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Magnesium in PDB 3nm3: 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: 3nm3 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) 46.00 / 3.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 105.191, 154.602, 148.650, 90.00, 102.10, 90.00
R / Rfree (%) 19.7 / 25.1

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 3nm3). 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: 3nm3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3nm3

Go back to Magnesium Binding Sites List in 3nm3
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:Mg3001

b:70.7
occ:1.00
 O2 A:POP4001 2.2 74.9 1.0
OD2 A:ASP76 2.3 86.3 1.0
OD2 A:ASP95 2.4 79.4 1.0
O4 A:POP4001 2.6 65.5 0.9
O6 A:POP4001 2.7 67.9 1.0
OD1 A:ASP95 2.9 87.0 1.0
CG A:ASP95 3.0 85.9 1.0
P2 A:POP4001 3.2 63.1 0.7
CG A:ASP76 3.2 93.3 1.0
P1 A:POP4001 3.6 80.3 1.0
OD1 A:ASP76 3.8 91.8 1.0
O A:POP4001 3.9 77.4 0.8
NZ A:LYS47 3.9 82.4 1.0
ND2 A:ASN75 4.2 85.6 1.0
CB A:ASP76 4.2 88.9 1.0
O5 A:POP4001 4.5 56.9 1.0
CB A:ASP95 4.5 88.1 1.0
O1 A:POP4001 4.5 80.9 1.0
O3 A:POP4001 4.5 80.8 0.6
N A:GLY92 4.6 84.0 1.0
CE A:LYS47 4.7 69.0 1.0
CA A:GLY92 4.7 83.5 1.0
NZ A:LYS146 4.9 82.1 1.0

Magnesium binding site 2 out of 6 in 3nm3

Go back to Magnesium Binding Sites List in 3nm3
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
B:Mg3002

b:61.3
occ:1.00
 OD2 B:ASP95 2.3 68.2 1.0
OD2 B:ASP76 2.3 82.2 1.0
O6 B:POP4002 2.4 67.4 0.9
O3 B:POP4002 2.6 67.0 1.0
O2 B:POP4002 3.0 57.2 1.0
CG B:ASP95 3.1 77.9 1.0
ND2 B:ASN75 3.2 75.8 1.0
N B:GLY92 3.2 76.1 1.0
CG B:ASP76 3.2 87.0 1.0
P1 B:POP4002 3.2 56.0 0.5
CB B:ASP76 3.5 80.3 1.0
OD1 B:ASP95 3.5 87.4 1.0
P2 B:POP4002 3.5 62.3 1.0
CA B:GLY92 3.6 74.3 1.0
O B:POP4002 3.7 58.7 1.0
C B:VAL91 4.0 72.0 1.0
O5 B:POP4002 4.1 57.9 1.0
CB B:ASP95 4.2 81.1 1.0
CA B:VAL91 4.2 69.8 1.0
OD1 B:ASP76 4.3 89.9 1.0
CG B:ASN75 4.5 77.2 1.0
O B:HIS90 4.6 75.4 1.0
NZ B:LYS47 4.6 74.2 1.0
O1 B:POP4002 4.6 48.7 1.0
C B:GLY92 4.8 76.0 1.0
O4 B:POP4002 4.8 70.2 0.9
O B:VAL91 4.9 69.3 1.0
CA B:ASP76 4.9 75.2 1.0

Magnesium binding site 3 out of 6 in 3nm3

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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
C:Mg3003

b:55.1
occ:1.00
 O2 C:POP4003 2.3 82.8 1.0
O6 C:POP4003 2.4 65.3 0.9
OD2 C:ASP76 2.4 87.3 1.0
OD2 C:ASP95 2.5 82.9 1.0
O3 C:POP4003 2.9 75.8 1.0
P1 C:POP4003 3.1 75.0 1.0
P2 C:POP4003 3.3 55.2 1.0
CG C:ASP95 3.3 92.8 1.0
CG C:ASP76 3.4 91.4 1.0
O4 C:POP4003 3.4 68.1 0.5
OD1 C:ASP95 3.4 95.9 1.0
O C:POP4003 3.7 73.6 0.0
ND2 C:ASN75 3.8 79.5 1.0
NZ C:LYS47 3.8 70.4 1.0
N C:GLY92 4.2 80.5 1.0
OD1 C:ASP76 4.2 83.0 1.0
CB C:ASP76 4.2 91.0 1.0
O1 C:POP4003 4.4 66.1 1.0
CA C:GLY92 4.5 76.5 1.0
O5 C:POP4003 4.7 71.8 0.5
CB C:ASP95 4.8 86.6 1.0
CE C:LYS47 4.9 76.6 1.0
CG C:ASN75 4.9 79.4 1.0

