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Manganese in PDB 4d8g: Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)

Enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)

All present enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn):
1.17.4.1;

Protein crystallography data

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn), PDB code: 4d8g was solved by L.M.K.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.74 / 1.75
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.387, 98.264, 100.390, 90.00, 97.67, 90.00
R / Rfree (%) 19.4 / 22.1

Other elements in 4d8g:

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) (pdb code 4d8g). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn), PDB code: 4d8g:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4d8g

Go back to Manganese Binding Sites List in 4d8g
Manganese binding site 1 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.8
occ:0.50
 OE1 A:GLU89 2.0 27.1 1.0
O A:HOH618 2.2 18.2 0.5
OE1 A:GLU120 2.2 29.4 1.0
OE1 A:GLU227 2.2 28.5 1.0
ND1 A:HIS123 2.3 15.9 1.0
O A:HOH619 2.4 23.2 0.5
CD A:GLU89 3.0 25.7 1.0
CE1 A:HIS123 3.1 16.3 1.0
CD A:GLU120 3.2 22.9 1.0
CD A:GLU227 3.3 29.7 1.0
FE A:FE402 3.3 17.1 0.5
OE2 A:GLU89 3.4 28.8 1.0
CG A:HIS123 3.5 14.8 1.0
OE2 A:GLU120 3.6 26.5 1.0
CE2 A:PHE197 3.9 25.2 1.0
CB A:HIS123 3.9 15.6 1.0
OE2 A:GLU227 4.1 26.4 1.0
CG A:GLU227 4.1 23.5 1.0
NE2 A:HIS123 4.3 14.6 1.0
CG A:GLU89 4.4 21.8 1.0
CD2 A:PHE197 4.5 25.2 1.0
CD2 A:HIS123 4.5 14.6 1.0
CG2 A:ILE223 4.6 17.8 1.0
CG A:GLU120 4.6 17.7 1.0
CA A:GLU120 4.6 14.0 1.0
CE1 A:HIS230 4.6 18.2 1.0
CB A:GLU89 4.7 18.9 1.0
ND1 A:HIS230 4.7 16.7 1.0
CZ A:PHE197 4.8 24.4 1.0
CB A:GLU120 4.9 13.9 1.0
CA A:GLU89 4.9 18.3 1.0
OE2 A:GLU193 4.9 27.4 1.0

Manganese binding site 2 out of 4 in 4d8g

Go back to Manganese Binding Sites List in 4d8g
Manganese binding site 2 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:24.9
occ:0.50
 OE1 B:GLU89 2.0 35.4 1.0
OE2 B:GLU227 2.1 27.8 1.0
O B:HOH590 2.2 26.9 0.5
ND1 B:HIS123 2.2 16.5 1.0
OE1 B:GLU120 2.2 30.1 1.0
O B:HOH578 2.3 23.6 0.5
CE1 B:HIS123 2.9 16.3 1.0
CD B:GLU89 3.0 32.5 1.0
CD B:GLU227 3.2 28.1 1.0
CD B:GLU120 3.3 27.3 1.0
FE B:FE402 3.3 24.2 0.5
OE2 B:GLU89 3.4 34.7 1.0
CG B:HIS123 3.4 15.9 1.0
OE2 B:GLU120 3.7 29.3 1.0
CB B:HIS123 3.9 15.2 1.0
OE1 B:GLU227 4.0 27.7 1.0
CG B:GLU227 4.1 21.5 1.0
CE2 B:PHE197 4.1 25.1 1.0
NE2 B:HIS123 4.1 19.4 1.0
CG B:GLU89 4.3 27.8 1.0
CD2 B:HIS123 4.4 15.5 1.0
CE1 B:HIS230 4.5 17.5 1.0
CG2 B:ILE223 4.5 15.8 1.0
CA B:GLU120 4.6 14.8 1.0
CB B:GLU89 4.6 24.6 1.0
CG B:GLU120 4.6 19.3 1.0
ND1 B:HIS230 4.6 19.7 1.0
CZ B:PHE197 4.7 23.6 1.0
CA B:GLU89 4.8 23.5 1.0
CB B:GLU120 4.9 16.5 1.0
OE2 B:GLU193 4.9 28.5 1.0
CD2 B:PHE197 5.0 23.6 1.0

