Magnesium in PDB 6cq2: Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium:
5.99.1.2;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium, PDB code: 6cq2 was solved by N.Cao, A.Thirunavukkaraus, K.Tan, Y.-C.Tse-Dinh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.28 / 3.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 67.625, 44.683, 128.866, 90.00, 90.61, 90.00
R / Rfree (%) 18.9 / 24.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium (pdb code 6cq2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium, PDB code: 6cq2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6cq2

Go back to Magnesium Binding Sites List in 6cq2
Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg801

b:57.2
occ:1.00
 OD1 A:ASP111 1.9 89.4 1.0
OE1 A:GLU24 2.0 91.0 1.0
OP1 B:DT7 2.1 87.6 1.0
O A:HOH903 2.1 64.4 1.0
O3' B:DC6 2.2 87.2 1.0
P B:DT7 2.7 81.3 1.0
CG A:ASP111 3.0 0.1 1.0
CD A:GLU24 3.1 82.1 1.0
C5' B:DT7 3.4 45.0 1.0
O5' B:DT7 3.5 62.2 1.0
C3' B:DC6 3.6 77.1 1.0
OE2 A:GLU24 3.8 86.9 1.0
OD2 A:ASP111 3.8 97.7 1.0
OP2 B:DT7 3.9 83.3 1.0
CB A:ASP111 4.0 0.1 1.0
C4' B:DC6 4.0 68.4 1.0
CB A:GLU24 4.1 37.2 1.0
O A:HOH905 4.1 63.0 1.0
CG A:GLU24 4.2 57.9 1.0
C2' B:DC6 4.3 72.4 1.0
OH A:TYR342 4.6 75.6 1.0
C5' B:DC6 4.6 70.7 1.0
C4' B:DT7 4.9 46.5 1.0

Magnesium binding site 2 out of 4 in 6cq2

Go back to Magnesium Binding Sites List in 6cq2
Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.2
occ:1.00
 OE2 A:GLU296 1.9 90.1 1.0
O A:HOH902 2.0 36.0 1.0
NE2 A:HIS492 2.2 83.3 1.0
OE1 A:GLU296 2.3 0.4 1.0
CD A:GLU296 2.4 93.9 1.0
CD2 A:HIS492 3.0 79.7 1.0
CE1 A:HIS492 3.2 88.8 1.0
CG A:GLU296 3.9 85.5 1.0
SD A:MET438 4.1 0.6 1.0
CG A:HIS492 4.2 85.3 1.0
ND1 A:HIS492 4.2 89.2 1.0
CB A:MET438 4.6 60.4 1.0
CB A:GLU296 4.7 77.6 1.0
CD1 A:LEU440 4.9 99.8 1.0

Magnesium binding site 3 out of 4 in 6cq2

Go back to Magnesium Binding Sites List in 6cq2
Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:63.3
occ:1.00
 OD1 A:ASP507 2.3 0.7 1.0
NE2 A:HIS509 3.0 67.0 1.0
CG A:ASP507 3.1 0.7 1.0
OD1 A:ASP220 3.3 82.0 1.0
CE1 A:HIS509 3.3 80.6 1.0
OD2 A:ASP507 3.3 0.1 1.0
OD2 A:ASP220 3.7 78.1 1.0
CG A:ASP220 3.9 79.5 1.0
CG A:ARG242 4.1 72.0 1.0
NE A:ARG242 4.2 88.2 1.0
CD2 A:HIS509 4.2 74.5 1.0
CB A:ASP507 4.5 98.8 1.0
CD A:ARG242 4.5 73.6 1.0
CB A:LEU222 4.5 71.5 1.0
ND1 A:HIS509 4.6 87.7 1.0
CD1 A:LEU222 4.8 59.6 1.0

Magnesium binding site 4 out of 4 in 6cq2

Go back to Magnesium Binding Sites List in 6cq2
Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Topoisomerase I in Complex with Oligonucleotide MTS2-12 and Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg804

b:73.3
occ:1.00
 OE2 A:GLU598 1.9 0.4 1.0
OE2 A:GLU589 2.0 0.0 1.0
OE1 A:GLU589 2.1 0.3 1.0
NE2 A:HIS613 2.1 81.5 1.0
CD A:GLU589 2.3 92.7 1.0
CD A:GLU598 2.8 92.8 1.0
OE1 A:GLU598 2.9 95.1 1.0
CE1 A:HIS613 3.0 81.7 1.0
CD2 A:HIS613 3.1 75.8 1.0
CG A:GLU589 3.7 79.7 1.0
OE1 A:GLU592 4.0 95.4 1.0
ND1 A:HIS613 4.0 78.8 1.0
CG A:HIS613 4.1 75.5 1.0
CG A:GLU598 4.2 88.7 1.0
CB A:GLU589 4.4 69.7 1.0
CD A:GLU592 4.5 89.4 1.0
CA A:GLU589 4.6 74.8 1.0
CD1 A:TRP603 4.8 87.9 1.0
NE1 A:TRP603 5.0 87.8 1.0
OE2 A:GLU592 5.0 95.2 1.0

Reference:

N.Cao, K.Tan, T.Annamalai, A.Joachimiak, Y.C.Tse-Dinh. Investigating Mycobacterial Topoisomerase I Mechanism From the Analysis of Metal and Dna Substrate Interactions at the Active Site. Nucleic Acids Res. V. 46 7296 2018.
ISSN: ESSN 1362-4962
PubMed: 29905859
DOI: 10.1093/NAR/GKY492
Page generated: Mon Dec 14 22:31:39 2020

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