Atomistry » Manganese » PDB 8dl1-8f4c » 8dq3
Atomistry »
  Manganese »
    PDB 8dl1-8f4c »
      8dq3 »

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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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

Go back to Manganese Binding Sites List in 8dq3
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: Sun Oct 6 11:33:38 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy