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Magnesium in PDB 3nl3: 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: 3nl3 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) 48.00 / 3.01
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.543, 154.292, 148.627, 90.00, 102.55, 90.00
R / Rfree (%) 21.3 / 24.2

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

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 3nl3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 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: 3nl3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3nl3

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Magnesium binding site 1 out of 12 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
A:Mg541

b:0.5
occ:1.00
 OG1 C:THR51 2.7 82.7 1.0
OD1 A:ASP95 2.8 97.1 1.0
OD2 A:ASP76 2.8 0.3 1.0
N C:THR51 3.7 78.8 1.0
CG A:ASP76 3.8 93.7 1.0
CG A:ASP95 3.9 85.7 1.0
CB C:THR51 4.0 70.7 1.0
OD1 A:ASP76 4.1 86.0 1.0
O C:ALA49 4.2 0.3 1.0
CA C:THR51 4.4 70.0 1.0
CA C:ASP50 4.4 0.5 1.0
OD2 A:ASP95 4.5 73.5 1.0
C C:ASP50 4.5 96.4 1.0
CB A:ASP95 4.9 67.0 1.0

Magnesium binding site 2 out of 12 in 3nl3

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Magnesium binding site 2 out of 12 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:Mg542

b:74.3
occ:1.00
 OD2 A:ASP424 3.0 70.0 1.0
OG1 A:THR426 3.0 64.4 1.0
OD1 A:ASP424 3.1 77.2 1.0
OG1 A:THR243 3.1 74.7 1.0
CG A:ASP424 3.2 72.0 1.0
N A:ILE427 3.4 67.6 1.0
O A:LEU241 3.4 75.0 1.0
N A:GLU428 3.7 61.4 1.0
CA A:THR243 3.8 78.5 1.0
CA A:ILE427 3.9 61.1 1.0
CB A:THR243 4.0 77.3 1.0
N A:THR243 4.1 78.8 1.0
C A:THR426 4.1 60.2 1.0
N A:THR426 4.2 44.0 1.0
CB A:THR426 4.3 42.0 1.0
O A:ASP424 4.3 60.2 1.0
C A:ILE427 4.3 53.8 1.0
CB A:ASP424 4.3 54.7 1.0
O A:SER242 4.4 75.4 1.0
CA A:THR426 4.4 50.2 1.0
C A:SER242 4.4 78.1 1.0
CG2 A:THR243 4.5 79.1 1.0
C A:LEU241 4.6 69.7 1.0
CA A:GLU428 4.7 63.1 1.0
CG A:GLU428 4.7 85.2 1.0
C A:ASP424 4.7 63.1 1.0

Magnesium binding site 3 out of 12 in 3nl3

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Magnesium binding site 3 out of 12 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
A:Mg543

b:41.7
occ:1.00
 O A:PRO341 2.7 79.2 1.0
OE2 A:GLU372 2.7 77.2 1.0
OE1 A:GLU372 2.7 68.3 1.0
OD2 A:ASP340 3.0 90.7 1.0
CD A:GLU372 3.1 69.8 1.0
C A:PRO341 3.7 82.5 1.0
CG A:ASP340 4.2 92.0 1.0
NZ A:LYS367 4.3 73.9 1.0
CA A:VAL342 4.3 76.9 1.0
ND2 A:ASN369 4.4 72.8 1.0
N A:VAL342 4.4 86.4 1.0
O A:ASP340 4.6 76.2 1.0
O A:LYS367 4.6 65.5 1.0
CG A:GLU372 4.6 55.9 1.0
C A:ASP340 4.6 66.5 1.0
N A:PRO341 4.7 65.7 1.0
CE A:LYS367 4.7 64.8 1.0
OD1 A:ASP340 4.8 96.3 1.0
CA A:PRO341 4.8 65.2 1.0

Magnesium binding site 4 out of 12 in 3nl3

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Magnesium binding site 4 out of 12 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 4 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:42.0
occ:1.00
 OE2 B:GLU372 2.5 71.2 1.0
O B:PRO341 2.7 81.3 1.0
OE1 B:GLU372 2.8 62.6 1.0
CD B:GLU372 3.0 67.4 1.0
OD2 B:ASP340 3.4 94.7 1.0
C B:PRO341 3.8 81.2 1.0
CA B:VAL342 4.2 78.6 1.0
ND2 B:ASN369 4.3 71.8 1.0
N B:VAL342 4.4 87.9 1.0
CG B:ASP340 4.6 91.9 1.0
CG B:GLU372 4.6 56.0 1.0
NZ B:LYS367 4.6 67.6 1.0
O B:ASP340 4.8 77.1 1.0
O B:LYS367 4.8 53.6 1.0
C B:ASP340 4.9 67.0 1.0
CA B:PRO341 4.9 66.3 1.0
C B:VAL342 4.9 79.5 1.0
N B:PRO341 4.9 65.5 1.0

Magnesium binding site 5 out of 12 in 3nl3

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Magnesium binding site 5 out of 12 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 5 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:83.7
occ:1.00
 OG1 A:THR51 2.6 87.6 1.0
OD1 C:ASP95 3.1 0.5 1.0
OD2 C:ASP76 3.1 96.2 1.0
N A:THR51 3.8 81.5 1.0
CB A:THR51 3.9 71.0 1.0
CG C:ASP95 4.2 89.4 1.0
CG C:ASP76 4.3 92.4 1.0
CA A:THR51 4.4 68.8 1.0
OD2 C:ASP95 4.6 71.3 1.0
O A:ALA49 4.6 94.5 1.0
OD1 C:ASP76 4.7 90.0 1.0
C A:ASP50 4.8 89.7 1.0
CA A:ASP50 4.8 0.7 1.0
CG2 A:THR51 5.0 65.6 1.0
OD1 A:ASP50 5.0 0.4 1.0

Magnesium binding site 6 out of 12 in 3nl3

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Magnesium binding site 6 out of 12 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 6 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:Mg542

b:47.2
occ:1.00
 O C:PRO341 2.4 73.4 1.0
OE2 C:GLU372 2.6 77.3 1.0
OE1 C:GLU372 2.6 65.5 1.0
CD C:GLU372 2.9 70.9 1.0
OD2 C:ASP340 3.0 97.7 1.0
C C:PRO341 3.5 78.3 1.0
CG C:ASP340 4.2 93.5 1.0
N C:VAL342 4.2 88.9 1.0
CA C:VAL342 4.3 75.9 1.0
O C:LYS367 4.4 60.7 1.0
O C:ASP340 4.4 74.5 1.0
NZ C:LYS367 4.4 68.6 1.0
C C:ASP340 4.4 64.2 1.0
N C:PRO341 4.4 66.8 1.0
CG C:GLU372 4.5 53.5 1.0
CA C:PRO341 4.5 71.2 1.0
ND2 C:ASN369 4.6 75.3 1.0
CE C:LYS367 4.8 65.9 1.0
OD1 C:ASP340 4.8 96.9 1.0
CA C:GLY368 4.9 55.8 1.0

Magnesium binding site 7 out of 12 in 3nl3

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Magnesium binding site 7 out of 12 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 7 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
D:Mg541

b:72.1
occ:1.00
 OG1 E:THR51 2.7 89.1 1.0
OD2 D:ASP76 2.8 98.4 1.0
OD1 D:ASP95 3.1 91.0 1.0
N E:THR51 3.5 90.3 1.0
CB E:THR51 3.8 75.3 1.0
CG D:ASP76 4.0 92.1 1.0
O E:ALA49 4.0 89.8 1.0
CG D:ASP95 4.1 86.2 1.0
CA E:THR51 4.2 74.6 1.0
CA E:ASP50 4.2 78.1 1.0
C E:ASP50 4.4 88.4 1.0
OD1 D:ASP76 4.4 80.5 1.0
OD2 D:ASP95 4.5 74.2 1.0
OD1 E:ASP50 4.9 91.5 1.0
C E:ALA49 5.0 0.7 1.0

Magnesium binding site 8 out of 12 in 3nl3

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Magnesium binding site 8 out of 12 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 8 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
D:Mg542

b:90.7
occ:1.00
 O D:ALA49 2.7 30.0 1.0
OD2 E:ASP76 2.8 95.8 1.0
N D:ASP50 2.9 0.9 1.0
OG1 D:THR51 2.9 86.7 1.0
C D:ALA49 2.9 30.0 1.0
OD1 E:ASP95 3.2 97.1 1.0
N D:THR51 3.6 86.0 1.0
CG E:ASP76 3.9 92.7 1.0
CA D:ASP50 4.0 94.1 1.0
C D:ASP50 4.1 88.9 1.0
CB D:THR51 4.1 77.3 1.0
CA D:ALA49 4.2 30.0 1.0
CG E:ASP95 4.2 88.4 1.0
OD1 E:ASP76 4.2 81.0 1.0
CB D:ALA49 4.3 30.0 1.0
CA D:THR51 4.4 70.6 1.0
OD2 E:ASP95 4.6 75.3 1.0

Magnesium binding site 9 out of 12 in 3nl3

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Magnesium binding site 9 out of 12 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 9 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
D:Mg543

b:37.9
occ:1.00
 OE2 D:GLU372 2.5 75.4 1.0
OE1 D:GLU372 2.7 59.6 1.0
O D:PRO341 2.7 81.0 1.0
CD D:GLU372 2.9 64.2 1.0
OD2 D:ASP340 3.3 94.0 1.0
C D:PRO341 3.8 81.7 1.0
CA D:VAL342 4.3 79.9 1.0
ND2 D:ASN369 4.3 74.7 1.0
N D:VAL342 4.4 93.3 1.0
CG D:GLU372 4.4 56.6 1.0
CG D:ASP340 4.5 91.0 1.0
NZ D:LYS367 4.5 67.7 1.0
O D:ASP340 4.7 75.8 1.0
O D:LYS367 4.8 68.9 1.0
C D:ASP340 4.8 65.6 1.0
N D:PRO341 4.8 66.4 1.0
CA D:PRO341 4.9 65.2 1.0
C D:VAL342 5.0 76.6 1.0

Magnesium binding site 10 out of 12 in 3nl3

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Magnesium binding site 10 out of 12 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 10 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
E:Mg541

b:34.9
occ:1.00
 OE2 E:GLU372 2.5 77.4 1.0
OE1 E:GLU372 2.5 65.2 1.0
O E:PRO341 2.8 76.0 1.0
CD E:GLU372 2.9 67.6 1.0
OD2 E:ASP340 3.3 92.5 1.0
C E:PRO341 3.9 80.4 1.0
ND2 E:ASN369 4.1 77.7 1.0
NZ E:LYS367 4.4 68.6 1.0
CG E:GLU372 4.4 52.8 1.0
CA E:VAL342 4.5 74.8 1.0
CG E:ASP340 4.5 91.6 1.0
N E:VAL342 4.6 90.4 1.0
O E:LYS367 4.6 62.5 1.0
O E:ASP340 4.8 74.6 1.0
CE E:LYS367 4.9 62.3 1.0
C E:ASP340 4.9 66.5 1.0
N E:PRO341 4.9 67.0 1.0
CA E:GLY368 4.9 58.0 1.0
CA E:PRO341 5.0 69.6 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 08:02:55 2024

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