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Manganese in PDB 4qnk: The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate

Enzymatic activity of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate

All present enzymatic activity of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate:
4.2.1.19;

Protein crystallography data

The structure of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate, PDB code: 4qnk was solved by C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 1.75
Space group I 2 3 1
Cell size a, b, c (Å), α, β, γ (°) 225.130, 225.130, 225.130, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.9

Other elements in 4qnk:

The structure of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate also contains other interesting chemical elements:

Sodium (Na) 8 atoms

Manganese Binding Sites:

Pages:

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

Binding sites:

The binding sites of Manganese atom in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate (pdb code 4qnk). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 16 binding sites of Manganese where determined in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate, PDB code: 4qnk:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 16 in 4qnk

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Manganese binding site 1 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:14.5
occ:1.00
 OE1 A:GLU173 2.2 15.7 1.0
O D:HOH478 2.2 30.0 1.0
NE2 A:HIS169 2.2 15.6 1.0
NE2 D:HIS74 2.2 14.0 1.0
NE2 A:HIS47 2.3 15.6 1.0
O A:HOH417 2.3 19.1 1.0
CE1 D:HIS74 3.0 19.7 1.0
CE1 A:HIS169 3.1 16.8 1.0
CE1 A:HIS47 3.2 20.5 1.0
CD A:GLU173 3.2 14.6 1.0
CD2 A:HIS169 3.3 13.4 1.0
CD2 A:HIS47 3.3 18.5 1.0
CD2 D:HIS74 3.4 17.3 1.0
OE2 A:GLU173 3.6 20.9 1.0
O D:HOH534 4.0 37.0 1.0
ND1 D:HIS74 4.2 19.2 1.0
ND1 A:HIS169 4.3 13.9 1.0
ND1 A:HIS47 4.3 15.6 1.0
CG A:HIS169 4.4 13.5 1.0
CG D:HIS74 4.4 16.5 1.0
CG A:HIS47 4.4 9.1 1.0
CG A:GLU173 4.5 10.5 1.0
O D:HOH417 4.8 15.5 1.0
CE A:MET48 4.9 13.4 1.0
CB A:GLU173 4.9 8.5 1.0

Manganese binding site 2 out of 16 in 4qnk

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Manganese binding site 2 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn302

b:10.6
occ:1.00
 O B:HOH410 2.2 12.8 1.0
O A:HOH424 2.2 18.0 1.0
NE2 B:HIS170 2.3 13.6 1.0
OE1 A:GLU77 2.3 10.7 1.0
NE2 A:HIS73 2.3 11.4 1.0
NE2 A:HIS145 2.3 10.9 1.0
CE1 B:HIS170 3.1 10.6 1.0
CE1 A:HIS73 3.2 13.6 1.0
CE1 A:HIS145 3.2 11.4 1.0
CD A:GLU77 3.3 19.0 1.0
CD2 A:HIS73 3.3 9.0 1.0
CD2 A:HIS145 3.3 11.3 1.0
CD2 B:HIS170 3.3 9.9 1.0
OE2 A:GLU77 3.7 15.6 1.0
OD2 B:ASP108 4.0 19.2 1.0
O A:HOH516 4.0 32.4 1.0
O A:HOH554 4.1 36.0 1.0
ND1 B:HIS170 4.3 12.3 1.0
ND1 A:HIS145 4.3 12.3 1.0
ND1 A:HIS73 4.3 9.3 1.0
CG A:HIS145 4.4 13.6 1.0
CG A:HIS73 4.4 12.1 1.0
CG B:HIS170 4.4 8.7 1.0
CG A:GLU77 4.5 20.8 1.0
O B:HOH548 4.8 30.7 1.0
CB A:GLU77 4.8 13.1 1.0
CD2 B:LEU107 4.8 22.7 1.0
O A:HOH401 4.8 11.0 1.0

