Atomistry » Manganese » PDB 8iri-8kfi » 8j4x
Atomistry »
  Manganese »
    PDB 8iri-8kfi »
      8j4x »

Manganese in PDB 8j4x: Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution

Enzymatic activity of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution

All present enzymatic activity of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution:
1.17.4.1;

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution, PDB code: 8j4x was solved by L.R.Yadav, S.C.Mande, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.27 / 3.04
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 160.5, 160.5, 312.08, 90, 90, 90
R / Rfree (%) 21.9 / 25.4

Manganese Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Manganese atom in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution (pdb code 8j4x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 12 binding sites of Manganese where determined in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution, PDB code: 8j4x:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 1 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1301

b:59.3
occ:1.00
 OE2 A:GLU197 2.1 73.2 1.0
OE2 A:GLU103 2.1 48.4 1.0
OE1 A:GLU163 2.1 56.3 1.0
ND1 A:HIS200 2.3 39.3 1.0
CD A:GLU163 2.8 69.7 1.0
CD A:GLU197 2.8 74.7 1.0
OE2 A:GLU163 2.8 61.3 1.0
OE1 A:GLU197 3.0 82.7 1.0
CD A:GLU103 3.1 58.1 1.0
CE1 A:HIS200 3.3 44.4 1.0
CG A:HIS200 3.3 38.3 1.0
CB A:HIS200 3.5 36.0 1.0
OE1 A:GLU103 3.7 62.7 1.0
MN A:MN1302 3.9 102.4 1.0
CA A:GLU197 4.1 41.3 1.0
CG A:GLU197 4.1 54.8 1.0
CG A:GLU103 4.2 48.9 1.0
CG A:GLU163 4.2 56.0 1.0
NE2 A:HIS200 4.4 44.8 1.0
CD2 A:HIS200 4.4 37.0 1.0
CB A:GLU197 4.5 44.2 1.0
CG2 A:ILE99 4.6 34.5 1.0
CG A:GLN75 4.6 37.7 1.0
N A:GLU197 4.7 40.9 1.0
CB A:GLU163 4.7 36.2 1.0
O A:ASP196 4.9 45.6 1.0
CE1 A:HIS106 4.9 41.4 1.0
ND1 A:HIS106 5.0 41.5 1.0
O A:GLU197 5.0 40.3 1.0

Manganese binding site 2 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 2 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1302

b:102.4
occ:1.00
 ND1 A:HIS106 2.3 41.5 1.0
OD1 A:ASP72 2.3 54.9 1.0
OE1 A:GLU103 2.4 62.7 1.0
OE2 A:GLU197 2.5 73.2 1.0
CD A:GLU197 2.9 74.7 1.0
CE1 A:HIS106 3.2 41.4 1.0
CD A:GLU103 3.3 58.1 1.0
CG A:HIS106 3.3 42.5 1.0
OE1 A:GLU197 3.3 82.7 1.0
CG A:ASP72 3.4 60.4 1.0
CB A:HIS106 3.6 43.0 1.0
OE2 A:GLU103 3.6 48.4 1.0
CZ A:PHE167 3.7 63.2 1.0
CG A:GLU197 3.8 54.8 1.0
HO A:OH1303 3.9 60.7 1.0
MN A:MN1301 3.9 59.3 1.0
OD2 A:ASP72 4.0 69.0 1.0
CE1 A:PHE167 4.0 55.7 1.0
CG2 A:ILE193 4.1 44.7 1.0
NE2 A:HIS106 4.4 49.8 1.0
CE2 A:PHE167 4.4 65.3 1.0
CD2 A:HIS106 4.4 49.7 1.0
CG A:GLU103 4.6 48.9 1.0
O A:OH1303 4.6 50.2 1.0
CB A:ASP72 4.6 42.5 1.0
CA A:GLU103 4.6 42.0 1.0
CD1 A:PHE167 4.8 44.7 1.0
CB A:GLU103 4.9 37.6 1.0
OE1 A:GLU163 5.0 56.3 1.0

Manganese binding site 3 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 3 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1301

b:86.2
occ:1.00
 OD2 B:ASP72 2.3 60.3 1.0
OE2 B:GLU197 2.5 68.8 1.0
ND1 B:HIS106 2.6 44.1 1.0
OE1 B:GLU103 2.6 54.9 1.0
CD B:GLU197 2.9 63.4 1.0
CG B:ASP72 3.3 57.9 1.0
CD B:GLU103 3.4 48.4 1.0
OE1 B:GLU197 3.4 75.4 1.0
CE1 B:HIS106 3.4 31.3 1.0
OE2 B:GLU103 3.5 53.8 1.0
CG B:GLU197 3.5 45.6 1.0
CZ B:PHE167 3.6 52.5 1.0
CE2 B:PHE167 3.6 44.2 1.0
CG B:HIS106 3.6 39.1 1.0
OD1 B:ASP72 3.7 67.9 1.0
MN B:MN1302 3.9 56.9 1.0
CB B:HIS106 4.0 26.2 1.0
CG2 B:ILE193 4.0 44.0 1.0
O B:OH1303 4.2 52.3 1.0
CE1 B:PHE167 4.4 62.8 1.0
CD2 B:PHE167 4.5 46.1 1.0
NE2 B:HIS106 4.6 27.4 1.0
CB B:ASP72 4.6 34.5 1.0
CD2 B:HIS106 4.7 41.7 1.0
CG B:GLU103 4.7 41.3 1.0
CA B:GLU103 4.8 37.6 1.0
HO B:OH1303 5.0 63.1 1.0
CA B:ASP72 5.0 42.7 1.0
CB B:GLU197 5.0 36.5 1.0
OE1 B:GLU163 5.0 67.2 1.0

Manganese binding site 4 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 4 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn1302

b:56.9
occ:1.00
 OE1 B:GLU163 2.0 67.2 1.0
OE2 B:GLU103 2.0 53.8 1.0
OE2 B:GLU197 2.1 68.8 1.0
ND1 B:HIS200 2.5 37.5 1.0
CD B:GLU197 2.8 63.4 1.0
CD B:GLU163 2.9 71.3 1.0
OE1 B:GLU197 2.9 75.4 1.0
CD B:GLU103 3.2 48.4 1.0
OE2 B:GLU163 3.3 73.1 1.0
CG B:HIS200 3.3 35.5 1.0
CB B:HIS200 3.4 40.7 1.0
CE1 B:HIS200 3.5 30.2 1.0
OE1 B:GLU103 3.8 54.9 1.0
MN B:MN1301 3.9 86.2 1.0
CG B:GLU197 4.1 45.6 1.0
CG B:GLU163 4.2 59.1 1.0
CA B:GLU197 4.2 38.9 1.0
CB B:GLU163 4.3 43.1 1.0
CG B:GLN75 4.4 31.1 1.0
CG B:GLU103 4.4 41.3 1.0
CD2 B:HIS200 4.5 38.4 1.0
NE2 B:HIS200 4.6 41.7 1.0
CB B:GLU197 4.6 36.5 1.0
CG2 B:ILE99 4.8 23.3 1.0
N B:GLU197 4.9 40.8 1.0
CA B:HIS200 4.9 38.9 1.0
O B:GLU197 5.0 43.4 1.0

Manganese binding site 5 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 5 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1301

b:60.1
occ:1.00
 OE2 C:GLU103 2.0 50.6 1.0
OE1 C:GLU163 2.0 54.1 1.0
OE2 C:GLU197 2.4 56.1 1.0
ND1 C:HIS200 2.5 46.4 1.0
OE1 C:GLU197 2.7 69.7 1.0
CD C:GLU197 2.8 60.5 1.0
CD C:GLU163 2.9 59.0 1.0
CD C:GLU103 3.0 50.1 1.0
OE2 C:GLU163 3.2 62.7 1.0
CE1 C:HIS200 3.4 43.3 1.0
CG C:HIS200 3.4 42.6 1.0
OE1 C:GLU103 3.6 60.0 1.0
CB C:HIS200 3.7 36.4 1.0
CG C:GLU103 4.1 32.2 1.0
CG C:GLN75 4.2 30.6 1.0
MN C:MN1302 4.3 87.4 1.0
CG C:GLU163 4.3 58.4 1.0
CG C:GLU197 4.3 47.9 1.0
CA C:GLU197 4.4 40.8 1.0
CG2 C:ILE99 4.5 31.5 1.0
NE2 C:HIS200 4.6 48.3 1.0
CB C:GLU163 4.6 40.6 1.0
CD2 C:HIS200 4.6 48.2 1.0
CE2 C:PHE167 4.7 49.0 1.0
CB C:GLU197 4.7 49.3 1.0

