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Manganese 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:

Magnesium (Mg) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 8 binding sites of Manganese where determined in the X-Ray Crystal Structure of Aggregatibacter Actinomycetemcomitans Dimanganese(II) Class Id Ribonucleotide Reductase Beta Subunit, PDB code: 8dq3:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 8dq3

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Manganese binding site 1 out of 8 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 Manganese with other atoms in the Mn 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:Mn401

b:7.6
occ:1.00
 OE2 A:GLU103 2.0 19.2 1.0
OE1 A:GLU200 2.0 10.8 1.0
OE1 A:GLU165 2.1 11.1 1.0
ND1 A:HIS203 2.3 9.2 1.0
CD A:GLU200 2.8 11.3 1.0
CD A:GLU165 2.9 17.9 1.0
OE2 A:GLU200 2.9 16.5 1.0
OE2 A:GLU165 3.1 16.5 1.0
CE1 A:HIS203 3.1 8.2 1.0
CD A:GLU103 3.2 13.3 1.0
CG A:HIS203 3.4 7.3 1.0
O A:HOH626 3.4 15.6 1.0
CB A:HIS203 3.7 8.1 1.0
OE1 A:GLU103 3.8 10.9 1.0
MN A:MN402 3.8 8.2 1.0
O A:HOH632 4.1 24.7 1.0
CG A:GLU165 4.2 13.0 1.0
O A:HOH614 4.2 18.5 1.0
NE1 A:TRP80 4.2 11.2 1.0
CG A:GLU200 4.3 8.4 1.0
CG A:GLU103 4.3 10.2 1.0
NE2 A:HIS203 4.3 7.9 1.0
CD2 A:HIS203 4.4 7.3 1.0
CA A:GLU200 4.6 6.7 1.0
CD1 A:TRP80 4.7 8.9 1.0
CB A:GLU165 4.8 11.6 1.0
CB A:GLU200 4.8 7.8 1.0

Manganese binding site 2 out of 8 in 8dq3

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Manganese binding site 2 out of 8 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 Manganese with other atoms in the Mn 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
A:Mn402

b:8.2
occ:1.00
 OE2 A:GLU200 2.0 16.5 1.0
OE1 A:GLU103 2.2 10.9 1.0
OE2 A:GLU73 2.2 11.2 1.0
ND1 A:HIS106 2.3 7.1 1.0
OE1 A:GLU73 2.3 11.8 1.0
O A:HOH626 2.3 15.6 1.0
CD A:GLU73 2.6 11.6 1.0
CD A:GLU103 3.1 13.3 1.0
CD A:GLU200 3.1 11.3 1.0
CE1 A:HIS106 3.2 8.6 1.0
OE2 A:GLU103 3.3 19.2 1.0
CG A:HIS106 3.3 7.8 1.0
CB A:HIS106 3.7 6.6 1.0
OE1 A:GLU200 3.8 10.8 1.0
MN A:MN401 3.8 7.6 1.0
CG A:GLU73 4.1 10.5 1.0
CG A:GLU200 4.1 8.4 1.0
NZ A:LYS77 4.2 9.1 1.0
NE2 A:HIS106 4.4 7.0 1.0
CD2 A:HIS106 4.4 7.8 1.0
O A:HOH614 4.5 18.5 1.0
CG A:GLU103 4.5 10.2 1.0
CG2 A:THR196 4.5 8.2 1.0
CA A:GLU103 4.8 7.6 1.0
CB A:GLU103 4.9 7.2 1.0
O A:HOH632 4.9 24.7 1.0
CD A:LYS77 5.0 12.3 1.0

Manganese binding site 3 out of 8 in 8dq3

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Manganese binding site 3 out of 8 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 Manganese with other atoms in the Mn 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
B:Mn401

