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Magnesium in PDB 1ru1: Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)

Enzymatic activity of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)

All present enzymatic activity of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form):
2.7.6.3;

Protein crystallography data

The structure of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form), PDB code: 1ru1 was solved by J.Blaszczyk, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.797, 68.752, 36.491, 90.00, 90.50, 90.00
R / Rfree (%) 15 / 19.8

Other elements in 1ru1:

The structure of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) (pdb code 1ru1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form), PDB code: 1ru1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1ru1

Go back to Magnesium Binding Sites List in 1ru1
Magnesium binding site 1 out of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:13.4
occ:1.00
 OD1 A:ASP95 2.0 15.3 1.0
O1A A:APC171 2.0 13.8 1.0
O A:HOH413 2.1 14.6 1.0
O1B A:APC171 2.1 12.1 1.0
OD1 A:ASP97 2.1 10.9 1.0
O A:HOH423 2.1 12.0 1.0
CG A:ASP95 2.9 14.3 1.0
OD2 A:ASP95 3.1 14.8 1.0
CG A:ASP97 3.1 11.5 1.0
PB A:APC171 3.2 14.5 1.0
PA A:APC171 3.2 16.2 1.0
MG A:MG162 3.5 13.3 1.0
C3A A:APC171 3.5 17.4 1.0
OD2 A:ASP97 3.6 12.7 1.0
O5' A:APC171 3.7 18.1 1.0
O2B A:APC171 3.9 14.3 1.0
OE2 A:GLU77 4.1 14.0 1.0
CB A:ASP95 4.3 12.5 1.0
O A:HOH681 4.4 28.0 1.0
O A:LEU96 4.4 11.9 1.0
CB A:ASP97 4.5 10.2 1.0
O2A A:APC171 4.5 14.9 1.0
O A:HOH539 4.5 24.5 1.0
O3B A:APC171 4.5 14.5 1.0
O A:HOH682 4.6 34.2 1.0
C A:LEU96 4.6 11.2 1.0
O3G A:APC171 4.6 12.8 1.0
O A:HOH442 4.7 19.1 1.0
N A:LEU96 4.7 12.1 1.0
O4 A:PH2181 4.7 17.2 1.0
N3 A:APC171 4.7 11.8 1.0
CA A:ASP97 4.7 10.5 1.0
O1G A:APC171 4.7 15.2 1.0
C2 A:APC171 4.7 10.4 1.0
N A:ASP97 4.8 12.1 1.0
CA A:ASP95 4.8 12.4 1.0
PG A:APC171 4.9 13.9 1.0

Magnesium binding site 2 out of 4 in 1ru1

Go back to Magnesium Binding Sites List in 1ru1
Magnesium binding site 2 out of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg162

b:13.3
occ:1.00
 OD2 A:ASP95 2.0 14.8 1.0
OD2 A:ASP97 2.0 12.7 1.0
O3G A:APC171 2.1 12.8 1.0
O A:HOH403 2.1 18.7 1.0
O1B A:APC171 2.1 12.1 1.0
O4 A:PH2181 2.1 17.2 1.0
CG A:ASP97 3.0 11.5 1.0
CG A:ASP95 3.1 14.3 1.0
PB A:APC171 3.2 14.5 1.0
PG A:APC171 3.2 13.9 1.0
OD1 A:ASP97 3.3 10.9 1.0
C11 A:PH2181 3.3 31.9 1.0
O3B A:APC171 3.4 14.5 1.0
MG A:MG161 3.5 13.4 1.0
OD1 A:ASP95 3.6 15.3 1.0
O1G A:APC171 3.9 15.2 1.0
O A:HOH419 4.0 22.2 1.0
O2B A:APC171 4.0 14.3 1.0
NH1 A:ARG121 4.1 15.5 1.0
NE2 A:HIS115 4.2 12.9 1.0
CB A:ASP97 4.3 10.2 1.0
C2 A:PH2181 4.3 38.1 1.0
O A:HOH708 4.4 35.6 1.0
CB A:ASP95 4.4 12.5 1.0
O2G A:APC171 4.4 15.8 1.0
N1 A:PH2181 4.4 38.2 1.0
O A:HOH423 4.5 12.0 1.0
O A:HOH713 4.6 37.4 1.0
C3A A:APC171 4.7 17.4 1.0
O A:HOH682 4.9 34.2 1.0
O1A A:APC171 4.9 13.8 1.0
O A:HOH539 5.0 24.5 1.0
O A:HOH519 5.0 27.1 1.0
CD2 A:HIS115 5.0 14.1 1.0

