Atomistry » Manganese » PDB 8sne-8v22 » 8ujg
Atomistry »
  Manganese »
    PDB 8sne-8v22 »
      8ujg »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy