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Manganese in PDB 8ujf: X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13

Enzymatic activity of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13

All present enzymatic activity of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13:
2.4.1.41;

Protein crystallography data

The structure of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13, PDB code: 8ujf was solved by P.Kumar, N.L.Samara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.01 / 2.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.233, 123.693, 165.724, 90, 90, 90
R / Rfree (%) 21.7 / 27.4

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13 (pdb code 8ujf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13, PDB code: 8ujf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8ujf

Go back to Manganese Binding Sites List in 8ujf
Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:29.8
occ:0.93
 OD2 A:ASP276 2.2 47.8 1.0
NE2 A:HIS278 2.3 58.3 1.0
NE2 A:HIS414 2.3 35.9 1.0
O2B A:UDP701 2.4 57.8 0.6
O1B A:UDP701 2.4 38.4 0.6
O3A A:UDP701 2.6 78.5 0.6
PB A:UDP701 2.6 80.5 0.6
CG A:ASP276 2.8 56.5 1.0
CE1 A:HIS278 3.0 58.8 1.0
OD1 A:ASP276 3.1 43.5 1.0
HE1 A:HIS278 3.1 70.5 1.0
CE1 A:HIS414 3.3 36.6 1.0
CD2 A:HIS414 3.3 34.6 1.0
CD2 A:HIS278 3.4 38.7 1.0
HE1 A:HIS414 3.4 44.0 1.0
HD2 A:HIS414 3.4 41.5 1.0
O1A A:UDP701 3.5 73.0 0.6
H5'1 A:UDP701 3.6 78.0 0.6
HD2 A:HIS278 3.6 46.4 1.0
PA A:UDP701 3.7 76.9 0.6
H3' A:UDP701 3.9 79.8 0.6
CB A:ASP276 4.1 45.9 1.0
O3B A:UDP701 4.1 64.7 0.6
HB3 A:ASP276 4.1 55.0 1.0
ND1 A:HIS278 4.2 44.2 1.0
HB2 A:ASP276 4.3 55.0 1.0
CG A:HIS278 4.4 31.0 1.0
ND1 A:HIS414 4.4 31.4 1.0
C5' A:UDP701 4.4 65.0 0.6
CG A:HIS414 4.4 39.3 1.0
O5' A:UDP701 4.5 62.5 0.6
NH1 A:ARG417 4.6 79.3 1.0
HH11 A:ARG417 4.7 95.1 1.0
O2A A:UDP701 4.7 73.5 0.6
CZ A:ARG417 4.8 87.8 1.0
HH12 A:ARG417 4.8 95.1 1.0
C3' A:UDP701 4.8 66.5 0.6
HD1 A:HIS278 4.9 53.0 1.0

Manganese binding site 2 out of 4 in 8ujf

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Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn703

b:57.9
occ:0.45
 OE1 A:GLU336 2.2 82.2 1.0
CD A:GLU336 2.2 77.2 1.0
O A:HOH806 2.2 47.9 1.0
O A:HOH805 2.2 52.7 1.0
NE2 A:HIS333 2.2 48.5 1.0
OE2 A:GLU336 2.4 71.4 1.0
HG2 A:GLU336 2.9 87.9 1.0
CG A:GLU336 3.1 73.3 1.0
CE1 A:HIS333 3.1 51.8 1.0
HE1 A:HIS333 3.2 62.1 1.0
CD2 A:HIS333 3.3 42.8 1.0
HH11 A:ARG567 3.4 128.3 1.0
HG3 A:GLU336 3.5 87.9 1.0
HD2 A:HIS333 3.5 51.4 1.0
NH1 A:ARG567 3.8 107.0 1.0
HH12 A:ARG567 4.0 128.3 1.0
O A:CYS566 4.3 60.4 1.0
ND1 A:HIS333 4.3 48.6 1.0
HB3 A:GLU336 4.4 71.7 1.0
CG A:HIS333 4.4 29.2 1.0
CB A:GLU336 4.4 59.7 1.0
HH22 A:ARG567 4.5 106.6 1.0
CZ A:ARG567 4.5 97.2 1.0
OE1 A:GLU554 4.7 49.3 1.0
HD21 A:LEU327 4.7 43.3 1.0
NH2 A:ARG567 4.8 88.8 1.0
HB2 A:GLU336 4.9 71.7 1.0