Manganese binding site 3 out of 16 in 4qnk

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Manganese binding site 3 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:14.5
occ:1.00
 O B:HOH548 2.2 30.7 1.0
OE1 B:GLU173 2.2 14.8 1.0
O B:HOH412 2.2 21.2 1.0
NE2 A:HIS74 2.3 16.0 1.0
NE2 B:HIS47 2.3 13.8 1.0
NE2 B:HIS169 2.3 16.0 1.0
CE1 A:HIS74 3.1 26.7 1.0
CE1 B:HIS47 3.2 17.1 1.0
CD B:GLU173 3.2 15.8 1.0
CE1 B:HIS169 3.2 16.5 1.0
CD2 B:HIS169 3.3 14.5 1.0
CD2 B:HIS47 3.3 14.8 1.0
CD2 A:HIS74 3.4 19.0 1.0
OE2 B:GLU173 3.6 18.9 1.0
O B:HOH560 4.1 37.4 1.0
ND1 A:HIS74 4.3 20.5 1.0
ND1 B:HIS47 4.3 17.1 1.0
ND1 B:HIS169 4.4 12.3 1.0
CG B:HIS169 4.4 13.4 1.0
CG A:HIS74 4.4 12.7 1.0
CG B:HIS47 4.4 11.5 1.0
CG B:GLU173 4.6 13.5 1.0
O A:HOH424 4.8 18.0 1.0
CE B:MET48 4.9 13.7 1.0
CB B:GLU173 4.9 8.7 1.0

Manganese binding site 4 out of 16 in 4qnk

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Manganese binding site 4 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn302

b:9.7
occ:1.00
 O C:HOH405 2.2 12.3 1.0
O B:HOH441 2.2 15.5 1.0
OE1 B:GLU77 2.2 13.6 1.0
NE2 B:HIS73 2.3 10.8 1.0
NE2 C:HIS170 2.3 10.8 1.0
NE2 B:HIS145 2.3 11.9 1.0
CE1 C:HIS170 3.2 11.2 1.0
CE1 B:HIS73 3.2 11.7 1.0
CE1 B:HIS145 3.2 11.4 1.0
CD B:GLU77 3.2 34.5 1.0
CD2 B:HIS73 3.3 8.1 1.0
CD2 B:HIS145 3.3 11.7 1.0
CD2 C:HIS170 3.3 9.9 1.0
OE2 B:GLU77 3.7 17.7 1.0
O B:HOH507 3.9 27.8 1.0
O B:HOH504 4.1 37.6 1.0
OD2 C:ASP108 4.1 20.6 1.0
ND1 B:HIS145 4.3 11.7 1.0
ND1 C:HIS170 4.3 10.4 1.0
ND1 B:HIS73 4.3 9.7 1.0
CG B:HIS145 4.4 9.7 1.0
CG B:HIS73 4.4 8.4 1.0
CG C:HIS170 4.4 11.4 1.0
CG B:GLU77 4.5 25.5 1.0
O C:HOH539 4.6 27.4 1.0
CB B:GLU77 4.8 14.6 1.0
O B:HOH401 4.8 11.5 1.0
CD2 C:LEU107 4.9 25.1 1.0

Manganese binding site 5 out of 16 in 4qnk

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Manganese binding site 5 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:13.3
occ:1.00
 OE1 C:GLU173 2.1 14.9 1.0
O C:HOH539 2.2 27.4 1.0
O C:HOH536 2.2 20.1 1.0
NE2 C:HIS47 2.3 14.0 1.0
NE2 C:HIS169 2.3 16.4 1.0
NE2 B:HIS74 2.3 20.4 1.0
CE1 B:HIS74 3.1 23.3 1.0
CE1 C:HIS169 3.2 13.0 1.0
CE1 C:HIS47 3.2 15.0 1.0
CD C:GLU173 3.2 16.1 1.0
CD2 C:HIS47 3.3 11.3 1.0
CD2 C:HIS169 3.3 15.4 1.0
CD2 B:HIS74 3.4 16.6 1.0
OE2 C:GLU173 3.6 19.0 1.0
O C:HOH558 4.1 44.2 1.0
ND1 C:HIS169 4.3 12.4 1.0
ND1 C:HIS47 4.3 20.1 1.0
ND1 B:HIS74 4.3 16.6 1.0
CG C:HIS47 4.4 10.1 1.0
CG C:HIS169 4.4 13.7 1.0
CG B:HIS74 4.4 12.7 1.0
CG C:GLU173 4.5 10.0 1.0
CE C:MET48 4.8 9.8 1.0
O B:HOH441 4.9 15.5 1.0
CB C:GLU173 4.9 7.8 1.0

