0
CB B:GLU145 4.7 29.4 1.0
CD2 A:LEU175 4.8 27.6 1.0
O B:HOH457 4.8 31.1 1.0

Manganese binding site 5 out of 16 in 8qay

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Manganese binding site 5 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:31.7
occ:1.00
 OE1 C:GLU241 2.1 29.8 1.0
O2 H:FMT304 2.3 34.7 1.0
NE2 H:HIS142 2.3 32.7 1.0
NE2 C:HIS115 2.3 30.1 1.0
O H:HOH453 2.3 39.1 1.0
NE2 C:HIS237 2.4 33.8 1.0
CD C:GLU241 3.2 31.1 1.0
CE1 H:HIS142 3.2 30.4 1.0
C H:FMT304 3.3 32.1 1.0
CE1 C:HIS115 3.3 28.5 1.0
CE1 C:HIS237 3.3 31.7 1.0
CD2 C:HIS115 3.3 30.0 1.0
CD2 C:HIS237 3.4 30.0 1.0
CD2 H:HIS142 3.4 35.4 1.0
OE2 C:GLU241 3.6 33.0 1.0
ND1 H:HIS142 4.4 32.1 1.0
O1 H:FMT304 4.4 31.8 1.0
ND1 C:HIS115 4.4 28.7 1.0
ND1 C:HIS237 4.4 30.9 1.0
CG C:GLU241 4.5 30.1 1.0
CG C:HIS115 4.5 29.0 1.0
CG H:HIS142 4.5 33.3 1.0
CG C:HIS237 4.5 28.6 1.0
OE2 H:GLU89 4.8 56.7 1.0
CB C:GLU241 4.9 27.8 1.0
O C:HOH452 5.0 40.8 1.0

Manganese binding site 6 out of 16 in 8qay

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Manganese binding site 6 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn303

b:29.1
occ:1.00
 O1 C:FMT301 2.2 30.5 1.0
OE1 C:GLU145 2.2 32.4 1.0
NE2 C:HIS141 2.3 27.3 1.0
O D:HOH401 2.3 30.2 1.0
NE2 D:HIS238 2.3 30.0 1.0
NE2 C:HIS213 2.3 27.8 1.0
C C:FMT301 3.2 31.9 1.0
CD2 C:HIS213 3.2 26.7 1.0
CD C:GLU145 3.2 32.9 1.0
CE1 C:HIS141 3.2 27.0 1.0
CE1 D:HIS238 3.2 26.0 1.0
CD2 C:HIS141 3.3 28.0 1.0
CE1 C:HIS213 3.3 29.1 1.0
CD2 D:HIS238 3.3 25.7 1.0
OE2 C:GLU145 3.6 29.8 1.0
OD2 D:ASP176 4.1 31.3 1.0
O2 C:FMT301 4.3 34.6 1.0
ND1 C:HIS141 4.3 21.9 1.0
CG C:HIS213 4.4 23.1 1.0
ND1 D:HIS238 4.4 27.4 1.0
ND1 C:HIS213 4.4 31.2 1.0
CG C:HIS141 4.4 27.9 1.0
CG C:GLU145 4.5 29.8 1.0
CG D:HIS238 4.5 27.8 1.0
CB C:GLU145 4.7 33.2 1.0
O C:HOH462 4.7 28.1 1.0
CD2 D:LEU175 4.8 27.6 1.0

Manganese binding site 7 out of 16 in 8qay

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Manganese binding site 7 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn304

b:32.1
occ:1.00
 O D:HOH411 2.0 26.9 1.0
O2 D:FMT302 2.1 33.0 1.0
OE1 D:GLU145 2.2 31.4 1.0
NE2 D:HIS141 2.3 31.8 1.0
NE2 G:HIS238 2.3 28.7 1.0
NE2 D:HIS213 2.3 33.2 1.0
C D:FMT302 3.1 34.7 1.0
CD D:GLU145 3.1 34.2 1.0
CE1 D:HIS141 3.2 35.4 1.0
CD2 D:HIS213 3.2 28.5 1.0
CE1 G:HIS238 3.2 27.1 1.0
CE1 D:HIS213 3.3 30.7 1.0
CD2 D:HIS141 3.3 29.7 1.0
CD2 G:HIS238 3.4 29.0 1.0
OE2 D:GLU145 3.4 39.3 1.0
OD2 G:ASP176 4.1 33.1 1.0
O1 D:FMT302 4.2 38.5 1.0
ND1 D:HIS141 4.4 31.3 1.0
CG D:HIS213 4.4 27.3 1.0
ND1 D:HIS213 4.4 29.4 1.0
CG D:GLU145 4.4 29.0 1.0
ND1 G:HIS238 4.4 26.6 1.0
CG D:HIS141 4.5 34.2 1.0
CG G:HIS238 4.5 27.0 1.0
CB D:GLU145 4.7 31.9 1.0
O D:HOH435 4.8 32.5 1.0
CD2 G:LEU175 4.9 33.0 1.0

Manganese binding site 8 out of 16 in 8qay

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Manganese binding site 8 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn305

b:31.6
occ:1.00
 OE1 D:GLU241 2.1 37.9 1.0
O D:HOH439 2.2 35.4 1.0
NE2 C:HIS142 2.2 32.4 1.0
NE2 D:HIS115 2.2 33.6 1.0
O2 C:FMT301 2.3 34.6 1.0
NE2 D:HIS237 2.4 28.8 1.0
CE1 C:HIS142 3.0 31.5 1.0
CE1 D:HIS115 3.2 33.0 1.0
CD D:GLU241 3.2 32.2 1.0
CD2 D:HIS115 3.2 34.9 1.0
CE1 D:HIS237 3.3 27.8 1.0
C C:FMT301 3.3 31.9 1.0
CD2 D:HIS237 3.4 25.2 1.0
CD2 C:HIS142 3.4 30.5 1.0
OE2 D:GLU241 3.6 40.6 1.0
ND1 C:HIS142 4.2 26.0 1.0
ND1 D:HIS115 4.3 35.5 1.0
CG D:HIS115 4.4 30.0 1.0
ND1 D:HIS237 4.4 32.3 1.0
CG C:HIS142 4.4 36.1 1.0
CG D:HIS237 4.5 27.4 1.0
CG D:GLU241 4.5 32.5 1.0
O1 C:FMT301 4.5 30.5 1.0
C2 C:EDO306 4.8 51.5 1.0
O2 C:EDO306 4.8 54.3 1.0
O D:HOH429 4.8 36.1 1.0
CB D:GLU241 4.9 28.2 1.0
CE D:MET116 5.0 27.7 1.0

Manganese binding site 9 out of 16 in 8qay

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Manganese binding site 9 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn303

b:33.4
occ:1.00
 O F:HOH411 2.0 29.3 1.0
O2 E:FMT302 2.1 33.7 1.0
NE2 E:HIS141 2.2 29.8 1.0
OE1 E:GLU145 2.2 33.8 1.0
NE2 E:HIS213 2.4 29.9 1.0
NE2 F:HIS238 2.4 30.2 1.0
C E:FMT302 3.0 35.1 1.0
CE1 E:HIS141 3.1 27.8 1.0
CD E:GLU145 3.2 32.8 1.0
CD2 E:HIS141 3.2 26.7 1.0
CD2 E:HIS213 3.3 28.7 1.0
CE1 F:HIS238 3.3 27.0 1.0
CE1 E:HIS213 3.4 27.1 1.0
CD2 F:HIS238 3.4 26.4 1.0
OE2 E:GLU145 3.5 31.8 1.0
OD2 F:ASP176 4.2 29.4 1.0
O1 E:FMT302 4.2 30.2 1.0
O E:HOH443 4.3 43.0 1.0
ND1 E:HIS141 4.3 26.4 1.0
CG E:HIS141 4.4 33.1 1.0
CG E:HIS213 4.4 29.4 1.0
ND1 E:HIS213 4.4 31.9 1.0
ND1 F:HIS238 4.4 25.9 1.0
CG E:GLU145 4.5 28.1 1.0
CG F:HIS238 4.5 27.1 1.0
CB E:GLU145 4.7 28.4 1.0
C2 E:EDO307 4.8 48.0 1.0
O E:HOH440 4.9 27.9 1.0
CD2 F:LEU175 4.9 33.5 1.0

Manganese binding site 10 out of 16 in 8qay

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Manganese binding site 10 out of 16 in the Medicago Truncatula HISN5 (Igpd) in Complex with Mn, Fmt, Act, Cit, Edo, SO4


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, Fmt, Act, Cit, Edo, SO4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn304

b:34.5
occ:1.00
 OE1 E:GLU241 2.2 33.4 1.0
O1 A:FMT301 2.2 34.0 1.0
NE2 E:HIS115 2.3 37.8 1.0
NE2 E:HIS237 2.3 35.9 1.0
NE2 A:HIS142 2.3 35.0 1.0
O E:HOH411 2.4 34.8 1.0
CE1 A:HIS142 3.2 32.7 1.0
C A:FMT301 3.2 33.8 1.0
CD E:GLU241 3.2 33.0 1.0
CE1 E:HIS237 3.2 32.3 1.0
CE1 E:HIS115 3.2 33.2 1.0
CD2 E:HIS115 3.3 34.7 1.0
CD2 E:HIS237 3.3 29.8 1.0
CD2 A:HIS142 3.4 34.4 1.0
OE2 E:GLU241 3.6 41.0 1.0
O2 A:FMT301 4.3 35.3 1.0
ND1 E:HIS237 4.3 33.8 1.0
ND1 A:HIS142 4.3 35.8 1.0
ND1 E:HIS115 4.3 33.8 1.0
CG E:HIS115 4.4 35.6 1.0
CG E:HIS237 4.4 28.8 1.0
CG E:GLU241 4.5 33.5 1.0
CG A:HIS142 4.5 36.0 1.0
O E:HOH432 4.7 43.2 1.0
O A:HOH491 4.8 52.5 1.0
CB E:GLU241 5.0 30.8 1.0

Reference:

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
Page generated: Sun Oct 6 13:40:12 2024

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