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Magnesium in PDB 8dq3: X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit

Enzymatic activity of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit

All present enzymatic activity of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit:
1.17.4.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit, PDB code: 8dq3 was solved by H.R.Rose, J.J.Jung, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.22 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.213, 156.54, 80.722, 90, 91.09, 90
R / Rfree (%) 17 / 19.5

Other elements in 8dq3:

The structure of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit (pdb code 8dq3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit, PDB code: 8dq3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 8dq3

Go back to Magnesium Binding Sites List in 8dq3
Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:27.8
occ:1.00
 OE2 A:GLU299 1.9 31.6 1.0
O A:HOH593 2.1 33.6 1.0
OE2 A:GLU194 2.1 20.3 1.0
O A:HOH514 2.2 23.4 1.0
O A:HOH572 2.2 33.5 1.0
O A:HOH507 2.3 33.6 1.0
CD A:GLU194 3.0 23.5 1.0
CD A:GLU299 3.0 33.0 1.0
OE1 A:GLU194 3.3 23.4 1.0
CG A:GLU299 3.7 29.3 1.0
NZ A:LYS198 3.9 25.5 1.0
OE1 A:GLU299 4.1 38.0 1.0
O A:GLU299 4.2 21.0 1.0
CG A:GLU194 4.4 13.6 1.0
CE A:LYS198 4.9 14.9 1.0
CB A:GLU299 4.9 21.9 1.0
C A:GLU299 5.0 20.2 1.0
CA A:GLU299 5.0 21.2 1.0

Magnesium binding site 2 out of 4 in 8dq3

Go back to Magnesium Binding Sites List in 8dq3
Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:29.1
occ:1.00
 OE2 B:GLU299 2.0 30.6 1.0
OE2 B:GLU194 2.0 18.4 1.0
O B:HOH549 2.1 27.3 1.0
O B:HOH550 2.2 30.8 1.0
O B:HOH538 2.3 26.5 1.0
CD B:GLU194 3.0 23.4 1.0
CD B:GLU299 3.2 30.3 1.0
OE1 B:GLU194 3.3 21.2 1.0
NZ B:LYS198 3.8 24.9 1.0
CG B:GLU299 3.9 25.6 1.0
OE1 B:GLU299 4.1 32.8 1.0
CG B:GLU194 4.4 13.3 1.0
O B:GLU299 4.4 21.8 1.0
CE B:LYS198 4.8 18.0 1.0

Magnesium binding site 3 out of 4 in 8dq3

Go back to Magnesium Binding Sites List in 8dq3
Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg403

b:38.0
occ:1.00
 OE2 C:GLU299 2.0 39.0 1.0
O C:HOH539 2.0 30.3 1.0
O C:HOH601 2.0 33.1 1.0
OE2 C:GLU194 2.1 25.8 1.0
O C:HOH560 2.2 36.9 1.0
O C:HOH516 2.3 26.5 1.0
CD C:GLU194 3.1 26.0 1.0
CD C:GLU299 3.2 32.2 1.0
OE1 C:GLU194 3.5 27.8 1.0
NZ C:LYS198 3.8 31.6 1.0
CG C:GLU299 3.8 31.9 1.0
OE1 C:GLU299 4.2 36.7 1.0
O C:GLU299 4.3 26.6 1.0
CG C:GLU194 4.4 16.2 1.0
CE C:LYS198 4.6 22.4 1.0

Magnesium binding site 4 out of 4 in 8dq3

Go back to Magnesium Binding Sites List in 8dq3
Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg403

b:31.7
occ:1.00
 O D:HOH535 2.0 31.4 1.0
OE2 D:GLU299 2.0 30.6 1.0
O D:HOH503 2.1 32.8 1.0
OE2 D:GLU194 2.1 19.6 1.0
O D:HOH527 2.3 29.1 1.0
CD D:GLU194 3.1 23.8 1.0
CD D:GLU299 3.2 32.5 1.0
OE1 D:GLU194 3.4 23.1 1.0
NZ D:LYS198 3.8 26.0 1.0
CG D:GLU299 4.0 25.4 1.0
OE1 D:GLU299 4.2 37.2 1.0
O D:GLU299 4.4 23.7 1.0
CG D:GLU194 4.4 13.3 1.0
CE D:LYS198 4.8 16.8 1.0
O D:SER302 4.9 53.0 1.0
O D:HOH595 5.0 24.8 1.0

Reference:

H.R.Rose, A.K.Boal. X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit To Be Published.
Page generated: Thu Dec 28 08:59:43 2023

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