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Magnesium in PDB 3nm1: 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: 3nm1 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) 38.55 / 3.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 104.938, 154.212, 148.704, 90.00, 102.10, 90.00
R / Rfree (%) 20.1 / 23.2

Other elements in 3nm1:

The structure of The Crystal Structure of Candida Glabrata THI6, A Bifunctional Enzyme Involved in Thiamin Biosyhthesis of Eukaryotes also contains other interesting chemical elements:

Fluorine (F) 18 atoms

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 3nm1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 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: 3nm1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3nm1

Go back to Magnesium Binding Sites List in 3nm1
Magnesium binding site 1 out of 6 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:Mg544

b:66.8
occ:1.00
OD2 A:ASP95 2.2 77.3 1.0
O6 A:POP543 2.4 84.8 1.0
O1 A:POP543 2.6 89.4 1.0
OD2 A:ASP76 2.7 89.7 1.0
O4 A:POP543 3.0 85.4 1.0
O3 A:POP543 3.0 80.7 1.0
CG A:ASP95 3.1 80.9 1.0
P2 A:POP543 3.1 91.5 1.0
P1 A:POP543 3.2 76.2 1.0
CG A:ASP76 3.2 90.7 1.0
OD1 A:ASP95 3.3 83.0 1.0
CB A:ASP76 3.6 87.9 1.0
O A:POP543 3.6 88.9 1.0
NZ A:LYS47 3.8 81.8 1.0
ND2 A:ASN75 3.9 80.1 1.0
N A:GLY92 4.1 74.8 1.0
OD1 A:ASP76 4.1 89.0 1.0
OD1 A:ASN75 4.4 84.2 1.0
CA A:GLY92 4.4 71.2 1.0
CB A:ASP95 4.5 77.3 1.0
CG A:ASN75 4.5 80.3 1.0
O5 A:POP543 4.6 80.3 1.0
O2 A:POP543 4.6 64.3 1.0
C A:VAL91 4.7 70.9 1.0
CA A:ASP76 4.8 81.2 1.0
N A:ASP76 4.8 78.0 1.0
CA A:VAL91 4.9 67.8 1.0
O A:HIS90 4.9 70.9 1.0

Magnesium binding site 2 out of 6 in 3nm1

Go back to Magnesium Binding Sites List in 3nm1
Magnesium binding site 2 out of 6 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
F:Mg544

b:60.4
occ:1.00
OD2 F:ASP95 2.3 76.3 1.0
OD2 F:ASP76 2.4 75.7 1.0
O4 F:POP543 2.7 80.8 1.0
O3 F:POP543 2.8 86.9 1.0
O6 F:POP543 2.9 81.3 1.0
CG F:ASP95 3.0 83.5 1.0
OD1 F:ASP95 3.1 85.9 1.0
O2 F:POP543 3.1 78.2 1.0
P2 F:POP543 3.2 86.6 1.0
CG F:ASP76 3.3 84.1 1.0
P1 F:POP543 3.3 81.1 1.0
O F:POP543 3.5 79.7 1.0
NZ F:LYS47 3.8 74.3 1.0
CB F:ASP76 3.9 83.8 1.0
OD1 F:ASP76 4.2 84.5 1.0
N F:GLY92 4.3 80.2 1.0
CB F:ASP95 4.5 80.8 1.0
CA F:GLY92 4.6 74.6 1.0
O5 F:POP543 4.6 68.8 1.0
ND2 F:ASN75 4.8 73.2 1.0
O1 F:POP543 4.8 69.5 1.0
CE F:LYS47 4.9 78.6 1.0

Magnesium binding site 3 out of 6 in 3nm1

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Magnesium binding site 3 out of 6 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
E:Mg544

b:61.7
occ:1.00
OD2 E:ASP95 2.4 83.3 1.0
O6 E:POP543 2.5 84.0 1.0
O2 E:POP543 2.7 79.1 1.0
OD2 E:ASP76 2.7 87.5 1.0
O3 E:POP543 2.8 85.8 1.0
CB E:ASP76 3.1 81.7 1.0
CG E:ASP95 3.1 82.1 1.0
OD1 E:ASP95 3.2 83.3 1.0
CG E:ASP76 3.2 84.8 1.0
P1 E:POP543 3.2 79.8 1.0
NZ E:LYS47 3.6 75.9 1.0
P2 E:POP543 3.7 90.6 1.0
ND2 E:ASN75 3.8 69.6 1.0
O E:POP543 3.9 84.4 1.0
OD1 E:ASN75 4.0 79.2 1.0
N E:GLY92 4.2 76.2 1.0
OD1 E:ASP76 4.3 83.8 1.0
CG E:ASN75 4.3 75.2 1.0
O4 E:POP543 4.4 73.8 1.0
CA E:ASP76 4.4 79.1 1.0
O1 E:POP543 4.6 64.1 1.0
CB E:ASP95 4.6 77.5 1.0
N E:ASP76 4.7 78.5 1.0
CA E:GLY92 4.8 74.3 1.0
CE E:LYS47 4.8 74.0 1.0
O5 E:POP543 4.9 88.9 1.0
C E:VAL91 5.0 76.4 1.0
CD E:LYS47 5.0 72.8 1.0
CA E:VAL91 5.0 71.7 1.0

Magnesium binding site 4 out of 6 in 3nm1

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Magnesium binding site 4 out of 6 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
D:Mg544

b:61.9
occ:1.00
OD2 D:ASP95 2.3 75.7 1.0
O6 D:POP543 2.4 72.6 1.0
OD1 D:ASP76 2.5 79.6 1.0
O3 D:POP543 2.6 72.3 1.0
CG D:ASP76 3.1 85.1 1.0
O2 D:POP543 3.2 72.6 1.0
P1 D:POP543 3.3 70.3 1.0
CG D:ASP95 3.3 79.4 1.0
P2 D:POP543 3.3 74.3 1.0
CB D:ASP76 3.4 79.5 1.0
O4 D:POP543 3.5 67.6 1.0
ND2 D:ASN75 3.5 74.0 1.0
N D:GLY92 3.7 75.8 1.0
OD1 D:ASP95 3.7 80.7 1.0
O D:POP543 3.8 74.2 1.0
NZ D:LYS47 4.0 78.7 1.0
OD2 D:ASP76 4.1 88.3 1.0
OD1 D:ASN75 4.1 77.9 1.0
CA D:GLY92 4.1 73.2 1.0
CG D:ASN75 4.2 74.6 1.0
C D:VAL91 4.4 70.6 1.0
N D:ASP76 4.4 74.7 1.0
CA D:ASP76 4.4 73.2 1.0
CB D:ASP95 4.6 76.2 1.0
CA D:VAL91 4.6 64.8 1.0
O5 D:POP543 4.7 73.1 1.0
O D:HIS90 4.7 71.8 1.0
O1 D:POP543 4.7 61.6 1.0

Magnesium binding site 5 out of 6 in 3nm1

Go back to Magnesium Binding Sites List in 3nm1
Magnesium binding site 5 out of 6 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:Mg544

b:57.0
occ:1.00
O6 C:POP543 2.2 72.9 1.0
OD1 C:ASP76 2.4 76.4 1.0
OD2 C:ASP95 2.5 73.2 1.0
O3 C:POP543 3.1 76.4 1.0
CG C:ASP76 3.1 79.9 1.0
OD1 C:ASP95 3.1 84.8 1.0
CG C:ASP95 3.2 76.4 1.0
P2 C:POP543 3.2 82.4 1.0
O2 C:POP543 3.4 66.7 1.0
O5 C:POP543 3.4 80.5 1.0
CB C:ASP76 3.5 77.3 1.0
P1 C:POP543 3.6 68.6 1.0
NZ C:LYS47 3.6 70.8 1.0
O C:POP543 3.7 75.3 1.0
OD2 C:ASP76 3.9 81.2 1.0
OD1 C:ASN75 4.2 65.6 1.0
N C:GLY92 4.3 69.6 1.0
ND2 C:ASN75 4.5 74.3 1.0
O4 C:POP543 4.5 72.1 1.0
CA C:GLY92 4.7 69.5 1.0
CB C:ASP95 4.7 68.1 1.0
CG C:ASN75 4.8 72.1 1.0
CA C:ASP76 4.9 68.5 1.0
CE C:LYS47 5.0 70.8 1.0

Magnesium binding site 6 out of 6 in 3nm1

Go back to Magnesium Binding Sites List in 3nm1
Magnesium binding site 6 out of 6 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
B:Mg544

b:56.1
occ:1.00
O3 B:POP543 2.5 81.9 1.0
O4 B:POP543 2.5 78.1 1.0
OD2 B:ASP95 2.8 87.7 1.0
OD1 B:ASP95 3.0 86.7 1.0
OD1 B:ASN75 3.1 80.6 1.0
CG B:ASP95 3.1 86.4 1.0
CG B:ASP76 3.2 91.7 1.0
CB B:ASP76 3.3 89.2 1.0
NZ B:LYS47 3.3 75.3 1.0
OD1 B:ASP76 3.4 88.7 1.0
OD2 B:ASP76 3.6 91.4 1.0
P2 B:POP543 3.6 81.6 1.0
P1 B:POP543 3.6 79.0 1.0
O6 B:POP543 3.7 87.5 1.0
O2 B:POP543 3.9 75.6 1.0
O B:POP543 4.1 81.0 1.0
CG B:ASN75 4.3 80.5 1.0
N B:GLY92 4.4 80.5 1.0
CB B:ASP95 4.5 80.8 1.0
CA B:ASP76 4.7 82.8 1.0
CE B:LYS47 4.8 79.7 1.0
O1 B:POP543 4.8 70.8 1.0
O5 B:POP543 4.9 75.9 1.0
CA B:GLY92 5.0 74.6 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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