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Mercury in PDB 1r7y: Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate

Enzymatic activity of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate

All present enzymatic activity of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate:
2.4.1.40;

Protein crystallography data

The structure of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate, PDB code: 1r7y was solved by H.P.Nguyen, N.O.L.Seto, Y.Cai, E.K.Leinala, S.N.Borisova, M.M.Palcic, S.V.Evans, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.13 / 1.75
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 52.500, 149.400, 79.400, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 21.6

Other elements in 1r7y:

The structure of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate also contains other interesting chemical elements:

Manganese (Mn) 1 atom

Mercury Binding Sites:

The binding sites of Mercury atom in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate (pdb code 1r7y). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 5 binding sites of Mercury where determined in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate, PDB code: 1r7y:
Jump to Mercury binding site number: 1; 2; 3; 4; 5;

Mercury binding site 1 out of 5 in 1r7y

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Mercury binding site 1 out of 5 in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg401

b:38.5
occ:0.50
 SG A:CYS284 2.7 30.1 1.0
OD1 A:ASP302 2.7 38.0 1.0
SD A:MET288 3.1 36.1 1.0
CB A:CYS284 3.5 25.3 1.0
C A:CYS284 3.7 24.9 1.0
N A:HIS285 3.7 25.0 1.0
O A:CYS284 3.8 24.1 1.0
CG A:MET288 3.9 31.3 1.0
CG A:ASP302 3.9 34.3 1.0
CA A:HIS285 4.0 27.0 1.0
CA A:CYS284 4.2 24.1 1.0
HG A:HG402 4.3 44.1 0.5
CB A:ASP302 4.6 30.4 1.0
CB A:MET288 4.7 28.4 1.0
CE A:MET288 4.7 37.4 1.0
CB A:HIS285 4.7 29.8 1.0
O A:THR281 4.8 21.7 1.0
O A:HOH613 4.9 47.8 1.0
OD2 A:ASP302 4.9 37.3 1.0
CA A:ASP302 5.0 25.5 1.0

Mercury binding site 2 out of 5 in 1r7y

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Mercury binding site 2 out of 5 in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg402

b:44.1
occ:0.50
 SG A:CYS284 2.7 30.1 1.0
O A:HOH613 2.8 47.8 1.0
CB A:CYS284 3.0 25.3 1.0
CD2 A:LEU280 3.6 19.1 1.0
O A:ASP302 3.8 23.2 1.0
CB A:LEU306 4.3 18.2 1.0
HG A:HG401 4.3 38.5 0.5
N A:LEU306 4.4 17.7 1.0
CA A:LEU306 4.4 18.1 1.0
CA A:CYS284 4.5 24.1 1.0
C A:ASP302 4.6 24.4 1.0
CB A:ASP302 4.6 30.4 1.0
O A:LEU280 4.7 19.5 1.0
CA A:ASP302 4.8 25.5 1.0
OD1 A:ASP302 4.9 38.0 1.0
CD1 A:LEU306 4.9 20.3 1.0
CG A:LEU280 5.0 18.1 1.0
C A:HIS305 5.0 18.9 1.0
CB A:HIS305 5.0 21.1 1.0
CA A:THR281 5.0 21.2 1.0

Mercury binding site 3 out of 5 in 1r7y

Go back to Mercury Binding Sites List in 1r7y
Mercury binding site 3 out of 5 in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg403

b:32.0
occ:1.00
 SG A:CYS209 2.4 24.6 1.0
O A:HOH612 2.5 27.1 1.0
OG1 A:THR119 2.9 21.8 1.0
CB A:CYS209 3.3 20.5 1.0
O A:HOH550 3.9 44.2 1.0
CB A:THR119 3.9 17.4 1.0
CG2 A:THR119 4.0 19.6 1.0
CG1 A:VAL277 4.2 14.9 1.0
CA A:CYS209 4.2 16.7 1.0
O A:HOH611 4.4 39.4 1.0
CD1 A:LEU207 4.6 20.3 1.0
N A:CYS209 4.7 17.2 1.0
CZ A:PHE270 4.9 17.7 1.0
CB A:LEU207 4.9 18.9 1.0
CD2 A:LEU207 5.0 19.6 1.0
CE1 A:PHE270 5.0 20.0 1.0

Mercury binding site 4 out of 5 in 1r7y

Go back to Mercury Binding Sites List in 1r7y
Mercury binding site 4 out of 5 in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg404

b:34.3
occ:0.50
 SG A:CYS80 2.8 51.4 1.0
O A:GLY98 2.8 24.9 1.0
CB A:CYS80 2.9 41.8 1.0
CA A:CYS80 3.0 38.9 1.0
C A:GLY98 4.0 22.4 1.0
C A:CYS80 4.0 36.8 1.0
N A:CYS80 4.1 37.3 1.0
O A:CYS80 4.1 37.2 1.0
O A:HOH593 4.3 38.9 1.0
CA A:THR99 4.3 19.6 1.0
N A:THR99 4.6 19.7 1.0
C A:THR99 4.8 19.4 1.0
C A:PRO79 4.9 36.1 1.0
O A:THR99 4.9 20.3 1.0
O A:PRO79 4.9 35.1 1.0

Mercury binding site 5 out of 5 in 1r7y

Go back to Mercury Binding Sites List in 1r7y
Mercury binding site 5 out of 5 in the Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Glycosyltransferase A in Complex with 3-Amino-Acceptor Analog Inhibitor and Uridine Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Hg405

b:48.8
occ:0.50
 O A:HOH517 2.7 25.0 1.0
O A:HOH550 2.8 44.2 1.0
O A:VAL210 3.4 17.4 1.0
N A:VAL210 3.6 15.3 1.0
C A:VAL210 3.7 17.4 1.0
C A:CYS209 3.7 15.8 1.0
CB A:CYS209 3.9 20.5 1.0
CA A:VAL210 4.0 16.2 1.0
O A:HOH482 4.0 21.0 1.0
O A:CYS209 4.0 15.1 1.0
CA A:CYS209 4.2 16.7 1.0
N A:ASP211 4.5 18.2 1.0
CE2 A:PHE270 4.5 20.6 1.0
OD1 A:ASP211 4.6 21.4 1.0
O A:THR119 4.7 17.8 1.0
O A:GLY267 4.8 20.6 1.0
CD1 A:PHE121 5.0 30.7 1.0

Reference:

H.P.Nguyen, N.O.L.Seto, Y.Cai, E.K.Leinala, S.N.Borisova, M.M.Palcic, S.V.Evans. The Influence of An Intramolecular Hydrogen Bond in Differential Recognition of Inhibitory Acceptor Analogs By Human Abo(H) Blood Group A and B Glycosyltransferases J.Biol.Chem. V. 278 49191 2003.
ISSN: ISSN 0021-9258
PubMed: 12972418
DOI: 10.1074/JBC.M308770200
Page generated: Sun Aug 11 01:23:27 2024

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