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Magnesium in PDB 2g9z: Thiamin Pyrophosphokinase From Candida Albicans

Enzymatic activity of Thiamin Pyrophosphokinase From Candida Albicans

All present enzymatic activity of Thiamin Pyrophosphokinase From Candida Albicans:
2.7.6.2;

Protein crystallography data

The structure of Thiamin Pyrophosphokinase From Candida Albicans, PDB code: 2g9z was solved by C.Abergel, S.Santini, V.Monchois, T.Rousselle, J.M.Claverie, Bacterialtargets At Igs-Cnrs, France (Bigs), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.44 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.825, 60.331, 63.722, 66.14, 89.94, 65.07
R / Rfree (%) 18.7 / 23.6

Other elements in 2g9z:

The structure of Thiamin Pyrophosphokinase From Candida Albicans also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thiamin Pyrophosphokinase From Candida Albicans (pdb code 2g9z). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Thiamin Pyrophosphokinase From Candida Albicans, PDB code: 2g9z:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 2g9z

Go back to Magnesium Binding Sites List in 2g9z
Magnesium binding site 1 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:24.7
occ:1.00
 OD2 A:ASP142 2.2 15.4 1.0
O1B A:VNP602 2.2 18.1 1.0
OD1 A:ASP113 2.3 16.5 1.0
OD1 A:ASP115 2.3 16.6 1.0
OD2 A:ASP78 2.3 17.8 1.0
O A:HOH906 2.4 21.2 1.0
CG A:ASP142 3.1 16.7 1.0
CG A:ASP113 3.3 19.9 1.0
OD1 A:ASP142 3.3 17.8 1.0
CG A:ASP78 3.4 16.6 1.0
CG A:ASP115 3.4 20.1 1.0
MG A:MG704 3.5 25.5 1.0
PB A:VNP602 3.6 19.6 1.0
CB A:ASP78 3.7 16.4 1.0
OD2 A:ASP113 3.7 18.0 1.0
OD2 A:ASP115 3.9 20.9 1.0
N A:ASP115 3.9 23.1 1.0
O2B A:VNP602 4.1 17.7 1.0
OG A:SER116 4.1 34.1 1.0
N A:PHE114 4.2 22.5 1.0
O A:HOH860 4.2 29.4 1.0
O1G A:VNP602 4.2 27.2 1.0
N A:ASP113 4.3 19.5 1.0
O A:HOH859 4.3 34.4 1.0
N A:SER116 4.4 23.6 1.0
OD1 A:ASP78 4.5 19.2 1.0
CB A:ASP142 4.5 14.6 1.0
MG A:MG801 4.5 14.7 1.0
O1 A:VNP602 4.5 18.4 1.0
CB A:ASP115 4.6 20.2 1.0
N3B A:VNP602 4.6 19.4 1.0
CB A:ASP113 4.6 19.7 1.0
CA A:ASP115 4.6 22.3 1.0
CB A:SER116 4.7 26.0 1.0
O2G A:VNP602 4.7 25.4 1.0
C A:ASP113 4.7 21.0 1.0
CA A:PHE114 4.8 23.2 1.0
CA A:ASP113 4.8 20.7 1.0
C A:ASP115 4.8 23.8 1.0
C A:PHE114 4.8 24.1 1.0
PG A:VNP602 4.9 23.1 1.0

Magnesium binding site 2 out of 6 in 2g9z

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Magnesium binding site 2 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg704

b:25.5
occ:1.00
 O2G A:VNP602 2.1 25.4 1.0
OD2 A:ASP115 2.1 20.9 1.0
O1B A:VNP602 2.2 18.1 1.0
OD2 A:ASP113 2.2 18.0 1.0
O1 A:PO4707 2.3 32.6 1.0
O1 A:VNP602 2.6 18.4 1.0
PB A:VNP602 2.9 19.6 1.0
CG A:ASP115 3.0 20.1 1.0
CG A:ASP113 3.1 19.9 1.0
OD1 A:ASP115 3.2 16.6 1.0
PG A:VNP602 3.3 23.1 1.0
OD1 A:ASP113 3.3 16.5 1.0
P A:PO4707 3.4 28.2 1.0
MG A:MG702 3.5 24.7 1.0
O3 A:PO4707 3.6 34.2 0.8
O1G A:VNP602 3.6 27.2 1.0
N3B A:VNP602 3.6 19.4 1.0
C7 A:VNP602 3.8 19.8 1.0
O4 A:PO4707 3.9 34.6 1.0
NH2 B:ARG303 3.9 20.6 1.0
O2B A:VNP602 4.2 17.7 1.0
O A:HOH1006 4.3 53.7 1.0
C12 A:VNP602 4.3 17.4 1.0
MG A:MG801 4.3 14.7 1.0
CB A:ASP115 4.4 20.2 1.0
O A:HOH906 4.4 21.2 1.0
CB A:ASP113 4.5 19.7 1.0
O3G A:VNP602 4.5 25.1 1.0
O2 A:PO4707 4.6 32.4 1.0
O A:HOH1032 4.7 55.8 1.0
OD2 A:ASP142 4.9 15.4 1.0

