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Magnesium in PDB 3nl5: The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes

Enzymatic activity of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes

All present enzymatic activity of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes:
2.5.1.3; 2.7.1.50;

Protein crystallography data

The structure of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes, PDB code: 3nl5 was solved by D.Paul, A.Chatterjee, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.00 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 161.327, 153.926, 108.581, 90.00, 117.60, 90.00
R / Rfree (%) 20.4 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes (pdb code 3nl5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes, PDB code: 3nl5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3nl5

Go back to Magnesium Binding Sites List in 3nl5
Magnesium binding site 1 out of 3 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg541

b:76.6
occ:1.00
O2B C:ACP999 2.9 91.6 1.0
O2G C:ACP999 3.1 1.0 1.0
C3B C:ACP999 3.3 0.7 1.0
O1G C:ACP999 3.4 98.3 1.0
PG C:ACP999 3.4 0.6 1.0
PB C:ACP999 3.6 0.0 1.0
OD2 C:ASP340 3.6 86.7 1.0
OD1 C:ASP340 3.6 82.4 1.0
NZ C:LYS367 3.9 76.1 1.0
OE2 C:GLU372 4.0 80.7 1.0
CG C:ASP340 4.0 85.3 1.0
CA C:GLY465 4.0 93.5 1.0
OE1 C:GLU372 4.1 81.4 1.0
C C:GLY465 4.3 87.5 1.0
CE C:LYS367 4.3 73.7 1.0
N C:CYS466 4.3 92.1 1.0
O1B C:ACP999 4.4 0.3 1.0
CD C:GLU372 4.5 78.3 1.0
N C:GLY465 4.7 94.7 1.0
O3G C:ACP999 4.9 95.4 1.0
O C:GLY465 4.9 79.5 1.0
SG C:CYS466 4.9 87.3 1.0
ND2 C:ASN369 5.0 81.2 1.0

Magnesium binding site 2 out of 3 in 3nl5

Go back to Magnesium Binding Sites List in 3nl5
Magnesium binding site 2 out of 3 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg541

b:65.1
occ:1.00
O2G A:ACP799 2.8 99.1 1.0
O2B A:ACP799 3.0 99.5 1.0
PG A:ACP799 3.5 0.6 1.0
PB A:ACP799 3.5 0.1 1.0
O1G A:ACP799 3.5 0.3 1.0
O1B A:ACP799 3.5 90.1 1.0
C3B A:ACP799 3.6 95.5 1.0
OD1 A:ASP340 3.7 81.2 1.0
OD2 A:ASP340 3.7 80.3 1.0
OE2 A:GLU372 4.0 74.0 1.0
OE1 A:GLU372 4.0 74.1 1.0
CG A:ASP340 4.1 80.6 1.0
NZ A:LYS367 4.2 77.7 1.0
CD A:GLU372 4.4 73.2 1.0
CG2 A:VAL342 4.5 68.1 1.0
CA A:GLY465 4.5 30.0 1.0
C A:GLY465 4.6 30.0 1.0
CE A:LYS367 4.7 74.2 1.0
CA A:VAL342 4.7 69.8 1.0
CG1 A:VAL342 4.7 77.8 1.0
O A:GLY465 4.8 30.0 1.0
SG A:CYS466 4.9 94.9 1.0
O3G A:ACP799 4.9 99.3 1.0
N A:CYS466 4.9 90.0 1.0
CB A:VAL342 4.9 66.5 1.0
C2' C:TZE542 5.0 48.7 1.0

Magnesium binding site 3 out of 3 in 3nl5

Go back to Magnesium Binding Sites List in 3nl5
Magnesium binding site 3 out of 3 in the The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg541

b:76.9
occ:1.00
O1B B:ACP899 2.4 97.2 1.0
OD2 B:ASP340 3.0 84.0 1.0
OD1 B:ASP340 3.2 82.7 1.0
CG B:ASP340 3.4 82.3 1.0
CG1 B:VAL342 3.7 70.2 1.0
PB B:ACP899 3.7 0.1 1.0
CB B:VAL342 3.7 69.4 1.0
N B:CYS466 3.8 89.7 1.0
C3B B:ACP899 3.8 1.0 1.0
O1G B:ACP899 3.8 0.8 1.0
SG B:CYS466 3.9 91.8 1.0
NZ B:LYS367 4.0 80.3 1.0
O2G B:ACP899 4.0 0.4 1.0
CE B:LYS367 4.1 74.6 1.0
C B:GLY465 4.1 87.8 1.0
PG B:ACP899 4.2 0.2 1.0
CA B:GLY465 4.3 87.1 1.0
OE2 B:GLU372 4.3 78.6 1.0
CG2 B:VAL342 4.4 72.7 1.0
CA B:CYS466 4.4 87.9 1.0
OE1 B:GLU372 4.4 79.1 1.0
O3A B:ACP899 4.7 0.5 1.0
O2B B:ACP899 4.7 0.4 1.0
O B:GLY465 4.8 82.7 1.0
CB B:CYS466 4.8 88.7 1.0
CD B:GLU372 4.9 80.8 1.0
C2' B:TZE542 4.9 42.8 1.0
N B:GLY465 4.9 91.2 1.0
OXT B:TZE542 4.9 42.2 1.0
CB B:ASP340 4.9 72.9 1.0
CA B:VAL342 4.9 73.0 1.0

Reference:

D.Paul, A.Chatterjee, T.P.Begley, S.E.Ealick. Domain Organization in Candida Glabrata THI6, A Bifunctional Enzyme Required For Thiamin Biosynthesis in Eukaryotes . Biochemistry V. 49 9922 2010.
ISSN: ISSN 0006-2960
PubMed: 20968298
DOI: 10.1021/BI101008U
Page generated: Thu Aug 15 08:02:54 2024

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