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Manganese in PDB 8ujg: X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and the Mono-Glycopeptide SRS13.2

Enzymatic activity of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and the Mono-Glycopeptide SRS13.2

All present enzymatic activity of X-Ray Crystal Structure of Toxoplasma Gondii Galnac-T3 in Complex with Udp-Galnac, MN2+, and the Mono-Glycopeptide SRS13.2:
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 the Mono-Glycopeptide SRS13.2, PDB code: 8ujg 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) 29.66 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.614, 122.624, 165.655, 90, 90, 90
R / Rfree (%) 19.2 / 23.7

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 the Mono-Glycopeptide SRS13.2 (pdb code 8ujg). 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 the Mono-Glycopeptide SRS13.2, PDB code: 8ujg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8ujg

Go back to Manganese Binding Sites List in 8ujg
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 the Mono-Glycopeptide SRS13.2


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 the Mono-Glycopeptide SRS13.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:32.5
occ:1.00
 O1A A:UDP703 2.1 46.5 0.9
OD2 A:ASP276 2.2 39.7 1.0
O A:HOH887 2.2 36.1 1.0
NE2 A:HIS414 2.2 32.7 1.0
NE2 A:HIS278 2.2 39.9 1.0
O2B A:UDP703 2.4 34.5 1.0
CE1 A:HIS414 3.0 35.9 1.0
HE1 A:HIS414 3.0 43.0 1.0
CE1 A:HIS278 3.2 40.1 1.0
CD2 A:HIS278 3.3 30.6 1.0
PA A:UDP703 3.3 39.0 1.0
HE1 A:HIS278 3.3 48.2 1.0
CG A:ASP276 3.3 50.2 1.0
PB A:UDP703 3.4 47.2 0.1
CD2 A:HIS414 3.4 40.3 1.0
HD2 A:HIS278 3.4 36.8 1.0
O3A A:UDP703 3.5 39.9 0.6
HB3 A:ASP276 3.6 50.9 1.0
HD2 A:HIS414 3.7 48.4 1.0
O3B A:UDP703 3.7 55.3 0.7
H5'1 A:UDP703 3.7 50.6 1.0
CB A:ASP276 4.0 42.4 1.0
H3' A:UDP703 4.1 52.1 1.0
ND1 A:HIS414 4.2 38.5 1.0
HB2 A:ASP276 4.3 50.9 1.0
O2A A:UDP703 4.3 44.3 1.0
ND1 A:HIS278 4.3 29.4 1.0
OD1 A:ASP276 4.3 51.8 1.0
O5' A:UDP703 4.4 37.1 1.0
CG A:HIS278 4.4 32.5 1.0
O A:ILE415 4.4 36.7 1.0
CG A:HIS414 4.4 29.2 1.0
C5' A:UDP703 4.5 42.2 1.0
HH21 A:ARG417 4.5 52.3 1.0
O1B A:UDP703 4.7 46.4 0.1
HE A:ARG417 4.8 61.9 1.0
HD1 A:HIS414 5.0 46.2 1.0
C3' A:UDP703 5.0 43.4 1.0

Manganese binding site 2 out of 4 in 8ujg

Go back to Manganese Binding Sites List in 8ujg
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 the Mono-Glycopeptide SRS13.2


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 the Mono-Glycopeptide SRS13.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:81.8
occ:0.50
 O A:HOH867 2.2 56.8 1.0
OE1 A:GLU336 2.2 82.9 1.0
O A:HOH906 2.2 56.8 1.0
O A:HOH924 2.2 66.8 1.0
O A:HOH806 2.2 97.3 1.0
CD A:GLU336 2.3 82.7 1.0
NE2 A:HIS333 2.5 56.2 1.0
OE2 A:GLU336 2.7 78.6 1.0
HG3 A:GLU336 2.8 82.4 1.0
CG A:GLU336 3.0 68.7 1.0
HG2 A:GLU336 3.3 82.4 1.0
HH21 A:ARG567 3.4 134.8 1.0
CE1 A:HIS333 3.4 44.8 1.0
CD2 A:HIS333 3.5 51.7 1.0
HE1 A:HIS333 3.5 53.8 1.0
HD2 A:HIS333 3.6 62.0 1.0
O A:HOH919 3.9 50.9 1.0
NH2 A:ARG567 4.2 112.3 1.0
O A:CYS566 4.3 51.1 1.0
CB A:GLU336 4.4 57.6 1.0
HE A:ARG567 4.4 124.6 1.0
O A:HOH818 4.5 55.3 1.0
HD21 A:LEU327 4.5 41.8 1.0
HB3 A:GLU336 4.5 69.2 1.0
ND1 A:HIS333 4.5 52.2 1.0
HH22 A:ARG567 4.5 134.8 1.0
H2 A:HOH818 4.5 66.4 1.0
CG A:HIS333 4.6 52.7 1.0
O A:HOH828 4.8 52.4 1.0
HB2 A:GLU336 4.8 69.2 1.0
HG2 A:GLU554 5.0 56.3 1.0

Manganese binding site 3 out of 4 in 8ujg

Go back to Manganese Binding Sites List in 8ujg
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 the Mono-Glycopeptide SRS13.2


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 the Mono-Glycopeptide SRS13.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:38.6
occ:1.00
 OD2 B:ASP276 2.2 49.6 1.0
O B:HOH801 2.2 54.4 1.0
NE2 B:HIS414 2.3 40.7 1.0
NE2 B:HIS278 2.3 37.1 1.0
O2B B:UDP703 2.3 41.6 0.5
O1A B:UDP703 2.4 44.6 0.7
O1B B:UDP703 2.4 44.6 0.8
PB B:UDP703 2.6 43.4 0.3
CG B:ASP276 2.7 53.4 1.0
O3A B:UDP703 2.7 47.6 0.4
OD1 B:ASP276 3.0 48.9 1.0
PA B:UDP703 3.1 45.9 0.4
CE1 B:HIS278 3.1 43.5 1.0
HE1 B:HIS278 3.2 52.3 1.0
CE1 B:HIS414 3.3 43.0 1.0
CD2 B:HIS414 3.3 37.2 1.0
CD2 B:HIS278 3.4 36.6 1.0
HE1 B:HIS414 3.4 51.6 1.0
HD2 B:HIS414 3.4 44.7 1.0
HD2 B:HIS278 3.6 43.9 1.0
H5'1 B:UDP703 3.6 53.1 0.9
H3' B:UDP703 3.9 67.6 0.8
CB B:ASP276 4.0 32.0 1.0
HB3 B:ASP276 4.0 38.4 1.0
O2A B:UDP703 4.1 47.0 0.6
O3B B:UDP703 4.1 46.2 0.4
HB2 B:ASP276 4.2 38.4 1.0
O5' B:UDP703 4.2 50.9 0.8
ND1 B:HIS278 4.3 45.5 1.0
C5' B:UDP703 4.4 44.2 0.9
HH21 B:ARG417 4.4 86.9 1.0
ND1 B:HIS414 4.4 41.9 1.0
CG B:HIS414 4.4 45.5 1.0
CG B:HIS278 4.4 42.1 1.0
HE B:ARG417 4.8 92.3 1.0
C3' B:UDP703 4.8 56.4 0.8
NH2 B:ARG417 4.9 72.4 1.0
O B:ILE415 5.0 43.6 1.0

Manganese binding site 4 out of 4 in 8ujg

Go back to Manganese Binding Sites List in 8ujg
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 the Mono-Glycopeptide SRS13.2


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 the Mono-Glycopeptide SRS13.2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:60.4
occ:0.46
 OE2 B:GLU336 2.2 86.2 1.0
O B:HOH821 2.2 36.0 1.0
O B:HOH811 2.2 59.6 1.0
O B:HOH898 2.2 56.1 1.0
O B:HOH804 2.2 66.6 1.0
NE2 B:HIS333 2.3 44.2 1.0
CD B:GLU336 2.4 77.5 1.0
HG2 B:GLU336 2.5 68.3 1.0
CG B:GLU336 2.7 56.9 1.0
HG3 B:GLU336 2.7 68.3 1.0
CD2 B:HIS333 3.2 38.9 1.0
CE1 B:HIS333 3.3 40.0 1.0
OE1 B:GLU336 3.3 77.2 1.0
HD2 B:HIS333 3.3 46.6 1.0
HE1 B:HIS333 3.4 48.0 1.0
HH12 B:ARG567 3.7 95.8 1.0
HH11 B:ARG567 3.8 95.8 1.0
NH1 B:ARG567 4.1 79.9 1.0
CB B:GLU336 4.2 49.8 1.0
ND1 B:HIS333 4.4 41.0 1.0
CG B:HIS333 4.4 41.8 1.0
HB3 B:GLU336 4.5 59.7 1.0
HB2 B:GLU336 4.6 59.7 1.0
O B:SER334 4.8 31.9 1.0
O B:CYS566 4.8 57.1 1.0
HA B:GLU336 4.9 49.0 1.0
OE1 B:GLU554 4.9 44.1 1.0
HD21 B:LEU327 5.0 49.5 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 14:01:11 2024

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