Magnesium binding site 3 out of 6 in 2g9z

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Magnesium binding site 3 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:14.7
occ:1.00
 OD1 A:ASP142 2.7 17.8 1.0
NZ A:LYS145 2.7 16.4 1.0
OD2 A:ASP113 3.1 18.0 1.0
CG A:ASP113 3.1 19.9 1.0
O1 A:VNP602 3.3 18.4 1.0
O2B A:VNP602 3.4 17.7 1.0
O A:TYR140 3.4 21.0 1.0
N A:ASP142 3.4 17.5 1.0
CE A:LYS145 3.5 16.0 1.0
OD1 A:ASP113 3.5 16.5 1.0
CG A:ASP142 3.6 16.7 1.0
C A:ASN141 3.7 19.1 1.0
PB A:VNP602 3.7 19.6 1.0
CB A:ASP113 3.7 19.7 1.0
CD A:LYS145 3.8 16.4 1.0
C12 A:VNP602 3.8 17.4 1.0
CA A:ASN141 3.8 19.3 1.0
N A:ASP113 3.8 19.5 1.0
O1B A:VNP602 3.9 18.1 1.0
C7 A:VNP602 3.9 19.8 1.0
CA A:ASP142 4.1 16.7 1.0
OD2 A:ASP142 4.2 15.4 1.0
MG A:MG704 4.3 25.5 1.0
O A:SER137 4.3 20.2 1.0
O A:ASN141 4.3 19.4 1.0
C A:TYR140 4.4 21.7 1.0
CA A:ASP113 4.4 20.7 1.0
O4 A:PO4707 4.4 34.6 1.0
CB A:ASP142 4.4 14.6 1.0
O A:GLN135 4.5 21.8 1.0
MG A:MG702 4.5 24.7 1.0
N A:ASN141 4.6 20.7 1.0
C A:GLY112 4.6 20.7 1.0
CA A:GLY112 4.8 20.4 1.0
CB A:ASN141 4.9 20.0 1.0
O1 A:PO4707 4.9 32.6 1.0
C11 A:VNP602 5.0 18.6 1.0

Magnesium binding site 4 out of 6 in 2g9z

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Magnesium binding site 4 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg701

b:20.3
occ:1.00
 O1B B:VNP601 2.2 19.2 1.0
OD2 B:ASP142 2.2 14.2 1.0
OD1 B:ASP113 2.2 14.9 1.0
OD2 B:ASP78 2.3 14.8 1.0
OD1 B:ASP115 2.3 19.0 1.0
O B:HOH874 2.3 22.8 1.0
CG B:ASP142 3.1 18.6 1.0
CG B:ASP78 3.3 15.0 1.0
CG B:ASP113 3.3 18.9 1.0
CG B:ASP115 3.3 19.5 1.0
OD1 B:ASP142 3.4 18.7 1.0
PB B:VNP601 3.5 20.5 1.0
MG B:MG703 3.6 23.8 1.0
CB B:ASP78 3.6 15.7 1.0
OD2 B:ASP113 3.7 17.0 1.0
OD2 B:ASP115 3.8 20.6 1.0
N B:ASP115 4.0 22.1 1.0
O2B B:VNP601 4.0 19.7 1.0
O1G B:VNP601 4.1 26.2 1.0
OG B:SER116 4.1 34.9 1.0
O B:HOH954 4.2 28.9 1.0
O B:HOH902 4.2 31.6 1.0
N B:PHE114 4.3 21.5 1.0
N B:ASP113 4.3 18.8 1.0
N B:SER116 4.4 22.9 1.0
OD1 B:ASP78 4.4 17.6 1.0
O1 B:VNP601 4.5 21.0 1.0
CB B:ASP142 4.5 17.5 1.0
N3B B:VNP601 4.5 20.4 1.0
CB B:ASP115 4.5 20.5 1.0
MG B:MG802 4.6 17.3 1.0
CB B:ASP113 4.6 17.1 1.0
CB B:SER116 4.6 24.9 1.0
CA B:ASP115 4.7 21.8 1.0
O2G B:VNP601 4.7 23.5 1.0
C B:ASP113 4.7 20.8 1.0
PG B:VNP601 4.8 22.2 1.0
CA B:ASP113 4.8 19.6 1.0
CA B:PHE114 4.8 22.6 1.0
C B:ASP115 4.9 23.0 1.0
C B:PHE114 4.9 23.1 1.0

Magnesium binding site 5 out of 6 in 2g9z

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Magnesium binding site 5 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:23.8
occ:1.00
 O2G B:VNP601 2.1 23.5 1.0
OD2 B:ASP115 2.1 20.6 1.0
OD2 B:ASP113 2.2 17.0 1.0
O3 B:PO4708 2.3 30.6 1.0
O1B B:VNP601 2.3 19.2 1.0
O1 B:VNP601 2.5 21.0 1.0
PB B:VNP601 2.9 20.5 1.0
CG B:ASP115 3.0 19.5 1.0
CG B:ASP113 3.1 18.9 1.0
PG B:VNP601 3.3 22.2 1.0
P B:PO4708 3.3 27.0 1.0
OD1 B:ASP115 3.4 19.0 1.0
OD1 B:ASP113 3.4 14.9 1.0
O1 B:PO4708 3.6 33.7 1.0
MG B:MG701 3.6 20.3 1.0
N3B B:VNP601 3.7 20.4 1.0
O1G B:VNP601 3.7 26.2 1.0
C7 B:VNP601 3.7 21.4 1.0
O2 B:PO4708 3.8 32.0 1.0
NH2 A:ARG303 3.8 19.9 1.0
C12 B:VNP601 4.2 20.3 1.0
O2B B:VNP601 4.2 19.7 1.0
CB B:ASP115 4.3 20.5 1.0
MG B:MG802 4.3 17.3 1.0
O B:HOH996 4.5 51.1 1.0
CB B:ASP113 4.5 17.1 1.0
O B:HOH874 4.5 22.8 1.0
O3G B:VNP601 4.5 24.4 1.0
O4 B:PO4708 4.6 30.7 1.0

Magnesium binding site 6 out of 6 in 2g9z

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Magnesium binding site 6 out of 6 in the Thiamin Pyrophosphokinase From Candida Albicans


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thiamin Pyrophosphokinase From Candida Albicans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:17.3
occ:1.00
 OD1 B:ASP142 2.7 18.7 1.0
NZ B:LYS145 2.7 15.9 1.0
OD2 B:ASP113 3.2 17.0 1.0
O B:TYR140 3.2 21.8 1.0
O1 B:VNP601 3.3 21.0 1.0
CG B:ASP113 3.3 18.9 1.0
O2B B:VNP601 3.4 19.7 1.0
CE B:LYS145 3.4 12.8 1.0
N B:ASP142 3.5 18.4 1.0
CG B:ASP142 3.6 18.6 1.0
C12 B:VNP601 3.6 20.3 1.0
C B:ASN141 3.6 19.9 1.0
OD1 B:ASP113 3.6 14.9 1.0
PB B:VNP601 3.7 20.5 1.0
CA B:ASN141 3.7 20.0 1.0
CD B:LYS145 3.7 13.4 1.0
CB B:ASP113 3.8 17.1 1.0
C7 B:VNP601 3.8 21.4 1.0
N B:ASP113 3.9 18.8 1.0
O1B B:VNP601 3.9 19.2 1.0
O B:SER137 4.1 19.9 1.0
CA B:ASP142 4.1 17.8 1.0
OD2 B:ASP142 4.2 14.2 1.0
C B:TYR140 4.2 22.6 1.0
O2 B:PO4708 4.3 32.0 1.0
O B:ASN141 4.3 19.1 1.0
MG B:MG703 4.3 23.8 1.0
CA B:ASP113 4.5 19.6 1.0
CB B:ASP142 4.5 17.5 1.0
N B:ASN141 4.5 21.8 1.0
O B:GLN135 4.5 20.4 1.0
MG B:MG701 4.6 20.3 1.0
C B:GLY112 4.8 20.8 1.0
CB B:ASN141 4.8 19.8 1.0
C11 B:VNP601 4.8 19.1 1.0
CA B:GLY112 4.9 19.9 1.0
CG B:LYS145 5.0 12.6 1.0

Reference:

S.Santini, V.Monchois, N.Mouz, C.Sigoillot, T.Rousselle, J.M.Claverie, C.Abergel. Structural Characterization of CA1462, the Candida Albicans Thiamine Pyrophosphokinase. Bmc Struct.Biol. V. 8 33 2008.
ISSN: ESSN 1472-6807
PubMed: 18652651
DOI: 10.1186/1472-6807-8-33
Page generated: Tue Aug 13 23:25:55 2024

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