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Sodium in PDB 8e4f: Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate

Enzymatic activity of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate

All present enzymatic activity of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate:
1.5.1.3;

Protein crystallography data

The structure of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate, PDB code: 8e4f was solved by K.Lange, K.M.Frey, N.M.Goodey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.61 / 2.47
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 133.877, 133.877, 75.876, 90, 90, 120
R / Rfree (%) 21.1 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate (pdb code 8e4f). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate, PDB code: 8e4f:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8e4f

Go back to Sodium Binding Sites List in 8e4f
Sodium binding site 1 out of 3 in the Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:39.5
occ:0.50
 O A:HOH423 3.2 28.2 1.0
N A:GLU96 3.5 31.4 1.0
CB A:PHE95 3.6 22.8 1.0
CB A:GLU96 3.9 35.3 1.0
N A:PHE95 4.2 29.8 1.0
CD2 A:LEU122 4.2 23.8 1.0
CA A:PHE95 4.2 29.4 1.0
CA A:GLU96 4.2 29.0 1.0
C A:PHE95 4.2 31.3 1.0
CD2 A:PHE95 4.5 27.6 1.0
CG A:PHE95 4.6 29.1 1.0

Sodium binding site 2 out of 3 in 8e4f

Go back to Sodium Binding Sites List in 8e4f
Sodium binding site 2 out of 3 in the Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:48.4
occ:1.00
 O A:GLU84 2.4 44.4 1.0
O A:VAL89 2.5 45.0 1.0
O A:ASN86 3.0 46.5 1.0
C A:GLU84 3.7 47.8 1.0
C A:VAL89 3.7 32.1 1.0
O A:HOH414 3.8 38.1 1.0
C A:ASN86 4.0 37.8 1.0
O A:SER85 4.2 46.3 1.0
CA A:VAL90 4.2 31.0 1.0
C A:SER85 4.2 45.2 1.0
N A:VAL90 4.4 30.0 1.0
CA A:GLU87 4.5 46.8 1.0
CA A:GLU84 4.5 50.1 1.0
CA A:SER85 4.6 50.5 1.0
N A:SER85 4.6 48.2 1.0
N A:ASN86 4.6 45.4 1.0
CB A:GLU84 4.7 36.6 1.0
N A:GLU84 4.7 48.0 1.0
N A:GLU87 4.7 39.0 1.0
CB A:VAL90 4.8 31.6 1.0
CA A:VAL89 4.8 36.0 1.0
N A:VAL89 4.8 35.1 1.0
CA A:ASN86 5.0 40.6 1.0
C A:GLU87 5.0 42.9 1.0

Sodium binding site 3 out of 3 in 8e4f

Go back to Sodium Binding Sites List in 8e4f
Sodium binding site 3 out of 3 in the Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dihydrofolate Reductase (Dhfr) From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:81.2
occ:1.00
 O A:HOH461 2.5 46.2 1.0
NE A:ARG149 2.8 25.1 1.0
CG A:ARG149 2.9 24.4 1.0
CD A:ARG149 3.3 29.6 1.0
CZ A:ARG149 3.7 25.5 1.0
NH2 A:ARG117 3.9 22.7 1.0
NH2 A:ARG149 4.0 22.0 1.0
CB A:ARG149 4.2 23.0 1.0
NH1 A:ARG149 4.7 25.2 1.0

Reference:

K.Lange, K.M.Frey, T.Eck, C.A.Janson, U.Gubler, N.M.Goodey. Crystal Structure of Dihydrofolate Reductase From the Filarial Nematode W. Bancrofti in Complex with Nadph and Folate. Plos Negl Trop Dis V. 17 11303 2023.
ISSN: ESSN 1935-2735
PubMed: 37104530
DOI: 10.1371/JOURNAL.PNTD.0011303
Page generated: Wed Oct 9 11:38:01 2024

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