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Manganese in PDB 8j4y: Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) Determined at 3 Angstrom Resolution

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

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

Protein crystallography data

The structure of Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) Determined at 3 Angstrom Resolution, PDB code: 8j4y 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) 91.58 / 3.02
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 160.43, 160.43, 310.4, 90, 90, 90
R / Rfree (%) 23 / 26.6

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 (Reduced) Determined at 3 Angstrom Resolution (pdb code 8j4y). 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 (Reduced) Determined at 3 Angstrom Resolution, PDB code: 8j4y:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 12 in 8j4y

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Manganese binding site 1 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:69.0
occ:1.00
 OE1 A:GLU163 2.0 61.9 1.0
OE2 A:GLU103 2.1 67.0 1.0
ND1 A:HIS200 2.4 50.0 1.0
OE1 A:GLU197 2.5 82.2 1.0
CD A:GLU163 2.9 62.1 1.0
CD A:GLU103 2.9 66.6 1.0
OE2 A:GLU197 3.0 69.6 1.0
CD A:GLU197 3.1 69.4 1.0
OE2 A:GLU163 3.1 67.3 1.0
CE1 A:HIS200 3.3 50.9 1.0
CG A:HIS200 3.4 49.2 1.0
OE1 A:GLU103 3.6 73.4 1.0
CB A:HIS200 3.7 48.2 1.0
MN A:MN402 3.7 94.8 1.0
CG A:GLU103 3.7 55.3 1.0
CG A:GLU163 4.3 58.8 1.0
CA A:GLU197 4.4 52.2 1.0
NE2 A:HIS200 4.4 50.7 1.0
CD2 A:HIS200 4.5 49.7 1.0
CG A:GLU197 4.5 69.5 1.0
CG2 A:ILE99 4.5 47.7 1.0
CG A:GLN75 4.5 47.0 1.0
CE2 A:PHE167 4.6 62.1 1.0
CB A:GLU163 4.7 47.2 1.0
CB A:GLU197 4.8 59.2 1.0
CE1 A:HIS106 4.8 55.1 1.0
ND1 A:HIS106 4.9 55.1 1.0
N A:GLU197 5.0 62.4 1.0

Manganese binding site 2 out of 12 in 8j4y

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Manganese binding site 2 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:94.8
occ:1.00
 OE1 A:GLU103 2.3 73.4 1.0
OD1 A:ASP72 2.3 84.9 1.0
ND1 A:HIS106 2.3 55.1 1.0
OE2 A:GLU197 2.4 69.6 1.0
CD A:GLU103 3.0 66.6 1.0
CD A:GLU197 3.0 69.4 1.0
CE1 A:HIS106 3.2 55.1 1.0
CG A:HIS106 3.3 56.6 1.0
OE1 A:GLU197 3.4 82.2 1.0
OE2 A:GLU103 3.4 67.0 1.0
CG A:ASP72 3.5 81.5 1.0
CB A:HIS106 3.6 57.2 1.0
CZ A:PHE167 3.7 63.3 1.0
MN A:MN401 3.7 69.0 1.0
CE2 A:PHE167 3.9 62.1 1.0
CG A:GLU103 4.2 55.3 1.0
CG A:GLU197 4.2 69.5 1.0
CG2 A:ILE193 4.3 58.0 1.0
OD2 A:ASP72 4.3 88.2 1.0
NE2 A:HIS106 4.3 61.1 1.0
CA A:GLU103 4.4 52.9 1.0
CD2 A:HIS106 4.4 62.9 1.0
CB A:ASP72 4.5 59.0 1.0
CE1 A:PHE167 4.5 76.7 1.0
CB A:GLU103 4.6 57.0 1.0
CD2 A:PHE167 4.8 51.4 1.0
CA A:ASP72 4.8 53.2 1.0
O A:GLU103 4.8 55.0 1.0

Manganese binding site 3 out of 12 in 8j4y

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Manganese binding site 3 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:56.0
occ:1.00
 OE2 B:GLU103 2.1 61.0 1.0
ND1 B:HIS200 2.4 40.0 1.0
OE2 B:GLU163 2.5 62.0 1.0
OE1 B:GLU197 2.6 71.5 1.0
CD B:GLU197 2.8 64.8 1.0
OE1 B:GLU163 2.9 64.1 1.0
OE2 B:GLU197 2.9 71.5 1.0
CD B:GLU163 2.9 65.2 1.0
CD B:GLU103 3.1 51.9 1.0
CG B:HIS200 3.3 36.4 1.0
CE1 B:HIS200 3.3 30.9 1.0
CB B:HIS200 3.5 32.8 1.0
OE1 B:GLU103 3.7 59.9 1.0
CG B:GLU197 4.0 54.8 1.0
MN B:MN402 4.0 79.8 1.0
CA B:GLU197 4.0 42.0 1.0
CG B:GLU163 4.2 50.3 1.0
CG B:GLU103 4.2 40.4 1.0
CD2 B:HIS200 4.4 39.0 1.0
NE2 B:HIS200 4.4 47.1 1.0
CB B:GLU197 4.4 45.6 1.0
CB B:GLU163 4.6 32.3 1.0
N B:GLU197 4.7 40.2 1.0
CG B:GLN75 4.8 40.0 1.0
O B:GLU197 4.8 40.5 1.0
O B:ASP196 4.8 43.3 1.0
CG2 B:ILE99 4.9 29.8 1.0
C B:GLU197 4.9 41.6 1.0
ND1 B:HIS106 4.9 33.3 1.0
CE1 B:HIS106 4.9 29.9 1.0
C B:ASP196 5.0 35.7 1.0
CA B:HIS200 5.0 32.2 1.0

Manganese binding site 4 out of 12 in 8j4y

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Manganese binding site 4 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:79.8
occ:1.00
 OE2 B:GLU197 2.2 71.5 1.0
ND1 B:HIS106 2.3 33.3 1.0
OD1 B:ASP72 2.6 62.3 1.0
OE1 B:GLU103 2.9 59.9 1.0
OE2 B:GLU103 2.9 61.0 1.0
CD B:GLU103 3.1 51.9 1.0
CG B:HIS106 3.2 38.3 1.0
CG B:ASP72 3.3 60.3 1.0
CD B:GLU197 3.4 64.8 1.0
CE1 B:HIS106 3.4 29.9 1.0
CB B:HIS106 3.4 33.2 1.0
OD2 B:ASP72 3.6 79.2 1.0
CG B:GLU197 4.0 54.8 1.0
MN B:MN401 4.0 56.0 1.0
HO B:OH403 4.0 55.8 1.0
O B:OH403 4.1 46.5 1.0
CZ B:PHE167 4.1 54.0 1.0
CG2 B:ILE193 4.1 42.8 1.0
CE1 B:PHE167 4.2 61.6 1.0
CA B:GLU103 4.3 34.3 1.0
OE1 B:GLU197 4.4 71.5 1.0
CD2 B:HIS106 4.4 46.0 1.0
CG B:GLU103 4.4 40.4 1.0
NE2 B:HIS106 4.4 30.1 1.0
CB B:ASP72 4.4 50.7 1.0
CB B:GLU103 4.7 45.2 1.0
O B:GLU103 4.8 37.2 1.0
CA B:ASP72 4.8 46.3 1.0
CE2 B:PHE167 4.8 57.8 1.0
CA B:HIS106 4.9 34.9 1.0

Manganese binding site 5 out of 12 in 8j4y

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Manganese binding site 5 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn401

b:63.8
occ:1.00
 OE2 C:GLU103 2.0 64.3 1.0
OE2 C:GLU197 2.4 68.6 1.0
OE1 C:GLU163 2.5 46.1 1.0
ND1 C:HIS200 2.5 63.4 1.0
OE1 C:GLU197 2.6 74.5 1.0
CD C:GLU197 2.8 63.1 1.0
CD C:GLU103 2.8 65.0 1.0
CE1 C:HIS200 3.3 54.9 1.0
CD C:GLU163 3.4 60.8 1.0
CG C:HIS200 3.4 45.9 1.0
OE1 C:GLU103 3.4 56.1 1.0
OE2 C:GLU163 3.5 66.3 1.0
CG C:GLU103 3.7 71.6 1.0
CB C:HIS200 3.7 44.1 1.0
MN C:MN402 3.9 83.0 1.0
CG C:GLU197 4.2 50.2 1.0
CA C:GLU197 4.2 45.1 1.0
NE2 C:HIS200 4.3 46.1 1.0
CG2 C:ILE99 4.3 43.5 1.0
CD2 C:HIS200 4.3 53.5 1.0
CG C:GLN75 4.6 49.5 1.0
CE1 C:HIS106 4.6 52.0 1.0
CB C:GLU197 4.6 44.2 1.0
ND1 C:HIS106 4.6 54.6 1.0
CG C:GLU163 4.8 69.7 1.0
N C:GLU197 4.8 56.9 1.0
CE2 C:PHE167 4.8 47.0 1.0
O C:ASP196 4.9 47.5 1.0

Manganese binding site 6 out of 12 in 8j4y

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Manganese binding site 6 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn402

b:83.0
occ:1.00
 OD1 C:ASP72 2.1 58.5 1.0
OE2 C:GLU197 2.1 68.6 1.0
OE1 C:GLU103 2.4 56.1 1.0
ND1 C:HIS106 2.5 54.6 1.0
CD C:GLU197 2.9 63.1 1.0
CG C:ASP72 3.2 65.5 1.0
CG C:HIS106 3.3 50.7 1.0
CD C:GLU103 3.4 65.0 1.0
CE1 C:HIS106 3.5 52.0 1.0
CB C:HIS106 3.5 44.5 1.0
CZ C:PHE167 3.6 59.5 1.0
CG2 C:ILE193 3.6 53.5 1.0
OE1 C:GLU197 3.7 74.5 1.0
OE2 C:GLU103 3.7 64.3 1.0
OD2 C:ASP72 3.7 82.1 1.0
CG C:GLU197 3.8 50.2 1.0
O C:OH403 3.8 51.8 1.0
MN C:MN401 3.9 63.8 1.0
CE1 C:PHE167 4.0 53.2 1.0
HO C:OH403 4.1 62.1 1.0
CE2 C:PHE167 4.2 47.0 1.0
CB C:ASP72 4.3 45.4 1.0
CD2 C:HIS106 4.5 66.1 1.0
NE2 C:HIS106 4.5 61.4 1.0
CG C:GLU103 4.7 71.6 1.0
CA C:GLU103 4.7 45.0 1.0
CA C:ASP72 4.8 39.3 1.0
CD1 C:PHE167 4.9 52.3 1.0
CD2 C:PHE167 5.0 51.6 1.0
CB C:GLU103 5.0 53.5 1.0

Manganese binding site 7 out of 12 in 8j4y

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Manganese binding site 7 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:52.2
occ:1.00
 OE1 D:GLU163 2.3 71.8 1.0
ND1 D:HIS200 2.3 32.6 1.0
OE2 D:GLU197 2.3 73.3 1.0
OE2 D:GLU103 2.5 65.9 1.0
CD D:GLU163 2.9 61.0 1.0
OE2 D:GLU163 2.9 62.6 1.0
CD D:GLU103 3.1 59.3 1.0
CD D:GLU197 3.1 70.0 1.0
CG D:HIS200 3.2 33.3 1.0
CE1 D:HIS200 3.2 32.9 1.0
OE1 D:GLU103 3.3 63.8 1.0
CB D:HIS200 3.4 33.4 1.0
MN D:MN402 3.6 69.3 1.0
OE1 D:GLU197 3.8 70.4 1.0
CG D:GLU197 4.0 60.6 1.0
CA D:GLU197 4.0 32.5 1.0
CG D:GLU103 4.2 36.1 1.0
CG D:GLU163 4.2 51.3 1.0
CD2 D:HIS200 4.3 34.1 1.0
NE2 D:HIS200 4.3 44.9 1.0
CB D:GLU197 4.5 37.5 1.0
CB D:GLU163 4.6 43.2 1.0
N D:GLU197 4.7 35.8 1.0
CG2 D:ILE99 4.7 25.8 1.0
CG D:GLN75 4.8 48.3 1.0
O D:GLU197 4.9 35.4 1.0
O D:ASP196 4.9 34.0 1.0
CA D:HIS200 4.9 34.5 1.0
CE1 D:HIS106 4.9 31.3 1.0
C D:GLU197 5.0 39.8 1.0
C D:ASP196 5.0 37.3 1.0

Manganese binding site 8 out of 12 in 8j4y

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Manganese binding site 8 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn402

b:69.3
occ:1.00
 OE2 D:GLU197 2.2 73.3 1.0
OD1 D:ASP72 2.3 58.2 1.0
ND1 D:HIS106 2.5 33.3 1.0
OE2 D:GLU103 2.5 65.9 1.0
OE1 D:GLU103 3.0 63.8 1.0
CD D:GLU103 3.1 59.3 1.0
CD D:GLU197 3.1 70.0 1.0
CE1 D:HIS106 3.3 31.3 1.0
CG D:ASP72 3.4 59.0 1.0
CG D:HIS106 3.5 25.2 1.0
CG D:GLU197 3.6 60.6 1.0
MN D:MN401 3.6 52.2 1.0
CZ D:PHE167 3.7 54.2 1.0
CE2 D:PHE167 3.7 41.1 1.0
OD2 D:ASP72 3.8 63.9 1.0
CB D:HIS106 3.9 24.9 1.0
OE1 D:GLU197 4.1 70.4 1.0
CG2 D:ILE193 4.1 30.4 1.0
O D:OH404 4.4 25.3 1.0
CG D:GLU103 4.4 36.1 1.0
NE2 D:HIS106 4.5 38.5 1.0
CA D:GLU103 4.6 29.2 1.0
CE1 D:PHE167 4.6 61.6 1.0
CD2 D:PHE167 4.6 32.5 1.0
CD2 D:HIS106 4.6 36.3 1.0
CB D:ASP72 4.7 44.9 1.0
OE1 D:GLU163 4.7 71.8 1.0
CB D:GLU103 4.8 32.7 1.0
HO D:OH404 5.0 30.4 1.0
CA D:ASP72 5.0 31.9 1.0

Manganese binding site 9 out of 12 in 8j4y

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Manganese binding site 9 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn401

b:84.8
occ:1.00
 OE2 E:GLU103 2.3 70.4 1.0
ND1 E:HIS200 2.5 71.2 1.0
OE1 E:GLU197 2.6 94.2 1.0
OE2 E:GLU163 2.9 92.8 1.0
OE2 E:GLU197 2.9 99.0 1.0
CD E:GLU197 3.1 84.6 1.0
CD E:GLU103 3.1 76.7 1.0
CG E:GLU163 3.1 64.6 1.0
CG E:HIS200 3.3 71.1 1.0
CD E:GLU163 3.4 80.7 1.0
CE1 E:HIS200 3.4 72.8 1.0
CB E:HIS200 3.5 69.6 1.0
OE1 E:GLU103 3.7 76.4 1.0
CG E:GLU103 4.1 67.8 1.0
CG E:GLN75 4.1 62.6 1.0
MN E:MN402 4.1 96.4 1.0
CB E:GLU163 4.2 65.0 1.0
CG2 E:ILE99 4.4 68.2 1.0
CD2 E:HIS200 4.4 72.8 1.0
NE2 E:HIS200 4.5 73.8 1.0
CG E:GLU197 4.5 76.2 1.0
CA E:GLU197 4.6 73.7 1.0
CE2 E:PHE167 4.6 69.4 1.0
OE1 E:GLU163 4.6 91.9 1.0
CB E:GLU197 5.0 78.0 1.0

Manganese binding site 10 out of 12 in 8j4y

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Manganese binding site 10 out of 12 in the Structure of Mycobacterium Tuberculosis NRDF2:Nrdicomplex (Reduced) 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 (Reduced) Determined at 3 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn402

b:96.4
occ:1.00
 OD1 E:ASP72 2.4 70.4 1.0
OE2 E:GLU197 2.6 99.0 1.0
CD E:GLU197 2.7 84.6 1.0
CD2 E:HIS106 2.9 76.0 1.0
OE2 E:GLU103 3.0 70.4 1.0
OE1 E:GLU103 3.0 76.4 1.0
OE1 E:GLU197 3.1 94.2 1.0
CD E:GLU103 3.3 76.7 1.0
CG E:ASP72 3.4 83.7 1.0
CZ E:PHE167 3.5 79.1 1.0
CG E:HIS106 3.6 76.4 1.0
CG E:GLU197 3.6 76.2 1.0
CE2 E:PHE167 3.7 69.4 1.0
NE2 E:HIS106 3.8 78.0 1.0
CG2 E:ILE193 3.8 77.6 1.0
OD2 E:ASP72 3.9 92.7 1.0
CB E:HIS106 3.9 75.8 1.0
CE1 E:PHE167 4.1 69.5 1.0
MN E:MN401 4.1 84.8 1.0
CD2 E:PHE167 4.5 66.3 1.0
ND1 E:HIS106 4.6 79.7 1.0
CB E:ASP72 4.7 69.2 1.0
CE1 E:HIS106 4.7 85.5 1.0
CG E:GLU103 4.8 67.8 1.0
CD1 E:PHE167 4.8 67.8 1.0
CA E:GLU103 4.9 71.2 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

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