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Cobalt in PDB 6vsg: Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17)

Enzymatic activity of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17)

All present enzymatic activity of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17):
1.5.1.3;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17), PDB code: 6vsg was solved by J.A.Ribeiro, M.V.B.Dias, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.54 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.912, 70.701, 72.135, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 22.2

Other elements in 6vsg:

The structure of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17) also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17) (pdb code 6vsg). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17), PDB code: 6vsg:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6vsg

Go back to Cobalt Binding Sites List in 6vsg
Cobalt binding site 1 out of 2 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co201

b:26.9
occ:1.00
 O B:HOH323 1.9 20.4 1.0
NE2 B:HIS38 2.0 19.8 1.0
NE2 A:HIS157 2.1 16.9 1.0
O B:HOH368 2.1 26.6 1.0
O B:HOH321 2.2 22.9 1.0
O B:HOH325 2.2 33.4 1.0
CE1 B:HIS38 2.8 20.5 1.0
CD2 A:HIS157 3.0 17.8 1.0
CE1 A:HIS157 3.1 18.3 1.0
CD2 B:HIS38 3.1 19.3 1.0
O B:ILE34 3.9 18.5 1.0
ND1 B:HIS38 4.0 23.0 1.0
OG1 A:THR108 4.0 35.7 1.0
OE1 B:GLU90 4.0 32.8 1.0
O B:MET36 4.1 18.6 1.0
CG B:HIS38 4.2 20.4 1.0
ND1 A:HIS157 4.2 20.8 1.0
CG A:HIS157 4.2 28.9 1.0
OE2 B:GLU90 4.3 40.9 1.0
O A:ARG158 4.3 37.6 1.0
CD B:GLU90 4.4 35.6 1.0
O B:HOH354 4.5 43.8 1.0
O B:GLU33 4.5 21.8 1.0
C B:ILE34 4.7 20.2 1.0

Cobalt binding site 2 out of 2 in 6vsg

Go back to Cobalt Binding Sites List in 6vsg
Cobalt binding site 2 out of 2 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (Trifluoromethyl)Benzene-1,2-Diamine(Fragment 17) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:32.4
occ:1.00
 CE1 A:HIS38 2.0 21.3 1.0
O B:HOH324 2.1 28.0 1.0
O B:HOH351 2.1 25.4 1.0
O A:HOH307 2.1 23.1 1.0
O A:HOH317 2.3 18.2 1.0
O A:HOH319 2.6 42.1 1.0
NE2 A:HIS38 2.8 23.7 1.0
ND1 A:HIS38 3.2 21.6 1.0
OE1 A:GLU90 3.7 24.9 1.0
O A:ILE34 3.8 20.0 1.0
O A:HOH335 3.9 30.6 1.0
CD2 A:HIS38 4.0 16.4 1.0
O A:MET36 4.2 21.4 1.0
CG A:HIS38 4.2 17.0 1.0
CD A:GLU90 4.2 24.5 1.0
O B:ARG158 4.3 38.7 1.0
O B:SER159 4.3 37.5 1.0
OE2 A:GLU90 4.4 36.5 1.0
O B:HOH372 4.4 58.9 1.0
O B:HOH337 4.5 39.4 1.0
O A:GLU33 4.5 30.5 1.0
CB B:THR108 4.6 23.3 1.0
CA B:SER159 4.7 35.1 1.0
CG2 B:THR108 4.7 21.9 1.0
OG1 B:THR108 4.7 31.1 1.0
O A:HOH304 4.7 44.7 1.0
C A:ILE34 4.7 20.3 1.0
C B:SER159 4.9 36.0 1.0

Reference:

J.A.Ribeiro, A.Hammer, G.A.Libreros-Zuniga, S.M.Chavez-Pacheco, P.Tyrakis, G.S.De Oliveira, T.Kirkman, J.El Bakali, S.A.Rocco, M.L.Sforca, R.Parise-Filho, A.G.Coyne, T.L.Blundell, C.Abell, M.V.B.Dias. Using A Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase Frommycobacterium Tuberculosis. Acs Infect Dis. V. 6 2192 2020.
ISSN: ESSN 2373-8227
PubMed: 32603583
DOI: 10.1021/ACSINFECDIS.0C00263
Page generated: Tue Jul 30 19:05:07 2024

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