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Cobalt in PDB 6vsf: Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16)

Enzymatic activity of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16)

All present enzymatic activity of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16):
1.5.1.3;

Protein crystallography data

The structure of Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16), PDB code: 6vsf 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) 46.77 / 2.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.556, 70.904, 71.940, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 21.1

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16) (pdb code 6vsf). 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- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16), PDB code: 6vsf:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6vsf

Go back to Cobalt Binding Sites List in 6vsf
Cobalt binding site 1 out of 2 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16)


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- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co202

b:17.0
occ:1.00
 NE2 B:HIS157 2.1 13.5 1.0
O A:HOH344 2.1 21.8 1.0
O B:HOH381 2.2 17.1 1.0
NE2 A:HIS38 2.2 13.3 1.0
O A:HOH343 2.2 12.8 1.0
O A:HOH322 2.3 9.9 1.0
CD2 B:HIS157 3.0 16.1 1.0
CE1 B:HIS157 3.1 17.0 1.0
CD2 A:HIS38 3.1 13.2 1.0
CE1 A:HIS38 3.2 16.9 1.0
OE1 A:GLU90 3.8 12.2 1.0
O A:ILE34 3.8 13.1 1.0
O A:MET36 4.0 12.0 1.0
OE2 A:GLU90 4.1 19.7 1.0
OG1 B:THR108 4.1 17.3 1.0
CG B:HIS157 4.2 14.7 1.0
ND1 B:HIS157 4.2 13.1 1.0
ND1 A:HIS38 4.3 13.9 1.0
CG A:HIS38 4.3 12.7 1.0
CD A:GLU90 4.3 13.8 1.0
O B:ARG158 4.3 22.1 1.0
O A:GLU33 4.4 11.0 1.0
C A:ILE34 4.6 9.6 1.0
O A:HOH380 4.7 31.9 1.0

Cobalt binding site 2 out of 2 in 6vsf

Go back to Cobalt Binding Sites List in 6vsf
Cobalt binding site 2 out of 2 in the Mycobacterium Tuberculosis Dihydrofolate Reductase in Complex with 4- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16)


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- (3,4-Dihydro-2H-Benzo[B][1,4]Dioxepin-7-Yl)-4-Oxobutanoic Acid(Fragment 16) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co203

b:25.4
occ:1.00
 O A:HOH384 1.9 27.4 1.0
NE2 B:HIS38 2.1 14.2 1.0
O B:HOH319 2.1 22.7 1.0
O B:HOH338 2.2 16.7 1.0
O B:HOH324 2.3 18.9 1.0
CE1 B:HIS38 3.0 9.0 1.0
CD2 B:HIS38 3.1 8.4 1.0
O A:HOH332 3.2 29.3 1.0
OE1 B:GLU90 3.8 22.7 1.0
O B:ILE34 3.8 10.0 1.0
ND1 B:HIS38 4.1 11.4 1.0
O B:MET36 4.2 12.9 1.0
OE2 B:GLU90 4.2 23.5 1.0
CG B:HIS38 4.2 13.1 1.0
O A:ARG158 4.3 24.0 1.0
CD B:GLU90 4.3 25.1 1.0
O B:GLU33 4.5 10.1 1.0
CB A:THR108 4.6 16.7 1.0
OG1 A:THR108 4.6 16.5 1.0
O B:HOH396 4.7 58.0 1.0
C B:ILE34 4.7 9.2 1.0
CA A:SER159 4.7 19.1 1.0
CG2 A:THR108 4.7 17.0 1.0
O A:SER159 4.9 28.4 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: Sun Dec 13 10:53:25 2020

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