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Manganese in PDB 4d8f: Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)

Enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn)

All present enzymatic activity of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn):
1.17.4.1;

Protein crystallography data

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High Mn), PDB code: 4d8f 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) 29.66 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.221, 97.998, 100.291, 90.00, 97.79, 90.00
R / Rfree (%) 18.6 / 23.5

Other elements in 4d8f:

The structure of Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High 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 1 - High Mn) (pdb code 4d8f). 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 1 - High Mn), PDB code: 4d8f:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 1 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High 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 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:36.8
occ:1.00
 OE1 A:GLU89 2.1 23.4 1.0
OE1 A:GLU120 2.2 19.3 1.0
ND1 A:HIS123 2.4 16.0 1.0
O A:HOH642 2.5 20.1 1.0
OE1 A:GLU227 2.9 28.8 1.0
FE A:FE401 3.1 38.4 1.0
CD A:GLU89 3.1 22.9 1.0
CE1 A:HIS123 3.1 15.4 1.0
CD A:GLU120 3.1 18.5 1.0
OE2 A:GLU120 3.4 20.4 1.0
OE2 A:GLU89 3.4 25.2 1.0
CG A:HIS123 3.5 15.5 1.0
CD A:GLU227 3.9 25.8 1.0
CE2 A:PHE197 4.0 21.1 1.0
CB A:HIS123 4.0 15.5 1.0
OE2 A:GLU227 4.2 26.6 1.0
NE2 A:HIS123 4.3 15.5 1.0
CG A:GLU89 4.4 20.4 1.0
CD2 A:PHE197 4.5 20.6 1.0
CG A:GLU120 4.5 16.2 1.0
CD2 A:HIS123 4.6 15.6 1.0
OE2 A:GLU193 4.6 22.1 1.0
CA A:GLU120 4.6 14.9 1.0
CE1 A:HIS230 4.6 15.4 1.0
CG2 A:ILE223 4.6 16.0 1.0
ND1 A:HIS230 4.7 13.9 1.0
CB A:GLU89 4.7 18.5 1.0
CB A:GLU120 4.8 14.8 1.0
CZ A:PHE197 4.9 20.7 1.0
CA A:GLU89 5.0 18.0 1.0

Manganese binding site 2 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 2 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High 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 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:43.1
occ:1.00
 OE1 B:GLU89 2.0 27.8 1.0
OE1 B:GLU227 2.2 27.5 1.0
OE1 B:GLU120 2.3 23.6 1.0
O B:HOH573 2.4 39.9 1.0
ND1 B:HIS123 2.5 14.7 1.0
CD B:GLU89 3.0 25.8 1.0
FE B:FE402 3.1 45.5 1.0
CD B:GLU120 3.3 21.5 1.0
CD B:GLU227 3.3 27.3 1.0
CE1 B:HIS123 3.3 15.4 1.0
OE2 B:GLU89 3.4 27.3 1.0
OE2 B:GLU120 3.5 22.9 1.0
CG B:HIS123 3.6 15.2 1.0
CE2 B:PHE197 3.8 28.0 1.0
OE2 B:GLU227 3.9 28.8 1.0
CB B:HIS123 4.1 15.5 1.0
CG B:GLU227 4.3 22.8 1.0
CG B:GLU89 4.3 22.9 1.0
NE2 B:HIS123 4.5 15.0 1.0
CE1 B:HIS230 4.6 15.2 1.0
ND1 B:HIS230 4.6 15.2 1.0
CG B:GLU120 4.6 18.1 1.0
CB B:GLU89 4.6 21.0 1.0
CA B:GLU120 4.6 15.7 1.0
CZ B:PHE197 4.6 27.8 1.0
CD2 B:PHE197 4.6 27.7 1.0
CG2 B:ILE223 4.7 17.0 1.0
OE2 B:GLU193 4.7 24.8 1.0
CD2 B:HIS123 4.7 15.2 1.0
CA B:GLU89 4.9 20.5 1.0
CB B:GLU120 4.9 16.1 1.0

Manganese binding site 3 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 3 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High 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 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:42.9
occ:1.00
 OE1 C:GLU89 2.0 30.5 1.0
OE1 C:GLU120 2.3 26.2 1.0
ND1 C:HIS123 2.4 17.8 1.0
OE1 C:GLU227 2.9 31.9 1.0
CD C:GLU89 3.1 28.6 1.0
FE C:FE401 3.1 47.1 1.0
CE1 C:HIS123 3.2 17.1 1.0
CD C:GLU120 3.3 23.9 1.0
OE2 C:GLU89 3.5 30.6 1.0
CG C:HIS123 3.6 18.6 1.0
OE2 C:GLU120 3.7 25.4 1.0
CD C:GLU227 3.8 30.3 1.0
CE2 C:PHE197 3.9 24.3 1.0
OE2 C:GLU227 4.0 31.5 1.0
CB C:HIS123 4.0 19.4 1.0
NE2 C:HIS123 4.4 18.6 1.0
CG C:GLU89 4.4 26.1 1.0
CD2 C:PHE197 4.4 25.2 1.0
CE1 C:HIS230 4.6 21.6 1.0
CD2 C:HIS123 4.6 17.4 1.0
CA C:GLU120 4.6 19.1 1.0
ND1 C:HIS230 4.6 21.3 1.0
CB C:GLU89 4.7 24.7 1.0
CG C:GLU120 4.7 20.9 1.0
CG2 C:ILE223 4.7 21.5 1.0
OE2 C:GLU193 4.8 28.5 1.0
CZ C:PHE197 4.8 24.6 1.0
CB C:GLU120 4.9 19.0 1.0
CA C:GLU89 5.0 24.3 1.0

Manganese binding site 4 out of 4 in 4d8f

Go back to Manganese Binding Sites List in 4d8f
Manganese binding site 4 out of 4 in the Chlamydia Trachomatis Nrdb with A Mn/Fe Cofactor (Procedure 1 - High 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 1 - High Mn) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:43.9
occ:1.00
 OE1 D:GLU89 2.2 30.4 1.0
ND1 D:HIS123 2.3 18.4 1.0
OE1 D:GLU227 2.3 27.5 1.0
OE1 D:GLU120 2.4 24.1 1.0
CE1 D:HIS123 3.0 18.4 1.0
CD D:GLU89 3.2 29.5 1.0
FE D:FE401 3.2 48.4 1.0
CD D:GLU227 3.3 26.7 1.0
CD D:GLU120 3.4 22.9 1.0
OE2 D:GLU89 3.5 30.8 1.0
CG D:HIS123 3.5 17.5 1.0
OE2 D:GLU120 3.7 24.2 1.0
OE2 D:GLU227 4.0 28.2 1.0
CB D:HIS123 4.0 17.1 1.0
CE2 D:PHE197 4.1 27.9 1.0
CG D:GLU227 4.2 23.6 1.0
NE2 D:HIS123 4.2 18.7 1.0
CD2 D:HIS123 4.5 17.8 1.0
CG D:GLU89 4.5 26.6 1.0
CE1 D:HIS230 4.5 18.9 1.0
CG2 D:ILE223 4.5 19.8 1.0
ND1 D:HIS230 4.6 18.8 1.0
CD2 D:PHE197 4.7 28.4 1.0
CA D:GLU120 4.7 18.4 1.0
CG D:GLU120 4.8 20.4 1.0
CB D:GLU89 4.8 25.1 1.0
CZ D:PHE197 4.9 28.9 1.0
OE2 D:GLU193 4.9 26.8 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: Sat Oct 5 18:59:07 2024

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