Manganese binding site 6 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 6 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn1302

b:87.4
occ:1.00
 OD1 C:ASP72 2.1 64.9 1.0
ND1 C:HIS106 2.5 39.3 1.0
CG C:ASP72 3.0 54.4 1.0
OE2 C:GLU197 3.1 56.1 1.0
CD C:GLU197 3.1 60.5 1.0
OD2 C:ASP72 3.2 66.2 1.0
OE1 C:GLU197 3.3 69.7 1.0
OE1 C:GLU103 3.3 60.0 1.0
CG C:HIS106 3.3 49.7 1.0
CE1 C:HIS106 3.4 43.6 1.0
OE2 C:GLU103 3.5 50.6 1.0
CG2 C:ILE193 3.5 47.1 1.0
CB C:HIS106 3.5 36.2 1.0
HO C:OH1304 3.6 49.4 1.0
CZ C:PHE167 3.7 57.3 1.0
CD C:GLU103 3.7 50.1 1.0
CG C:GLU197 3.9 47.9 1.0
O C:OH1304 3.9 40.9 1.0
CE2 C:PHE167 4.0 49.0 1.0
CE1 C:PHE167 4.1 45.8 1.0
MN C:MN1301 4.3 60.1 1.0
CB C:ASP72 4.4 32.5 1.0
CD2 C:HIS106 4.5 59.2 1.0
NE2 C:HIS106 4.5 57.2 1.0
CD2 C:PHE167 4.8 44.8 1.0
CD1 C:PHE167 4.8 44.0 1.0
CA C:ASP72 4.9 33.0 1.0
CB C:ILE193 4.9 48.9 1.0
CA C:GLU103 5.0 31.1 1.0

Manganese binding site 7 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 7 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1301

b:95.5
occ:1.00
 ND1 D:HIS106 2.4 38.0 1.0
OD1 D:ASP72 2.4 57.3 1.0
OE2 D:GLU197 2.6 56.4 1.0
CD D:GLU197 2.8 64.6 1.0
OE1 D:GLU103 3.0 52.4 1.0
CE1 D:HIS106 3.2 45.5 1.0
OE1 D:GLU197 3.3 72.2 1.0
OE2 D:GLU103 3.4 63.4 1.0
CG D:ASP72 3.4 45.3 1.0
CG D:HIS106 3.4 32.1 1.0
CG D:GLU197 3.4 50.9 1.0
CD D:GLU103 3.5 57.9 1.0
OD2 D:ASP72 3.7 57.5 1.0
CG2 D:ILE193 3.8 36.1 1.0
CB D:HIS106 3.8 29.9 1.0
CZ D:PHE167 3.8 64.7 1.0
MN D:MN1302 4.0 56.7 1.0
CE1 D:PHE167 4.1 51.8 1.0
HO D:OH1303 4.2 65.0 1.0
O D:OH1303 4.3 53.9 1.0
CE2 D:PHE167 4.3 63.1 1.0
NE2 D:HIS106 4.4 45.9 1.0
CD2 D:HIS106 4.5 52.7 1.0
CB D:ASP72 4.7 34.2 1.0
CD1 D:PHE167 4.8 46.0 1.0
CG D:GLU103 4.8 39.7 1.0
CB D:GLU197 4.9 34.6 1.0
CA D:GLU103 4.9 31.4 1.0
CD2 D:PHE167 4.9 50.3 1.0

Manganese binding site 8 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 8 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1302

b:56.7
occ:1.00
 OE2 D:GLU103 2.1 63.4 1.0
OE2 D:GLU197 2.3 56.4 1.0
ND1 D:HIS200 2.6 32.9 1.0
OE1 D:GLU197 2.6 72.2 1.0
CD D:GLU197 2.7 64.6 1.0
CD D:GLU103 3.0 57.9 1.0
OE2 D:GLU163 3.1 66.9 1.0
CG D:GLU163 3.2 58.1 1.0
CD D:GLU163 3.2 66.7 1.0
CG D:HIS200 3.4 40.7 1.0
OE1 D:GLU103 3.5 52.4 1.0
CB D:HIS200 3.5 34.6 1.0
CE1 D:HIS200 3.6 34.2 1.0
CB D:GLU163 4.0 37.2 1.0
MN D:MN1301 4.0 95.5 1.0
OE1 D:GLU163 4.1 81.2 1.0
CG D:GLU103 4.2 39.7 1.0
CG D:GLU197 4.2 50.9 1.0
CG D:GLN75 4.3 31.2 1.0
CA D:GLU197 4.4 38.1 1.0
CG2 D:ILE99 4.6 28.6 1.0
CD2 D:HIS200 4.6 37.8 1.0
CB D:GLU197 4.7 34.6 1.0
NE2 D:HIS200 4.7 43.7 1.0
CE2 D:PHE167 4.8 63.1 1.0
NE2 D:GLN75 4.8 50.5 1.0
CA D:GLU163 4.9 37.9 1.0