Magnesium binding site 4 out of 6 in 3nm3

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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:Mg3004

b:61.6
occ:1.00
 O6 D:POP4004 2.2 65.4 0.8
OD2 D:ASP95 2.3 78.0 1.0
O2 D:POP4004 2.4 59.3 1.0
OD2 D:ASP76 2.6 79.7 1.0
O3 D:POP4004 2.8 60.7 0.9
P1 D:POP4004 3.0 62.9 1.0
NZ D:LYS47 3.2 74.9 1.0
P2 D:POP4004 3.3 53.6 1.0
CG D:ASP95 3.3 81.0 1.0
CG D:ASP76 3.5 85.9 1.0
OD1 D:ASP95 3.7 85.5 1.0
O D:POP4004 3.7 63.0 0.1
O4 D:POP4004 3.7 62.8 0.9
N D:GLY92 3.8 76.4 1.0
CA D:GLY92 4.0 72.5 1.0
ND2 D:ASN75 4.0 71.9 1.0
CB D:ASP76 4.1 77.7 1.0
OD1 D:ASP76 4.3 90.8 1.0
O1 D:POP4004 4.4 68.7 0.4
CE D:LYS47 4.5 73.9 1.0
O5 D:POP4004 4.7 60.6 1.0
CB D:ASP95 4.7 73.5 1.0
C D:VAL91 4.8 70.8 1.0

Magnesium binding site 5 out of 6 in 3nm3

Go back to Magnesium Binding Sites List in 3nm3
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
E:Mg3005

b:48.6
occ:1.00
 O6 E:POP4005 2.3 62.6 0.8
OD2 E:ASP95 2.4 70.5 1.0
O2 E:POP4005 2.4 63.9 0.8
OD2 E:ASP76 2.6 72.8 1.0
O3 E:POP4005 2.8 63.0 0.8
P1 E:POP4005 3.1 61.1 1.0
CG E:ASP95 3.3 76.5 1.0
P2 E:POP4005 3.4 57.6 1.0
OD1 E:ASP95 3.5 80.4 1.0
CG E:ASP76 3.5 83.9 1.0
N E:GLY92 3.6 73.7 1.0
NZ E:LYS47 3.6 85.4 1.0
O4 E:POP4005 3.7 60.3 0.7
O E:POP4005 3.7 62.7 0.0
ND2 E:ASN75 3.8 78.6 1.0
CA E:GLY92 3.8 73.7 1.0
CB E:ASP76 4.1 78.6 1.0
OD1 E:ASP76 4.4 84.8 1.0
O1 E:POP4005 4.5 64.6 0.6
C E:VAL91 4.6 66.8 1.0
O5 E:POP4005 4.7 61.0 1.0
CB E:ASP95 4.7 73.7 1.0
C E:GLY92 4.8 71.5 1.0
CG E:ASN75 4.9 75.8 1.0
CA E:VAL91 5.0 67.4 1.0

Magnesium binding site 6 out of 6 in 3nm3

Go back to Magnesium Binding Sites List in 3nm3
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
F:Mg3006

b:63.4
occ:1.00
 OD2 F:ASP76 2.4 82.1 1.0
OD2 F:ASP95 2.4 84.0 1.0
O3 F:POP4006 2.5 68.9 0.8
O6 F:POP4006 2.6 67.4 0.8
O2 F:POP4006 2.7 69.9 1.0
P1 F:POP4006 3.0 63.1 1.0
O4 F:POP4006 3.2 69.6 1.0
P2 F:POP4006 3.3 66.7 1.0
CG F:ASP95 3.4 90.2 1.0
O F:POP4006 3.5 62.9 0.7
CG F:ASP76 3.5 91.2 1.0
OD1 F:ASP95 3.7 89.6 1.0
N F:GLY92 4.0 82.5 1.0
ND2 F:ASN75 4.0 82.3 1.0
CA F:GLY92 4.2 79.0 1.0
OD1 F:ASP76 4.3 97.9 1.0
CB F:ASP76 4.4 91.7 1.0
O1 F:POP4006 4.4 63.8 0.8
O5 F:POP4006 4.8 56.0 1.0
CB F:ASP95 4.8 87.8 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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