b:6.3
occ:1.00
 OE2 B:GLU103 2.0 16.6 1.0
OE1 B:GLU165 2.0 7.8 1.0
OE1 B:GLU200 2.1 8.8 1.0
ND1 B:HIS203 2.2 7.9 1.0
CD B:GLU165 2.8 8.3 1.0
CD B:GLU200 3.0 7.7 1.0
CE1 B:HIS203 3.0 6.5 1.0
OE2 B:GLU165 3.0 10.9 1.0
OE2 B:GLU200 3.2 11.3 1.0
CD B:GLU103 3.2 10.1 1.0
CG B:HIS203 3.3 6.4 1.0
O B:HOH646 3.7 10.2 1.0
CB B:HIS203 3.7 7.1 1.0
OE1 B:GLU103 4.0 8.2 1.0
MN B:MN402 4.0 6.7 1.0
CG B:GLU103 4.1 7.2 1.0
NE1 B:TRP80 4.2 8.7 1.0
NE2 B:HIS203 4.2 6.9 1.0
CG B:GLU165 4.2 9.1 1.0
CD2 B:HIS203 4.4 7.7 1.0
CG B:GLU200 4.4 6.2 1.0
CD1 B:TRP80 4.6 8.2 1.0
CA B:GLU200 4.6 6.4 1.0
CB B:GLU200 4.8 7.7 1.0
CB B:GLU165 4.8 6.0 1.0

Manganese binding site 4 out of 8 in 8dq3

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Manganese binding site 4 out of 8 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 Manganese with other atoms in the Mn 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
B:Mn402

b:6.7
occ:0.97
 OE2 B:GLU200 2.0 11.3 1.0
OE1 B:GLU103 2.2 8.2 1.0
O B:HOH646 2.2 10.2 1.0
OE2 B:GLU73 2.3 10.6 1.0
OE1 B:GLU73 2.3 9.0 1.0
ND1 B:HIS106 2.3 8.2 1.0
CD B:GLU73 2.6 9.3 1.0
CD B:GLU103 2.9 10.1 1.0
OE2 B:GLU103 3.0 16.6 1.0
CE1 B:HIS106 3.2 8.0 1.0
CD B:GLU200 3.2 7.7 1.0
CG B:HIS106 3.3 6.0 1.0
CB B:HIS106 3.7 5.7 1.0
OE1 B:GLU200 3.8 8.8 1.0
MN B:MN401 4.0 6.3 1.0
NZ B:LYS77 4.1 8.8 1.0
CG B:GLU73 4.1 8.7 1.0
CG B:GLU200 4.3 6.2 1.0
NE2 B:HIS106 4.4 6.3 1.0
CG2 B:THR196 4.4 7.5 1.0
CG B:GLU103 4.4 7.2 1.0
CD2 B:HIS106 4.5 6.4 1.0
CD B:LYS77 4.8 9.9 1.0
CA B:GLU103 4.8 5.7 1.0
CB B:GLU103 4.9 6.9 1.0

Manganese binding site 5 out of 8 in 8dq3

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Manganese binding site 5 out of 8 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 Manganese with other atoms in the Mn binding site number 5 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:Mn401

b:9.3
occ:1.00
 OE2 C:GLU103 1.9 20.3 1.0
OE1 C:GLU200 2.1 13.6 1.0
OE1 C:GLU165 2.2 11.1 1.0
ND1 C:HIS203 2.3 11.7 1.0
CD C:GLU200 2.8 12.9 1.0
OE2 C:GLU200 2.8 16.8 1.0
CD C:GLU165 2.9 20.5 1.0
CE1 C:HIS203 3.1 9.8 1.0
CD C:GLU103 3.1 14.9 1.0
OE2 C:GLU165 3.2 19.0 1.0
CG C:HIS203 3.4 8.5 1.0
O C:HOH618 3.5 18.8 1.0
OE1 C:GLU103 3.7 12.4 1.0
CB C:HIS203 3.8 10.4 1.0
MN C:MN402 3.8 9.4 1.0
O C:HOH625 3.9 24.0 1.0
O C:HOH612 4.2 19.2 1.0
NE1 C:TRP80 4.2 11.4 1.0
NE2 C:HIS203 4.3 7.7 1.0
CG C:GLU165 4.3 14.8 1.0
CG C:GLU103 4.3 9.0 1.0
CG C:GLU200 4.3 10.4 1.0
CD2 C:HIS203 4.4 8.1 1.0
CA C:GLU200 4.6 7.9 1.0
CD1 C:TRP80 4.7 11.2 1.0
CB C:GLU165 4.8 13.2 1.0
CB C:GLU200 4.8 8.8 1.0