Manganese binding site 3 out of 4 in 4d8g

Go back to Manganese Binding Sites List in 4d8g
Manganese binding site 3 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:23.0
occ:0.50
 OE1 C:GLU89 1.9 32.1 1.0
OE1 C:GLU227 2.2 33.6 1.0
OE1 C:GLU120 2.2 31.9 1.0
O C:HOH575 2.2 26.6 0.5
ND1 C:HIS123 2.2 18.4 1.0
O C:HOH574 2.4 34.0 0.5
CD C:GLU89 2.9 33.0 1.0
CE1 C:HIS123 3.0 22.2 1.0
CD C:GLU120 3.2 30.5 1.0
FE C:FE402 3.3 23.5 0.5
CD C:GLU227 3.3 33.0 1.0
OE2 C:GLU89 3.4 36.5 1.0
CG C:HIS123 3.4 19.5 1.0
OE2 C:GLU120 3.6 30.4 1.0
CB C:HIS123 3.9 18.8 1.0
CE2 C:PHE197 4.0 29.6 1.0
OE2 C:GLU227 4.1 32.6 1.0
CG C:GLU227 4.2 26.5 1.0
NE2 C:HIS123 4.2 20.3 1.0
CG C:GLU89 4.3 29.6 1.0
CD2 C:HIS123 4.4 18.3 1.0
CD2 C:PHE197 4.5 27.6 1.0
CB C:GLU89 4.5 27.5 1.0
CE1 C:HIS230 4.6 22.1 1.0
CG C:GLU120 4.6 23.1 1.0
CA C:GLU120 4.6 19.3 1.0
CG2 C:ILE223 4.6 22.9 1.0
ND1 C:HIS230 4.6 22.6 1.0
OE2 C:GLU193 4.7 31.4 1.0
CB C:GLU120 4.8 20.1 1.0
CA C:GLU89 4.9 26.4 1.0
CZ C:PHE197 4.9 28.8 1.0

Manganese binding site 4 out of 4 in 4d8g

Go back to Manganese Binding Sites List in 4d8g
Manganese binding site 4 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 2 - Low Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:24.8
occ:0.50
 OE1 D:GLU89 1.9 35.1 1.0
OE1 D:GLU227 2.2 30.2 1.0
ND1 D:HIS123 2.3 16.9 1.0
OE1 D:GLU120 2.3 34.3 1.0
O D:HOH568 2.3 20.2 0.5
O D:HOH501 2.5 35.0 0.5
CD D:GLU89 3.0 33.8 1.0
CE1 D:HIS123 3.0 16.3 1.0
CD D:GLU227 3.3 29.3 1.0
CD D:GLU120 3.3 28.7 1.0
FE D:FE402 3.3 26.8 0.5
OE2 D:GLU89 3.3 36.1 1.0
CG D:HIS123 3.5 16.7 1.0
OE2 D:GLU120 3.6 30.9 1.0
CB D:HIS123 3.9 16.9 1.0
CE2 D:PHE197 3.9 27.0 1.0
OE2 D:GLU227 4.0 28.4 1.0
CG D:GLU227 4.2 24.2 1.0
NE2 D:HIS123 4.3 20.1 1.0
CG D:GLU89 4.3 29.2 1.0
CD2 D:HIS123 4.5 16.5 1.0
CB D:GLU89 4.5 26.1 1.0
CE1 D:HIS230 4.6 22.2 1.0
CG2 D:ILE223 4.6 18.4 1.0
CZ D:PHE197 4.6 26.4 1.0
CA D:GLU120 4.7 18.0 1.0
CG D:GLU120 4.7 23.4 1.0
ND1 D:HIS230 4.7 20.8 1.0
CD2 D:PHE197 4.7 28.3 1.0
OE2 D:GLU193 4.8 31.6 1.0
CA D:GLU89 4.9 25.2 1.0
CB D:GLU120 5.0 19.4 1.0

Reference:

L.M.Dassama, A.K.Boal, C.Krebs, A.C.Rosenzweig, J.M.Bollinger. Evidence That the Beta Subunit of Chlamydia Trachomatis Ribonucleotide Reductase Is Active with the Manganese Ion of Its Manganese(IV)/Iron(III) Cofactor in Site 1. J.Am.Chem.Soc. V. 134 2520 2012.
ISSN: ISSN 0002-7863
PubMed: 22242660
DOI: 10.1021/JA211314P
Page generated: Tue Dec 15 04:19:10 2020

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