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Manganese in PDB 5oey: Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.

Enzymatic activity of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.

All present enzymatic activity of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.:
3.1.3.11;

Protein crystallography data

The structure of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form., PDB code: 5oey was solved by M.Yuan, M.G.Vasquez-Valdivieso, I.W.Mcnae, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.14 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 92.010, 104.150, 137.740, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.1

Other elements in 5oey:

The structure of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. also contains other interesting chemical elements:

Potassium (K) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. (pdb code 5oey). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form., PDB code: 5oey:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 5oey

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Manganese binding site 1 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:35.3
occ:1.00
 O2 A:PO4701 1.9 34.8 1.0
OE1 A:GLU97 2.2 38.0 1.0
OD1 A:ASP118 2.2 27.3 1.0
O A:LEU120 2.2 26.9 1.0
CG A:ASP118 3.2 23.9 1.0
C A:LEU120 3.2 26.3 1.0
CD A:GLU97 3.2 36.8 1.0
OE2 A:GLU98 3.2 38.9 1.0
P A:PO4701 3.3 36.7 1.0
OD2 A:ASP118 3.4 24.2 1.0
K A:K704 3.5 27.4 1.0
OD1 A:ASP74 3.6 44.7 1.0
O1 A:PO4701 3.7 40.8 1.0
CG A:GLU97 3.7 36.3 1.0
N A:ASP121 4.0 28.6 1.0
N A:LEU120 4.0 24.9 1.0
CA A:ASP121 4.1 30.7 1.0
MN A:MN703 4.1 34.2 1.0
CA A:LEU120 4.1 24.6 1.0
OG A:SER123 4.1 48.8 1.0
O3 A:PO4701 4.2 36.3 1.0
OE2 A:GLU97 4.3 42.2 1.0
O4 A:PO4701 4.4 34.5 1.0
CD A:GLU98 4.5 38.4 1.0
CB A:ASP118 4.5 22.5 1.0
CD A:PRO119 4.7 22.3 1.0
CG A:ASP74 4.7 40.5 1.0
CB A:LEU120 4.7 24.6 1.0
CB A:GLU97 4.7 34.5 1.0
C A:ASP118 4.9 21.9 1.0
CA A:ASP118 4.9 22.0 1.0
N A:PRO119 4.9 21.6 1.0

Manganese binding site 2 out of 8 in 5oey

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Manganese binding site 2 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:34.2
occ:1.00
 OE2 A:GLU284 2.2 36.2 1.0
OD1 A:ASP121 2.2 27.1 1.0
OD2 A:ASP118 2.2 24.2 1.0
O3 A:PO4701 2.5 36.3 1.0
O2 A:PO4701 2.6 34.8 1.0
P A:PO4701 2.7 36.7 1.0
O4 A:PO4701 2.8 34.5 1.0
CG A:ASP121 3.2 31.6 1.0
CD A:GLU284 3.3 36.0 1.0
CG A:ASP118 3.3 23.9 1.0
CB A:ASP121 3.5 31.6 1.0
CA A:ASP121 3.7 30.7 1.0
OD1 A:ASP118 3.9 27.3 1.0
CG A:GLU284 3.9 33.5 1.0
OE1 A:GLU97 4.1 38.0 1.0
MN A:MN702 4.1 35.3 1.0
NH2 A:ARG280 4.2 49.1 1.0
O1 A:PO4701 4.2 40.8 1.0
OE1 A:GLU284 4.3 39.8 1.0
OD2 A:ASP121 4.3 31.1 1.0
N A:GLY122 4.4 30.4 1.0
CB A:ASP118 4.4 22.5 1.0
C A:ASP121 4.6 30.3 1.0
N A:ASP121 4.7 28.6 1.0
CD A:GLU97 4.8 36.8 1.0
O A:LEU120 4.8 26.9 1.0
OE2 A:GLU97 5.0 42.2 1.0
CD1 A:ILE135 5.0 15.5 1.0

