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Magnesium in PDB 1ru2: Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form)

Enzymatic activity of Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form)

All present enzymatic activity of Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic 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-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form), PDB code: 1ru2 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 / 1.48
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 51.609, 63.156, 36.201, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 19.7

Other elements in 1ru2:

The structure of Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic 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-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form) (pdb code 1ru2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 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-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form), PDB code: 1ru2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1ru2

Go back to Magnesium Binding Sites List in 1ru2
Magnesium binding site 1 out of 2 in the Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic 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-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg161

b:23.6
occ:1.00
 OD1 A:ASP95 2.0 18.4 1.0
O A:HOH249 2.0 18.4 1.0
O A:HOH207 2.1 19.2 1.0
O1A A:APC171 2.1 25.5 1.0
OD1 A:ASP97 2.1 17.1 1.0
O1B A:APC171 2.3 23.9 1.0
CG A:ASP95 3.0 17.8 1.0
CG A:ASP97 3.2 15.6 1.0
PA A:APC171 3.2 24.7 1.0
PB A:APC171 3.3 23.7 1.0
OD2 A:ASP95 3.3 16.6 1.0
C3A A:APC171 3.3 33.3 1.0
OD2 A:ASP97 3.5 19.7 1.0
MG A:MG162 3.7 19.6 1.0
O5' A:APC171 3.7 24.8 1.0
O A:HOH257 3.8 26.7 1.0
OE2 A:GLU77 4.0 17.9 1.0
O2B A:APC171 4.0 25.3 1.0
O A:HOH208 4.1 27.3 1.0
O A:LEU96 4.3 17.4 1.0
CB A:ASP95 4.3 16.4 1.0
O A:HOH210 4.4 26.0 1.0
O A:HOH204 4.4 24.0 1.0
CB A:ASP97 4.5 12.8 1.0
O2A A:APC171 4.5 26.4 1.0
O3B A:APC171 4.5 23.6 1.0
C A:LEU96 4.6 15.3 1.0
N3 A:APC171 4.6 21.2 1.0
N A:LEU96 4.6 13.5 1.0
O3G A:APC171 4.7 19.6 1.0
CA A:ASP97 4.7 14.6 1.0
C2 A:APC171 4.7 18.7 1.0
O A:HOH216 4.7 32.8 1.0
CA A:ASP95 4.8 13.7 1.0
N A:ASP97 4.8 13.7 1.0
O6A A:HHR181 5.0 23.7 1.0
O1G A:APC171 5.0 27.0 1.0
C A:ASP95 5.0 11.6 1.0

Magnesium binding site 2 out of 2 in 1ru2

Go back to Magnesium Binding Sites List in 1ru2
Magnesium binding site 2 out of 2 in the Crystal Structure of A Ternary Complex of E.Coli Hppk(V83G/DEL84-89) with Mgampcpp and 6-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic 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-Hydroxymethylpterin at 1.48 Angstrom Resolution (Orthorhombic Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg162

b:19.6
occ:1.00
 O3G A:APC171 2.0 19.6 1.0
O1B A:APC171 2.0 23.9 1.0
O6A A:HHR181 2.0 23.7 1.0
OD2 A:ASP95 2.0 16.6 1.0
O A:HOH247 2.1 21.3 1.0
OD2 A:ASP97 2.1 19.7 1.0
CG A:ASP97 3.1 15.6 1.0
CG A:ASP95 3.1 17.8 1.0
PB A:APC171 3.2 23.7 1.0
PG A:APC171 3.2 23.7 1.0
C6A A:HHR181 3.2 28.4 1.0
O3B A:APC171 3.3 23.6 1.0
OD1 A:ASP97 3.5 17.1 1.0
OD1 A:ASP95 3.6 18.4 1.0
MG A:MG161 3.7 23.6 1.0
NH1 A:ARG121 3.9 26.4 1.0
O2B A:APC171 4.0 25.3 1.0
O A:HOH211 4.0 19.9 1.0
O1G A:APC171 4.0 27.0 1.0
N5 A:HHR181 4.2 33.3 1.0
C6 A:HHR181 4.2 33.1 1.0
O A:HOH281 4.3 33.6 1.0
O2G A:APC171 4.3 26.1 1.0
NE2 A:HIS115 4.3 17.7 1.0
CB A:ASP97 4.3 12.8 1.0
CB A:ASP95 4.4 16.4 1.0
O A:HOH224 4.5 35.9 1.0
O A:HOH207 4.6 19.2 1.0
C3A A:APC171 4.6 33.3 1.0
O A:HOH260 4.9 32.6 1.0
CE A:MET124 4.9 21.0 1.0
O A:HOH210 5.0 26.0 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 13:08:02 2024

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