Magnesium binding site 3 out of 4 in 1ru1

Go back to Magnesium Binding Sites List in 1ru1
Magnesium binding site 3 out of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg361

b:10.1
occ:1.00
 OD1 B:ASP297 2.1 11.9 1.0
O1B B:APC371 2.1 11.2 1.0
O B:HOH668 2.1 13.6 1.0
OD1 B:ASP295 2.1 12.5 1.0
O B:HOH426 2.1 12.6 1.0
O1A B:APC371 2.1 12.2 1.0
CG B:ASP295 3.0 13.0 1.0
CG B:ASP297 3.1 12.7 1.0
PA B:APC371 3.2 11.6 1.0
PB B:APC371 3.2 11.9 1.0
OD2 B:ASP295 3.3 11.4 1.0
C3A B:APC371 3.4 10.9 1.0
OD2 B:ASP297 3.5 11.7 1.0
MG B:MG362 3.5 11.6 1.0
O5' B:APC371 3.8 12.2 1.0
O2B B:APC371 4.0 13.5 1.0
OE2 B:GLU277 4.2 14.4 1.0
O B:HOH425 4.2 14.8 1.0
O B:LEU296 4.2 10.6 1.0
O B:HOH510 4.4 19.2 1.0
O B:HOH420 4.4 19.6 1.0
CB B:ASP295 4.4 11.5 1.0
O3B B:APC371 4.4 11.5 1.0
CB B:ASP297 4.4 10.3 1.0
O2A B:APC371 4.5 12.7 1.0
N3 B:APC371 4.5 10.8 1.0
O B:HOH415 4.6 11.2 1.0
C B:LEU296 4.6 10.4 1.0
C2 B:APC371 4.6 9.9 1.0
O1G B:APC371 4.6 12.8 1.0
O B:HOH772 4.6 31.1 1.0
O3G B:APC371 4.6 11.2 1.0
N B:LEU296 4.6 9.3 1.0
CA B:ASP297 4.7 10.4 1.0
O4 B:PH2381 4.7 12.7 1.0
CA B:ASP295 4.8 12.0 1.0
N B:ASP297 4.8 10.4 1.0
PG B:APC371 4.9 12.4 1.0
C B:ASP295 5.0 10.1 1.0

Magnesium binding site 4 out of 4 in 1ru1

Go back to Magnesium Binding Sites List in 1ru1
Magnesium binding site 4 out of 4 in the Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Ternary Complex of E. Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethyl-7,8- Dihydropterin at 1.40 Angstrom Resolution (Monoclinic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg362

b:11.6
occ:1.00
 OD2 B:ASP297 2.0 11.7 1.0
O3G B:APC371 2.0 11.2 1.0
O B:HOH401 2.1 11.2 1.0
OD2 B:ASP295 2.1 11.4 1.0
O4 B:PH2381 2.1 12.7 1.0
O1B B:APC371 2.2 11.2 1.0
CG B:ASP297 2.9 12.7 1.0
CG B:ASP295 3.1 13.0 1.0
PG B:APC371 3.2 12.4 1.0
PB B:APC371 3.2 11.9 1.0
C11 B:PH2381 3.3 14.0 1.0
OD1 B:ASP297 3.3 11.9 1.0
O3B B:APC371 3.3 11.5 1.0
MG B:MG361 3.5 10.1 1.0
OD1 B:ASP295 3.6 12.5 1.0
O1G B:APC371 3.9 12.8 1.0
O2B B:APC371 4.0 13.5 1.0
O B:HOH407 4.0 13.0 1.0
NH1 B:ARG321 4.1 12.3 1.0
N1 B:PH2381 4.1 13.5 1.0
C2 B:PH2381 4.2 15.7 1.0
O B:HOH588 4.2 25.5 1.0
CB B:ASP297 4.3 10.3 1.0
NE2 B:HIS315 4.3 10.9 1.0
O2G B:APC371 4.3 14.6 1.0
CB B:ASP295 4.4 11.5 1.0
O B:HOH461 4.4 18.1 1.0
O B:HOH426 4.6 12.6 1.0
C3A B:APC371 4.7 10.9 1.0
O B:HOH446 4.9 18.1 1.0
O B:HOH772 5.0 31.1 1.0

Reference:

J.Blaszczyk, Y.Li, Y.Wu, G.Shi, X.Ji, H.Yan. Essential Roles of A Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase. Biochemistry V. 43 1469 2004.
ISSN: ISSN 0006-2960
PubMed: 14769023
DOI: 10.1021/BI036053L
Page generated: Tue Aug 13 13:08:03 2024

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