Manganese binding site 3 out of 8 in 5oey

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Manganese binding site 3 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:15.7
occ:1.00
 O B:HOH801 2.1 8.9 1.0
OE1 B:GLU97 2.1 18.9 1.0
O B:LEU120 2.1 21.5 1.0
OD1 B:ASP118 2.2 13.8 1.0
O1 B:PO4701 3.0 45.3 1.0
C B:LEU120 3.1 21.2 1.0
CG B:ASP118 3.1 14.2 1.0
CD B:GLU97 3.1 20.1 1.0
OD2 B:ASP118 3.3 16.3 1.0
O4 B:PO4701 3.4 39.1 1.0
MN B:MN703 3.4 21.0 1.0
OE2 B:GLU98 3.5 36.0 1.0
OE2 B:GLU97 3.6 22.6 1.0
P B:PO4701 3.7 49.3 1.0
OD1 B:ASP74 3.8 27.1 1.0
N B:ASP121 3.8 24.6 1.0
CA B:ASP121 3.8 27.4 1.0
OG B:SER123 4.1 24.9 1.0
N B:LEU120 4.1 17.7 1.0
O2 B:PO4701 4.1 40.9 1.0
CA B:LEU120 4.1 18.9 1.0
CG B:GLU97 4.4 20.1 1.0
CB B:ASP118 4.5 14.1 1.0
CD B:GLU98 4.7 30.9 1.0
CB B:LEU120 4.8 18.7 1.0
CB B:ASP121 4.8 30.4 1.0
C B:ASP121 4.8 26.7 1.0
N B:GLY122 4.8 26.8 1.0
CB B:GLU97 4.8 20.0 1.0
CD B:PRO119 4.9 15.7 1.0
CG B:ASP74 4.9 27.2 1.0
CA B:ASP118 5.0 13.8 1.0
C B:ASP118 5.0 14.3 1.0

Manganese binding site 4 out of 8 in 5oey

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Manganese binding site 4 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:21.0
occ:1.00
 O1 B:PO4701 1.5 45.3 1.0
OE2 B:GLU284 1.9 18.2 1.0
OE2 B:GLU97 2.1 22.6 1.0
OD2 B:ASP118 2.3 16.3 1.0
P B:PO4701 2.9 49.3 1.0
CD B:GLU97 3.0 20.1 1.0
CD B:GLU284 3.1 16.8 1.0
CG B:ASP118 3.1 14.2 1.0
OE1 B:GLU97 3.3 18.9 1.0
MN B:MN702 3.4 15.7 1.0
O2 B:PO4701 3.5 40.9 1.0
OD1 B:ASP118 3.5 13.8 1.0
OD1 B:ASP121 3.5 39.9 1.0
O3 B:PO4701 3.6 42.3 1.0
O4 B:PO4701 3.9 39.1 1.0
CG B:GLU284 3.9 16.0 1.0
OE1 B:GLU284 4.0 16.2 1.0
O B:HOH835 4.1 20.0 1.0
CB B:ASP118 4.3 14.1 1.0
CG B:GLU97 4.4 20.1 1.0
CG B:ASP121 4.5 35.4 1.0
CA B:ASP121 4.5 27.4 1.0
CB B:ASP121 4.5 30.4 1.0
O B:HOH823 4.6 17.2 1.0
O B:LEU120 4.9 21.5 1.0

Manganese binding site 5 out of 8 in 5oey

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Manganese binding site 5 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn702

b:31.4
occ:1.00
 O4 C:PO4701 1.6 41.5 1.0
O C:HOH801 1.8 33.9 1.0
OD1 C:ASP118 2.1 24.0 1.0
OE1 C:GLU97 2.1 34.1 1.0
O C:LEU120 2.3 25.9 1.0
CG C:ASP118 2.9 21.9 1.0
OD2 C:ASP118 3.0 20.6 1.0
P C:PO4701 3.1 38.4 1.0
C C:LEU120 3.2 24.6 1.0
CD C:GLU97 3.2 34.6 1.0
MN C:MN703 3.6 21.0 1.0
O1 C:PO4701 3.6 41.6 1.0
K C:K704 3.6 25.9 1.0
OE2 C:GLU97 3.7 34.7 1.0
OE2 C:GLU98 3.7 36.7 1.0
CA C:ASP121 3.8 29.1 1.0
N C:ASP121 3.8 26.6 1.0
O2 C:PO4701 3.9 35.2 1.0
OD1 C:ASP74 4.0 37.9 1.0
O3 C:PO4701 4.0 39.4 1.0
N C:LEU120 4.2 21.5 1.0
CA C:LEU120 4.2 23.2 1.0
OG C:SER123 4.3 48.9 1.0
CB C:ASP118 4.3 22.2 1.0
CG C:GLU97 4.5 34.1 1.0
CB C:ASP121 4.6 29.3 1.0
CB C:GLU97 4.8 34.1 1.0
CA C:ASP118 4.8 21.9 1.0
C C:ASP121 4.8 30.0 1.0
N C:GLY122 4.9 33.1 1.0
OE2 C:GLU284 4.9 24.4 1.0
NH1 C:ARG280 4.9 40.8 1.0
C C:ASP118 4.9 21.3 1.0
CB C:LEU120 4.9 23.8 1.0
CD C:GLU98 4.9 35.6 1.0
CD C:PRO119 5.0 23.1 1.0

