Atomistry » Calcium » PDB 7rcd-7s5k » 7rgj
Atomistry »
  Calcium »
    PDB 7rcd-7s5k »
      7rgj »

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: Thu Jul 10 00:47:45 2025

Last articles

Mg in 6I1K
Mg in 6HZ9
Mg in 6HZ8
Mg in 6I0V
Mg in 6I0U
Mg in 6I0S
Mg in 6HZM
Mg in 6I03
Mg in 6HZ7
Mg in 6HZ6
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy