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Magnesium in PDB 1g6c: Thiamin Phosphate Synthase

Enzymatic activity of Thiamin Phosphate Synthase

All present enzymatic activity of Thiamin Phosphate Synthase:
2.5.1.3;

Protein crystallography data

The structure of Thiamin Phosphate Synthase, PDB code: 1g6c was solved by D.H.Peapus, H.-J.Chiu, N.Campobasso, J.J.Reddick, 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) 42.86 / 1.40
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 76.650, 76.650, 140.070, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 23.7

Other elements in 1g6c:

The structure of Thiamin Phosphate Synthase also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thiamin Phosphate Synthase (pdb code 1g6c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Thiamin Phosphate Synthase, PDB code: 1g6c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1g6c

Go back to Magnesium Binding Sites List in 1g6c
Magnesium binding site 1 out of 2 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg2007

b:9.2
occ:1.00
OD1 A:ASP93 2.1 12.1 1.0
O A:HOH2102 2.1 17.5 1.0
O5 A:POP2003 2.1 10.1 1.0
OD2 A:ASP112 2.1 10.8 1.0
O2 A:POP2003 2.2 6.7 0.3
O2 A:POP2003 2.2 15.1 0.3
O A:HOH2101 2.3 14.5 1.0
CG A:ASP93 3.1 13.8 1.0
CG A:ASP112 3.1 13.9 1.0
P1 A:POP2003 3.1 11.9 0.3
P1 A:POP2003 3.2 9.2 0.3
P2 A:POP2003 3.3 9.4 1.0
OD1 A:ASP112 3.4 14.9 1.0
OD2 A:ASP93 3.4 17.7 1.0
O A:POP2003 3.4 11.7 1.0
O1 A:POP2003 3.5 14.2 0.3
O3 A:POP2003 3.6 11.5 0.3
N A:GLY109 3.9 8.7 1.0
NZ A:LYS61 3.9 14.1 1.0
ND2 A:ASN92 4.1 12.9 1.0
O A:HOH2103 4.1 26.7 1.0
OD1 A:ASN92 4.1 14.5 1.0
O4 A:POP2003 4.3 10.4 1.0
O6 A:POP2003 4.3 9.4 1.0
CA A:GLY109 4.3 10.7 1.0
CB A:ASP93 4.4 11.4 1.0
CB A:ASP112 4.5 13.6 1.0
CG A:ASN92 4.5 11.0 1.0
O3 A:POP2003 4.6 13.7 0.3
O1 A:POP2003 4.6 9.6 0.3
C A:ILE108 4.7 8.3 1.0
CA A:ASP93 4.8 10.0 1.0
CA A:ILE108 4.8 9.2 1.0
N A:ASP93 4.9 8.6 1.0

Magnesium binding site 2 out of 2 in 1g6c

Go back to Magnesium Binding Sites List in 1g6c
Magnesium binding site 2 out of 2 in the Thiamin Phosphate Synthase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thiamin Phosphate Synthase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2008

b:9.2
occ:1.00
OD1 B:ASP1093 2.1 11.9 1.0
O5 B:POP2004 2.1 10.7 1.0
O2 B:POP2004 2.1 12.6 0.3
O B:HOH2202 2.1 14.4 1.0
O2 B:POP2004 2.1 11.5 0.3
O B:HOH2201 2.1 10.9 1.0
OD2 B:ASP1112 2.2 10.9 1.0
P1 B:POP2004 3.0 13.1 0.3
CG B:ASP1093 3.1 13.7 1.0
CG B:ASP1112 3.2 12.7 1.0
P1 B:POP2004 3.3 9.8 0.3
P2 B:POP2004 3.3 9.3 1.0
O B:POP2004 3.3 11.0 1.0
OD1 B:ASP1112 3.4 14.5 1.0
OD2 B:ASP1093 3.4 16.1 1.0
O1 B:POP2004 3.5 14.8 0.3
N B:GLY1109 3.9 8.1 1.0
O3 B:POP2004 4.0 12.5 0.3
NZ B:LYS1061 4.0 13.4 1.0
O B:HOH2203 4.0 16.0 1.0
OD1 B:ASN1092 4.1 14.4 1.0
ND2 B:ASN1092 4.1 13.4 1.0
O6 B:POP2004 4.2 11.2 1.0
O4 B:POP2004 4.3 9.6 1.0
CA B:GLY1109 4.3 9.5 1.0
CB B:ASP1093 4.5 12.7 1.0
O3 B:POP2004 4.5 13.0 0.3
CG B:ASN1092 4.5 11.7 1.0
O1 B:POP2004 4.5 10.8 0.3
CB B:ASP1112 4.6 11.9 1.0
C B:ILE1108 4.7 8.5 1.0
CA B:ASP1093 4.8 12.2 1.0
CA B:ILE1108 4.9 7.9 1.0
N B:ASP1093 4.9 10.7 1.0

Reference:

D.H.Peapus, H.J.Chiu, N.Campobasso, J.J.Reddick, T.P.Begley, S.E.Ealick. Structural Characterization of the Enzyme-Substrate, Enzyme-Intermediate, and Enzyme-Product Complexes of Thiamin Phosphate Synthase. Biochemistry V. 40 10103 2001.
ISSN: ISSN 0006-2960
PubMed: 11513589
DOI: 10.1021/BI0104726
Page generated: Mon Dec 14 05:57:20 2020

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