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Calcium in PDB 7rgj: DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223)

Enzymatic activity of DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223)

All present enzymatic activity of DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223):
1.5.1.3;

Protein crystallography data

The structure of DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223), PDB code: 7rgj 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) 30.29 / 1.44
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 72.279, 72.279, 120.148, 90, 90, 120
R / Rfree (%) 19.8 / 22.7

Calcium Binding Sites:

The binding sites of Calcium atom in the DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223) (pdb code 7rgj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223), PDB code: 7rgj:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7rgj

Go back to Calcium Binding Sites List in 7rgj
Calcium binding site 1 out of 2 in the DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:41.4
occ:1.00
 OG A:SER105 3.3 30.2 1.0
N6A A:NAP201 3.4 25.9 1.0
CB A:SER105 4.0 24.8 1.0
CD1 A:ILE80 4.0 27.8 1.0
C6A A:NAP201 4.7 26.2 1.0
CA A:SER105 5.0 24.7 1.0
N7A A:NAP201 5.0 28.3 1.0

Calcium binding site 2 out of 2 in 7rgj

Go back to Calcium Binding Sites List in 7rgj
Calcium binding site 2 out of 2 in the DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DFRA1 Complexed with Nadph and 5-(3-(7-(4-(Aminomethyl)Phenyl) Benzo[D][1,3]Dioxol-5-Yl)But-1-Yn-1-Yl)-6-Ethylpyrimidine-2,4-Diamine (UCP1223) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:37.6
occ:1.00
 N B:ILE80 3.3 28.6 1.0
N6A B:NAP201 3.3 30.0 1.0
N B:LYS81 3.6 32.0 1.0
CB B:SER79 3.7 30.2 1.0
CB B:ILE80 3.7 27.3 1.0
CA B:ILE80 3.9 29.3 1.0
C B:SER79 4.1 28.7 1.0
CG B:LYS81 4.1 42.7 1.0
CA B:SER79 4.2 28.2 1.0
O B:HOH370 4.2 41.6 1.0
C B:ILE80 4.2 28.8 1.0
C6A B:NAP201 4.3 26.7 1.0
N1A B:NAP201 4.3 27.9 1.0
CB B:LYS81 4.4 35.7 1.0
OG B:SER79 4.4 31.6 1.0
CG1 B:ILE80 4.4 29.4 1.0
CA B:LYS81 4.6 29.3 1.0
O B:HOH343 4.7 42.3 1.0
CD1 B:ILE80 4.8 29.8 1.0
CG2 B:ILE80 4.8 30.2 1.0
CD B:LYS81 4.9 52.0 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 Apr 4 18:38:05 2023

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