Manganese binding site 6 out of 16 in 4qnk

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Manganese binding site 6 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn302

b:10.0
occ:1.00
 O D:HOH514 2.2 13.2 1.0
O C:HOH547 2.2 17.9 1.0
OE1 C:GLU77 2.2 9.7 1.0
NE2 C:HIS73 2.2 10.4 1.0
NE2 C:HIS145 2.3 12.7 1.0
NE2 D:HIS170 2.3 13.2 1.0
CE1 C:HIS145 3.2 12.2 1.0
CE1 C:HIS73 3.2 17.7 1.0
CE1 D:HIS170 3.2 11.0 1.0
CD C:GLU77 3.2 19.3 1.0
CD2 C:HIS73 3.3 9.8 1.0
CD2 C:HIS145 3.3 10.0 1.0
CD2 D:HIS170 3.3 9.9 1.0
OE2 C:GLU77 3.7 13.3 1.0
O C:HOH516 3.9 31.4 1.0
OD2 D:ASP108 4.1 17.8 1.0
O C:HOH549 4.2 33.9 1.0
ND1 C:HIS145 4.3 10.5 1.0
ND1 C:HIS73 4.3 11.9 1.0
ND1 D:HIS170 4.4 8.7 1.0
CG C:HIS145 4.4 9.5 1.0
CG C:HIS73 4.4 9.0 1.0
CG D:HIS170 4.4 8.7 1.0
CG C:GLU77 4.5 14.6 1.0
O D:HOH471 4.7 28.3 1.0
CB C:GLU77 4.8 9.8 1.0
CD2 D:LEU107 4.8 24.5 1.0
O C:HOH402 4.9 10.1 1.0

Manganese binding site 7 out of 16 in 4qnk

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Manganese binding site 7 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:9.9
occ:1.00
 O A:HOH408 2.2 10.7 1.0
NE2 D:HIS73 2.2 10.7 1.0
O D:HOH417 2.2 15.5 1.0
NE2 A:HIS170 2.3 10.9 1.0
OE1 D:GLU77 2.3 13.2 1.0
NE2 D:HIS145 2.3 9.5 1.0
CE1 A:HIS170 3.1 12.7 1.0
CE1 D:HIS73 3.1 15.1 1.0
CD2 D:HIS145 3.2 7.5 1.0
CD D:GLU77 3.2 36.8 1.0
CE1 D:HIS145 3.2 11.2 1.0
CD2 D:HIS73 3.2 9.2 1.0
CD2 A:HIS170 3.3 9.4 1.0
OE2 D:GLU77 3.7 15.2 1.0
OD2 A:ASP108 4.1 18.1 1.0
O D:HOH536 4.1 34.4 1.0
ND1 A:HIS170 4.3 12.4 1.0
ND1 D:HIS73 4.3 11.5 1.0
ND1 D:HIS145 4.3 12.6 1.0
CG D:HIS145 4.4 10.4 1.0
CG D:HIS73 4.4 10.1 1.0
CG A:HIS170 4.4 8.5 1.0
CG D:GLU77 4.5 13.2 1.0
O D:HOH478 4.7 30.0 1.0
CB D:GLU77 4.7 12.4 1.0
CD2 A:LEU107 4.8 25.3 1.0
O D:HOH401 4.9 11.2 1.0

Manganese binding site 8 out of 16 in 4qnk

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Manganese binding site 8 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn302