Manganese binding site 9 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 9 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1301

b:95.4
occ:1.00
 OE2 E:GLU163 1.9 90.0 1.0
OE2 E:GLU103 2.0 89.1 1.0
ND1 E:HIS200 2.4 78.2 1.0
OE2 E:GLU197 2.4 92.9 1.0
CD E:GLU163 2.7 90.4 1.0
OE1 E:GLU163 2.9 80.8 1.0
CD E:GLU197 3.0 99.3 1.0
OE1 E:GLU197 3.0 109.7 1.0
CG E:HIS200 3.2 77.6 1.0
CD E:GLU103 3.2 86.9 1.0
CB E:HIS200 3.4 75.6 1.0
CE1 E:HIS200 3.4 79.4 1.0
OE1 E:GLU103 4.0 93.3 1.0
MN E:MN1302 4.1 120.5 1.0
CG E:GLU163 4.1 84.2 1.0
CA E:GLU197 4.2 82.1 1.0
CG E:GLU103 4.2 69.6 1.0
CG E:GLU197 4.3 80.1 1.0
CD2 E:HIS200 4.4 80.5 1.0
CB E:GLU163 4.5 68.8 1.0
NE2 E:HIS200 4.5 81.5 1.0
CG2 E:ILE99 4.5 70.8 1.0
CG E:GLN75 4.6 62.2 1.0
CB E:GLU197 4.7 81.2 1.0
O E:GLU197 4.9 80.3 1.0
CA E:HIS200 4.9 77.7 1.0
N E:GLU197 4.9 85.9 1.0

Manganese binding site 10 out of 12 in 8j4x

Go back to Manganese Binding Sites List in 8j4x
Manganese binding site 10 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Oxidised) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn1302

b:120.5
occ:1.00
 OD2 E:ASP72 2.1 91.7 1.0
OE2 E:GLU197 2.6 92.9 1.0
CD2 E:HIS106 2.7 81.6 1.0
OE1 E:GLU103 2.9 93.3 1.0
CD E:GLU197 2.9 99.3 1.0
OE2 E:GLU103 3.1 89.1 1.0
OE1 E:GLU197 3.2 109.7 1.0
CG E:ASP72 3.3 90.5 1.0
CD E:GLU103 3.3 86.9 1.0
CG E:HIS106 3.5 83.5 1.0
NE2 E:HIS106 3.7 84.7 1.0
CZ E:PHE167 3.8 83.2 1.0
OD1 E:ASP72 3.8 91.0 1.0
CB E:HIS106 3.8 82.2 1.0
CG E:GLU197 3.9 80.1 1.0
CG2 E:ILE193 4.0 86.8 1.0
MN E:MN1301 4.1 95.4 1.0
CE2 E:PHE167 4.1 87.4 1.0
HO E:OH1303 4.1 105.4 1.0
CE1 E:PHE167 4.3 75.0 1.0
CB E:ASP72 4.5 76.8 1.0
CG E:GLU103 4.6 69.6 1.0
O E:OH1303 4.6 87.5 1.0
ND1 E:HIS106 4.6 87.8 1.0
CA E:GLU103 4.7 74.1 1.0
CE1 E:HIS106 4.7 88.4 1.0
CD2 E:PHE167 4.8 73.5 1.0
OE2 E:GLU163 4.9 90.0 1.0
CA E:ASP72 4.9 67.9 1.0
CB E:GLU103 5.0 70.9 1.0

Reference:

L.R.Yadav, V.Sharma, M.Shanmugam, S.C.Mande. Structural Insights Into the Initiation of Free Radical Formation in the Class Ib Ribonucleotide Reductases in Mycobacteria Curr Res Struct Biol V. 8 00157 2024.
ISSN: ESSN 2665-928X
DOI: 10.1016/J.CRSTBI.2024.100157
Page generated: Thu Oct 31 22:42:47 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy