Chlorine in PDB 7rgo: DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228)

Enzymatic activity of DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228)

All present enzymatic activity of DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228):
1.5.1.3;

Protein crystallography data

The structure of DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228), PDB code: 7rgo was solved by M.N.Lombardo, D.L.Wright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.95 / 1.92
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 98.855, 98.855, 43.14, 90, 90, 90
R / Rfree (%) 19.2 / 22.7

Chlorine Binding Sites:

The binding sites of Chlorine atom in the DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228) (pdb code 7rgo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228), PDB code: 7rgo:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 7rgo

Go back to Chlorine Binding Sites List in 7rgo
Chlorine binding site 1 out of 2 in the DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:37.1
occ:1.00
 CL29 A:4SI203 0.0 37.1 1.0
C28 A:4SI203 1.7 34.7 1.0
C27 A:4SI203 2.7 33.8 1.0
C14 A:4SI203 2.7 34.6 1.0
C13 A:4SI203 3.0 32.9 1.0
C30 A:4SI203 3.8 32.9 1.0
C6N A:NAP201 3.9 35.4 1.0
CB A:SER50 4.0 39.1 1.0
C26 A:4SI203 4.0 38.3 1.0
C15 A:4SI203 4.0 34.0 1.0
CD1 A:ILE21 4.0 31.5 1.0
O2D A:NAP201 4.0 42.1 1.0
CG2 A:THR47 4.1 30.2 1.0
C2D A:NAP201 4.1 36.0 1.0
C5N A:NAP201 4.1 34.4 1.0
C12 A:4SI203 4.3 31.6 1.0
O A:THR47 4.3 34.8 1.0
N1N A:NAP201 4.4 34.5 1.0
C16 A:4SI203 4.5 41.0 1.0
CB A:MET51 4.5 39.3 1.0
CG1 A:ILE21 4.5 35.1 1.0
N A:MET51 4.5 39.3 1.0
CA A:THR47 4.7 32.1 1.0
CB A:THR47 4.8 33.1 1.0
C A:SER50 4.8 40.8 1.0
C4N A:NAP201 4.8 31.8 1.0
C1D A:NAP201 4.9 33.5 1.0
OG A:SER50 4.9 51.5 1.0
OG1 A:THR47 4.9 33.8 1.0
CA A:MET51 4.9 39.4 1.0
C A:THR47 5.0 33.5 1.0

Chlorine binding site 2 out of 2 in 7rgo

Go back to Chlorine Binding Sites List in 7rgo
Chlorine binding site 2 out of 2 in the DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of DFRA5 Complexed with Nadph and 4'-Chloro-3'-(4-(2,4-Diamino-6- Ethylpyrimidin-5-Yl)But-3-Yn-2-Yl)-[1,1'-Biphenyl]-4-Carboxamide (UCP1228) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:54.7
occ:1.00
 CL29 B:4SI204 0.0 54.7 1.0
C28 B:4SI204 1.7 53.0 1.0
C27 B:4SI204 2.7 53.7 1.0
C14 B:4SI204 2.8 53.3 1.0
C13 B:4SI204 3.1 48.5 1.0
CB B:SER50 3.6 42.8 1.0
O2D B:NAP201 3.9 49.3 1.0
C30 B:4SI204 3.9 41.9 1.0
C6N B:NAP201 4.0 36.6 1.0
C26 B:4SI204 4.0 55.0 1.0
CD1 B:ILE21 4.0 40.7 1.0
C2D B:NAP201 4.1 46.2 1.0
C15 B:4SI204 4.1 53.4 1.0
O B:THR47 4.2 38.6 1.0
C5N B:NAP201 4.2 38.9 1.0
CG2 B:THR47 4.3 36.6 1.0
CG1 B:ILE21 4.3 40.6 1.0
N1N B:NAP201 4.4 38.4 1.0
C12 B:4SI204 4.4 40.5 1.0
C B:SER50 4.5 43.5 1.0
OG B:SER50 4.5 56.1 1.0
C16 B:4SI204 4.5 62.4 1.0
N B:MET51 4.6 48.6 1.0
O B:SER50 4.7 50.8 1.0
CA B:SER50 4.7 43.0 1.0
CA B:THR47 4.7 36.0 1.0
CB B:MET51 4.8 52.5 1.0
C1D B:NAP201 4.8 42.2 1.0
C4N B:NAP201 4.9 35.8 1.0
CB B:THR47 4.9 36.1 1.0
C B:THR47 4.9 39.3 1.0
CA B:MET51 5.0 50.9 1.0
OG1 B:THR47 5.0 36.2 1.0
C2N B:NAP201 5.0 35.0 1.0
O B:PRO19 5.0 53.7 1.0

Reference:

J.Krucinska, M.N.Lombardo, H.Erlandsen, A.Estrada, D.Si, K.Viswanathan, D.L.Wright. Structure-Guided Functional Studies of Plasmid-Encoded Dihydrofolate Reductases Reveal A Common Mechanism of Trimethoprim Resistance in Gram-Negative Pathogens. Commun Biol V. 5 459 2022.
ISSN: ESSN 2399-3642
PubMed: 35562546
DOI: 10.1038/S42003-022-03384-Y
Page generated: Tue Jul 30 03:36:24 2024

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