Manganese binding site 6 out of 8 in 5oey

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Manganese binding site 6 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn703

b:21.0
occ:1.00
 OD2 C:ASP118 2.1 20.6 1.0
OE2 C:GLU284 2.2 24.4 1.0
OD1 C:ASP121 2.2 27.0 1.0
O2 C:PO4701 2.2 35.2 1.0
O4 C:PO4701 2.9 41.5 1.0
P C:PO4701 3.0 38.4 1.0
CG C:ASP121 3.1 30.3 1.0
CG C:ASP118 3.3 21.9 1.0
CD C:GLU284 3.3 23.9 1.0
CB C:ASP121 3.4 29.3 1.0
MN C:MN702 3.6 31.4 1.0
CA C:ASP121 3.6 29.1 1.0
O1 C:PO4701 3.6 41.6 1.0
OD1 C:ASP118 3.9 24.0 1.0
CG C:GLU284 3.9 23.6 1.0
OE1 C:GLU97 4.1 34.1 1.0
OE1 C:GLU284 4.3 23.5 1.0
NH1 C:ARG280 4.3 40.8 1.0
OD2 C:ASP121 4.3 35.0 1.0
O3 C:PO4701 4.4 39.4 1.0
CB C:ASP118 4.4 22.2 1.0
N C:GLY122 4.4 33.1 1.0
O C:HOH824 4.4 14.3 1.0
C C:ASP121 4.5 30.0 1.0
N C:ASP121 4.6 26.6 1.0
O C:LEU120 4.8 25.9 1.0
O C:HOH828 4.8 39.0 1.0
CD1 C:ILE135 4.9 14.5 1.0

Manganese binding site 7 out of 8 in 5oey

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Manganese binding site 7 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn702

b:70.9
occ:1.00
 OD2 D:ASP74 2.7 56.1 1.0
O3 D:PO4701 2.8 85.5 1.0
OE2 D:GLU98 2.8 56.7 1.0
OE1 D:GLU98 2.9 78.8 1.0
CD D:GLU98 3.2 64.4 1.0
O2 D:PO4701 3.5 84.7 1.0
K D:K704 3.5 12.9 1.0
O D:HOH803 3.7 13.6 1.0
CG D:ASP74 3.7 53.4 1.0
P D:PO4701 3.8 83.4 1.0
OE2 D:GLU97 4.0 37.6 1.0
OD1 D:ASP74 4.5 61.0 1.0
CB D:ASP74 4.5 48.6 1.0
OG D:SER123 4.7 39.0 1.0
O4 D:PO4701 4.7 81.5 1.0
CG D:GLU98 4.7 59.7 1.0
CD D:GLU97 4.9 36.9 1.0
O1 D:PO4701 4.9 87.5 1.0
CG D:GLU97 4.9 39.2 1.0

Manganese binding site 8 out of 8 in 5oey

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Manganese binding site 8 out of 8 in the Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Leishmania Major Fructose-1,6-Bisphosphatase in Holo Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn703

b:27.5
occ:1.00
 OE2 D:GLU284 1.9 27.8 1.0
O4 D:PO4701 1.9 81.5 1.0
OD2 D:ASP118 2.2 20.8 1.0
OD1 D:ASP121 2.5 34.3 1.0
OE1 D:GLU97 2.7 36.2 1.0
OE2 D:GLU97 2.7 37.6 1.0
CD D:GLU97 3.1 36.9 1.0
CG D:ASP118 3.1 19.9 1.0
CD D:GLU284 3.1 24.8 1.0
P D:PO4701 3.2 83.4 1.0
OD1 D:ASP118 3.5 19.3 1.0
O3 D:PO4701 3.7 85.5 1.0
CG D:ASP121 3.7 39.0 1.0
K D:K704 3.8 12.9 1.0
CG D:GLU284 3.9 23.7 1.0
O1 D:PO4701 3.9 87.5 1.0
OE1 D:GLU284 4.0 23.3 1.0
CB D:ASP118 4.2 19.6 1.0
CB D:ASP121 4.3 37.8 1.0
O2 D:PO4701 4.3 84.7 1.0
CA D:ASP121 4.3 35.6 1.0
CG D:GLU97 4.5 39.2 1.0
NH1 D:ARG280 4.6 41.9 1.0
OD2 D:ASP121 4.8 42.4 1.0
O D:LEU120 4.9 27.1 1.0

Reference:

M.Yuan, M.G.Vasquez-Valdivieso, I.W.Mcnae, P.A.M.Michels, L.A.Fothergill-Gilmore, M.D.Walkinshaw. Structures of Leishmania Fructose-1,6-Bisphosphatase Reveal Species-Specific Differences in the Mechanism of Allosteric Inhibition. J. Mol. Biol. V. 429 3075 2017.
ISSN: ESSN 1089-8638
PubMed: 28882541
DOI: 10.1016/J.JMB.2017.08.010
Page generated: Sun Oct 6 02:16:19 2024

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