b:14.2
occ:1.00
 OE1 D:GLU173 2.2 15.6 1.0
O D:HOH471 2.2 28.3 1.0
NE2 C:HIS74 2.2 17.7 1.0
NE2 D:HIS169 2.2 12.4 1.0
NE2 D:HIS47 2.3 17.1 1.0
O D:HOH428 2.3 17.3 1.0
CE1 C:HIS74 3.1 20.1 1.0
CE1 D:HIS169 3.2 15.1 1.0
CD D:GLU173 3.2 15.4 1.0
CE1 D:HIS47 3.2 21.2 1.0
CD2 D:HIS169 3.3 13.5 1.0
CD2 C:HIS74 3.3 18.7 1.0
CD2 D:HIS47 3.3 12.4 1.0
OE2 D:GLU173 3.6 15.2 1.0
ND1 C:HIS74 4.3 19.2 1.0
ND1 D:HIS169 4.3 13.1 1.0
ND1 D:HIS47 4.4 14.1 1.0
CG D:HIS169 4.4 12.8 1.0
CG C:HIS74 4.4 17.8 1.0
CG D:HIS47 4.5 13.0 1.0
CG D:GLU173 4.5 10.8 1.0
O C:HOH547 4.8 17.9 1.0
CB D:GLU173 4.9 10.4 1.0
CE D:MET48 4.9 12.4 1.0

Manganese binding site 9 out of 16 in 4qnk

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Manganese binding site 9 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:13.6
occ:1.00
 OE1 E:GLU173 2.2 13.0 1.0
O H:HOH535 2.2 28.4 1.0
O E:HOH404 2.2 16.0 1.0
NE2 H:HIS74 2.2 16.7 1.0
NE2 E:HIS169 2.3 13.0 1.0
NE2 E:HIS47 2.3 11.3 1.0
CE1 H:HIS74 3.1 22.2 1.0
CE1 E:HIS169 3.2 12.8 1.0
CD E:GLU173 3.2 17.7 1.0
CE1 E:HIS47 3.2 15.2 1.0
CD2 E:HIS169 3.3 12.3 1.0
CD2 E:HIS47 3.3 12.8 1.0
CD2 H:HIS74 3.3 16.0 1.0
OE2 E:GLU173 3.5 18.4 1.0
ND1 H:HIS74 4.3 19.1 1.0
ND1 E:HIS169 4.3 12.4 1.0
ND1 E:HIS47 4.4 16.2 1.0
CG E:HIS169 4.4 12.4 1.0
CG H:HIS74 4.4 13.8 1.0
CG E:HIS47 4.5 12.3 1.0
CG E:GLU173 4.5 12.7 1.0
CB E:GLU173 4.8 8.4 1.0
O H:HOH429 4.9 16.1 1.0
CE E:MET48 4.9 12.4 1.0

Manganese binding site 10 out of 16 in 4qnk

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Manganese binding site 10 out of 16 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn302

b:10.1
occ:1.00
 O F:HOH408 2.2 10.2 1.0
O E:HOH456 2.2 16.6 1.0
NE2 E:HIS73 2.2 12.2 1.0
NE2 F:HIS170 2.3 7.7 1.0
OE1 E:GLU77 2.3 12.2 1.0
NE2 E:HIS145 2.3 8.9 1.0
CE1 E:HIS73 3.2 11.6 1.0
CE1 F:HIS170 3.2 12.2 1.0
CD2 F:HIS170 3.3 8.8 1.0
CD E:GLU77 3.3 17.9 1.0
CD2 E:HIS73 3.3 12.4 1.0
CE1 E:HIS145 3.3 12.6 1.0
CD2 E:HIS145 3.3 10.9 1.0
OE2 E:GLU77 3.7 12.5 1.0
O E:HOH554 4.0 30.5 1.0
OD2 F:ASP108 4.1 19.1 1.0
ND1 E:HIS73 4.3 11.0 1.0
ND1 F:HIS170 4.3 10.0 1.0
ND1 E:HIS145 4.4 10.0 1.0
CG F:HIS170 4.4 10.0 1.0
CG E:HIS73 4.4 12.8 1.0
CG E:HIS145 4.4 11.4 1.0
CG E:GLU77 4.5 16.4 1.0
O F:HOH469 4.7 28.2 1.0
CB E:GLU77 4.8 11.8 1.0
O E:HOH401 4.8 9.4 1.0
CD2 F:LEU107 4.8 27.7 1.0

Reference:

C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice. Crystal Structures Reveal That the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled By Switching Mn(II) Coordination. Structure V. 23 1236 2015.
ISSN: ISSN 0969-2126
PubMed: 26095028
DOI: 10.1016/J.STR.2015.05.012
Page generated: Sat Oct 5 21:01:34 2024

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