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Manganese in PDB 4m1i: X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb

Enzymatic activity of X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb

All present enzymatic activity of X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb:
1.17.4.1;

Protein crystallography data

The structure of X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb, PDB code: 4m1i was solved by A.K.Boal, A.C.Rosenzweig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.85 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 74.897, 97.455, 99.315, 90.00, 97.77, 90.00
R / Rfree (%) 17.2 / 20.2

Other elements in 4m1i:

The structure of X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb (pdb code 4m1i). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb, PDB code: 4m1i:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4m1i

Go back to Manganese Binding Sites List in 4m1i
Manganese binding site 1 out of 4 in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb


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 Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:14.4
occ:0.95
 OE1 A:GLU89 2.1 14.7 1.0
OE1 A:GLU120 2.1 13.9 1.0
OE2 A:GLU227 2.2 17.2 1.0
ND1 A:HIS123 2.3 10.2 1.0
O A:HOH502 2.3 13.5 1.0
O A:HOH501 2.3 17.9 1.0
CD A:GLU89 3.1 15.2 1.0
CE1 A:HIS123 3.1 10.5 1.0
CD A:GLU120 3.1 13.1 1.0
FE A:FE402 3.2 16.4 1.0
CD A:GLU227 3.2 19.3 1.0
OE2 A:GLU89 3.4 16.2 1.0
CG A:HIS123 3.4 9.6 1.0
OE2 A:GLU120 3.5 13.5 1.0
CB A:HIS123 3.9 10.4 1.0
CE2 A:PHE197 4.0 17.2 1.0
OE1 A:GLU227 4.0 16.1 1.0
CG A:GLU227 4.1 16.2 1.0
NE2 A:HIS123 4.3 9.1 1.0
CG A:GLU89 4.4 14.5 1.0
CE1 A:HIS230 4.5 10.0 1.0
CD2 A:HIS123 4.5 9.3 1.0
CG A:GLU120 4.5 10.2 1.0
CD2 A:PHE197 4.5 16.6 1.0
CA A:GLU120 4.5 9.2 1.0
ND1 A:HIS230 4.6 9.9 1.0
CG2 A:ILE223 4.6 12.7 1.0
CB A:GLU89 4.8 12.8 1.0
CB A:GLU120 4.8 8.9 1.0
CZ A:PHE197 4.9 17.0 1.0
CA A:GLU89 4.9 12.1 1.0
OE2 A:GLU193 4.9 15.6 1.0

Manganese binding site 2 out of 4 in 4m1i

Go back to Manganese Binding Sites List in 4m1i
Manganese binding site 2 out of 4 in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb


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 Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:15.3
occ:0.85
 OE1 B:GLU89 2.0 18.8 1.0
OE1 B:GLU120 2.1 16.7 1.0
OE1 B:GLU227 2.2 15.2 1.0
O B:HOH501 2.2 12.3 1.0
O B:HOH502 2.2 17.9 1.0
ND1 B:HIS123 2.3 11.6 1.0
CD B:GLU89 3.0 18.9 1.0
CE1 B:HIS123 3.1 10.5 1.0
CD B:GLU120 3.2 15.0 1.0
CD B:GLU227 3.2 17.8 1.0
FE B:FE401 3.2 17.9 1.0
OE2 B:GLU89 3.4 19.8 1.0
CG B:HIS123 3.5 11.6 1.0
OE2 B:GLU120 3.5 14.6 1.0
OE2 B:GLU227 3.9 16.4 1.0
CB B:HIS123 3.9 11.4 1.0
CG B:GLU227 4.0 14.4 1.0
CE2 B:PHE197 4.1 18.9 1.0
NE2 B:HIS123 4.3 10.6 1.0
CG B:GLU89 4.4 17.2 1.0
CE1 B:HIS230 4.5 9.8 1.0
CD2 B:HIS123 4.5 10.0 1.0
CG B:GLU120 4.5 10.9 1.0
CA B:GLU120 4.5 9.9 1.0
ND1 B:HIS230 4.5 11.3 1.0
CZ B:PHE197 4.7 18.5 1.0
CG2 B:ILE223 4.7 13.0 1.0
CB B:GLU89 4.7 15.7 1.0
CB B:GLU120 4.8 10.2 1.0
CA B:GLU89 4.9 15.0 1.0
CD2 B:PHE197 5.0 17.9 1.0

Manganese binding site 3 out of 4 in 4m1i

Go back to Manganese Binding Sites List in 4m1i
Manganese binding site 3 out of 4 in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb


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 Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:16.6
occ:0.85
 OE1 C:GLU89 2.0 21.5 1.0
OE1 C:GLU120 2.1 19.0 1.0
O C:HOH502 2.2 16.6 1.0
OE1 C:GLU227 2.2 17.9 1.0
O C:HOH501 2.3 18.4 1.0
ND1 C:HIS123 2.3 13.1 1.0
CD C:GLU89 3.0 21.4 1.0
CE1 C:HIS123 3.1 13.3 1.0
CD C:GLU120 3.1 17.1 1.0
FE C:FE401 3.2 18.0 1.0
CD C:GLU227 3.2 20.1 1.0
OE2 C:GLU89 3.3 22.6 1.0
CG C:HIS123 3.4 13.5 1.0
OE2 C:GLU120 3.5 15.5 1.0
CB C:HIS123 3.9 13.7 1.0
OE2 C:GLU227 3.9 18.2 1.0
CE2 C:PHE197 4.0 22.2 1.0
CG C:GLU227 4.1 17.1 1.0
NE2 C:HIS123 4.3 12.5 1.0
CG C:GLU89 4.4 19.6 1.0
CE1 C:HIS230 4.4 12.6 1.0
CD2 C:HIS123 4.5 13.6 1.0
CG C:GLU120 4.5 14.2 1.0
ND1 C:HIS230 4.5 12.7 1.0
CD2 C:PHE197 4.5 21.2 1.0
CA C:GLU120 4.6 13.3 1.0
CG2 C:ILE223 4.6 13.8 1.0
CB C:GLU89 4.7 18.5 1.0
CB C:GLU120 4.8 13.7 1.0
OE2 C:GLU193 4.9 17.1 1.0
CZ C:PHE197 4.9 22.8 1.0
CA C:GLU89 4.9 17.6 1.0

Manganese binding site 4 out of 4 in 4m1i

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Manganese binding site 4 out of 4 in the X-Ray Crystal Structure of Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb


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 Chlamydia Trachomatis Mn(II)Fe(II)-Nrdb within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:15.9
occ:0.85
 OE1 D:GLU89 2.0 19.9 1.0
OE1 D:GLU120 2.1 18.0 1.0
OE1 D:GLU227 2.2 19.0 1.0
O D:HOH502 2.2 20.8 1.0
ND1 D:HIS123 2.2 12.2 1.0
O D:HOH501 2.3 17.3 1.0
CE1 D:HIS123 3.0 13.0 1.0
CD D:GLU89 3.0 19.9 1.0
FE D:FE401 3.2 19.3 1.0
CD D:GLU120 3.2 16.0 1.0
CD D:GLU227 3.2 21.1 1.0
OE2 D:GLU89 3.4 21.3 1.0
CG D:HIS123 3.4 11.7 1.0
OE2 D:GLU120 3.5 15.6 1.0
CB D:HIS123 3.9 11.1 1.0
OE2 D:GLU227 4.0 18.9 1.0
CG D:GLU227 4.0 17.0 1.0
CE2 D:PHE197 4.1 19.2 1.0
NE2 D:HIS123 4.2 12.5 1.0
CG D:GLU89 4.4 18.3 1.0
CD2 D:HIS123 4.4 11.8 1.0
CE1 D:HIS230 4.5 12.5 1.0
CG D:GLU120 4.5 13.3 1.0
ND1 D:HIS230 4.5 12.3 1.0
CA D:GLU120 4.6 11.8 1.0
CG2 D:ILE223 4.6 13.0 1.0
CB D:GLU89 4.7 16.8 1.0
CD2 D:PHE197 4.7 20.0 1.0
CB D:GLU120 4.8 11.9 1.0
CZ D:PHE197 4.8 19.9 1.0
OE2 D:GLU193 4.9 19.4 1.0
CA D:GLU89 4.9 16.7 1.0

Reference:

L.M.Dassama, C.Krebs, J.M.Bollinger, A.C.Rosenzweig, A.K.Boal. Structural Basis For Assembly of the Mn(IV)/Fe(III) Cofactor in the Class Ic Ribonucleotide Reductase From Chlamydia Trachomatis. Biochemistry V. 52 6424 2013.
ISSN: ISSN 0006-2960
PubMed: 23924396
DOI: 10.1021/BI400819X
Page generated: Sat Oct 5 20:18:00 2024

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