Manganese binding site 6 out of 8 in 8dq3

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Manganese binding site 6 out of 8 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 Manganese with other atoms in the Mn binding site number 6 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:Mn402

b:9.4
occ:0.97
 OE2 C:GLU200 2.1 16.8 1.0
OE2 C:GLU73 2.2 12.6 1.0
OE1 C:GLU103 2.2 12.4 1.0
OE1 C:GLU73 2.2 12.5 1.0
ND1 C:HIS106 2.3 9.8 1.0
O C:HOH618 2.3 18.8 1.0
CD C:GLU73 2.5 11.0 1.0
CE1 C:HIS106 3.2 10.6 1.0
CD C:GLU103 3.2 14.9 1.0
CD C:GLU200 3.2 12.9 1.0
CG C:HIS106 3.3 8.8 1.0
OE2 C:GLU103 3.4 20.3 1.0
CB C:HIS106 3.7 7.6 1.0
MN C:MN401 3.8 9.3 1.0
OE1 C:GLU200 3.9 13.6 1.0
CG C:GLU73 4.1 11.8 1.0
CG C:GLU200 4.1 10.4 1.0
NZ C:LYS77 4.2 10.1 1.0
NE2 C:HIS106 4.3 9.7 1.0
CD2 C:HIS106 4.4 9.1 1.0
O C:HOH612 4.5 19.2 1.0
CG C:GLU103 4.5 9.0 1.0
CG2 C:THR196 4.5 10.0 1.0
CA C:GLU103 4.8 8.1 1.0
O C:HOH625 4.8 24.0 1.0
CB C:GLU103 4.9 9.4 1.0
CB C:GLU73 4.9 11.1 1.0
CD C:LYS77 5.0 14.0 1.0

Manganese binding site 7 out of 8 in 8dq3

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Manganese binding site 7 out of 8 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 Manganese with other atoms in the Mn binding site number 7 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:Mn401

b:7.7
occ:0.98
 OE2 D:GLU200 2.0 12.7 1.0
OE1 D:GLU103 2.2 11.1 1.0
OE2 D:GLU73 2.2 14.0 1.0
OE1 D:GLU73 2.3 12.2 1.0
ND1 D:HIS106 2.3 9.0 1.0
CD D:GLU73 2.6 11.9 1.0
CD D:GLU103 2.9 10.9 1.0
OE2 D:GLU103 2.9 19.9 1.0
CD D:GLU200 3.2 10.1 1.0
CE1 D:HIS106 3.2 8.9 1.0
CG D:HIS106 3.3 6.5 1.0
CB D:HIS106 3.7 6.4 1.0
OE1 D:GLU200 3.9 10.1 1.0
MN D:MN402 4.0 7.1 1.0
NZ D:LYS77 4.1 9.7 1.0
CG D:GLU73 4.1 7.9 1.0
CG D:GLU200 4.2 8.5 1.0
CG2 D:THR196 4.4 6.0 1.0
NE2 D:HIS106 4.4 7.9 1.0
CG D:GLU103 4.4 9.9 1.0
CD2 D:HIS106 4.5 7.7 1.0
CA D:GLU103 4.8 6.7 1.0
CD D:LYS77 4.8 11.1 1.0
CB D:GLU103 5.0 7.8 1.0
CB D:GLU73 5.0 8.8 1.0

Manganese binding site 8 out of 8 in 8dq3

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Manganese binding site 8 out of 8 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 Manganese with other atoms in the Mn binding site number 8 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:Mn402

b:7.1
occ:1.00
 OE1 D:GLU165 2.0 8.9 1.0
OE1 D:GLU200 2.1 10.1 1.0
OE2 D:GLU103 2.1 19.9 1.0
ND1 D:HIS203 2.2 8.8 1.0
CD D:GLU165 2.8 9.5 1.0
CD D:GLU200 2.9 10.1 1.0
CE1 D:HIS203 3.0 7.6 1.0
OE2 D:GLU165 3.0 12.3 1.0
OE2 D:GLU200 3.1 12.7 1.0
CD D:GLU103 3.2 10.9 1.0
CG D:HIS203 3.3 7.6 1.0
CB D:HIS203 3.7 7.3 1.0
OE1 D:GLU103 4.0 11.1 1.0
MN D:MN401 4.0 7.7 1.0
CG D:GLU103 4.1 9.9 1.0
NE2 D:HIS203 4.2 7.7 1.0
NE1 D:TRP80 4.2 10.4 1.0
CG D:GLU165 4.2 9.9 1.0
CD2 D:HIS203 4.3 9.3 1.0
CG D:GLU200 4.4 8.5 1.0
CD1 D:TRP80 4.6 10.7 1.0
CA D:GLU200 4.6 8.3 1.0
CB D:GLU200 4.8 8.2 1.0
CB D:GLU165 4.9 8.5 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 11:04:43 2023

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