Manganese binding site 3 out of 4 in 8ujf

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Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn703

b:30.6
occ:1.00
 NE2 B:HIS414 2.1 37.9 1.0
OD2 B:ASP276 2.2 67.1 1.0
O B:HOH801 2.2 44.8 1.0
NE2 B:HIS278 2.2 35.5 1.0
O1A B:UDP701 2.3 61.4 1.0
O1B B:UDP701 2.4 94.2 1.0
O2B B:UDP701 2.7 79.6 1.0
CE1 B:HIS414 3.0 47.6 1.0
PB B:UDP701 3.1 75.1 1.0
CD2 B:HIS414 3.1 45.2 1.0
CD2 B:HIS278 3.1 39.0 1.0
HD2 B:HIS278 3.2 46.7 1.0
HE1 B:HIS414 3.2 57.1 1.0
HD2 B:HIS414 3.3 54.2 1.0
CE1 B:HIS278 3.3 40.7 1.0
CG B:ASP276 3.3 63.0 1.0
PA B:UDP701 3.5 57.7 1.0
HE1 B:HIS278 3.5 48.8 1.0
O3A B:UDP701 3.6 80.7 1.0
HB3 B:ASP276 3.6 37.8 1.0
H5'1 B:UDP701 3.9 70.2 1.0
CB B:ASP276 4.0 31.5 1.0
ND1 B:HIS414 4.2 49.5 1.0
HB2 B:ASP276 4.2 37.8 1.0
CG B:HIS414 4.2 41.0 1.0
CG B:HIS278 4.3 38.4 1.0
OD1 B:ASP276 4.3 69.8 1.0
ND1 B:HIS278 4.3 40.0 1.0
O2A B:UDP701 4.4 56.0 1.0
O B:ILE415 4.4 36.1 1.0
O3B B:UDP701 4.4 39.9 1.0
H3' B:UDP701 4.5 52.4 1.0
O5' B:UDP701 4.6 75.9 1.0
C5' B:UDP701 4.7 58.5 1.0
HD1 B:HIS414 4.9 59.4 1.0

Manganese binding site 4 out of 4 in 8ujf

Go back to Manganese Binding Sites List in 8ujf
Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and MUC5AC-3,13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn704

b:76.9
occ:0.51
 CD B:GLU336 2.1 82.8 1.0
OE2 B:GLU336 2.1 102.2 1.0
O B:HOH805 2.3 31.0 1.0
O B:HOH810 2.3 49.5 1.0
NE2 B:HIS333 2.3 73.7 1.0
OE1 B:GLU336 2.4 63.5 1.0
HG2 B:GLU336 2.8 80.2 1.0
HE1 B:HIS333 2.9 85.1 1.0
CE1 B:HIS333 2.9 70.9 1.0
CG B:GLU336 3.0 66.8 1.0
HG3 B:GLU336 3.2 80.2 1.0
CD2 B:HIS333 3.5 66.5 1.0
HD2 B:HIS333 3.8 79.8 1.0
HH11 B:ARG567 4.0 100.1 1.0
ND1 B:HIS333 4.1 54.5 1.0
CB B:GLU336 4.3 61.7 1.0
CG B:HIS333 4.4 49.8 1.0
HB3 B:GLU336 4.4 74.0 1.0
HH12 B:ARG567 4.4 100.1 1.0
O B:CYS566 4.4 48.1 1.0
NH1 B:ARG567 4.5 83.5 1.0
OE1 B:GLU554 4.6 52.8 1.0
HB2 B:GLU336 4.8 74.0 1.0
HD1 B:HIS333 4.8 65.4 1.0
O B:SER334 4.9 50.3 1.0
HD3 B:ARG567 4.9 93.5 1.0
HD21 B:LEU327 4.9 56.4 1.0

Reference:

P.Kumar, T.Tomita, T.A.Gerken, C.J.Ballard, Y.S.Lee, L.M.Weiss, N.L.Samara. A Toxoplasma Gondii O-Glycosyltransferase That Modulates Bradyzoite Cyst Wall Rigidity Is Distinct From Host Homologues Nat Commun V. 15 3792 2024.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-024-48253-W
Page generated: Sun Oct 6 14:00:52 2024

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