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Magnesium in PDB 6cw7: E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate

Enzymatic activity of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate

All present enzymatic activity of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate:
1.5.1.3;

Protein crystallography data

The structure of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate, PDB code: 6cw7 was solved by H.Cao, J.Rodrigues, J.Benach, A.Frommelt, L.Morisco, J.Koss, E.Shakhnovich, J.Skolnick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.06 / 1.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.861, 51.529, 77.841, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 20.6

Other elements in 6cw7:

The structure of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate (pdb code 6cw7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate, PDB code: 6cw7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6cw7

Go back to Magnesium Binding Sites List in 6cw7
Magnesium binding site 1 out of 4 in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:12.6
occ:1.00
 O A:HOH388 2.1 12.9 1.0
OE1 A:GLU101 2.1 9.9 1.0
O A:HOH331 2.2 12.1 1.0
CD A:GLU101 3.1 8.3 1.0
OE2 A:GLU101 3.4 9.2 1.0
HB2 A:ASP127 3.6 19.1 1.0
H A:ASP127 3.8 16.1 1.0
O A:HOH377 3.9 13.8 1.0
HB3 A:PRO126 4.1 12.7 1.0
O A:ASP127 4.4 14.2 1.0
N A:ASP127 4.5 13.4 1.0
CG A:GLU101 4.5 9.5 1.0
CB A:ASP127 4.5 15.9 1.0
HG3 A:GLU101 4.5 11.4 1.0
HA A:PRO126 4.8 11.5 1.0
HG2 A:GLU101 4.8 11.4 1.0
CB A:PRO126 4.9 10.5 1.0
O A:HOH455 4.9 34.3 1.0
OD1 A:ASP127 5.0 37.6 1.0
CA A:ASP127 5.0 13.7 1.0
CG A:ASP127 5.0 24.5 1.0

Magnesium binding site 2 out of 4 in 6cw7

Go back to Magnesium Binding Sites List in 6cw7
Magnesium binding site 2 out of 4 in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:10.9
occ:1.00
 O A:HOH367 2.3 9.6 1.0
OE2 A:GLU101 2.3 9.2 1.0
O A:HOH457 2.5 19.0 1.0
HB2 A:GLU101 3.0 11.1 1.0
CD A:GLU101 3.3 8.3 1.0
HA A:PRO126 3.3 11.5 1.0
HG2 A:GLU101 3.6 11.4 1.0
CG A:GLU101 3.7 9.5 1.0
CB A:GLU101 3.8 9.2 1.0
O A:HOH331 3.9 12.1 1.0
HG3 A:PRO126 4.0 18.1 1.0
CA A:PRO126 4.2 9.6 1.0
OE1 A:GLU101 4.2 9.9 1.0
HB3 A:PRO126 4.2 12.7 1.0
HB3 A:GLU101 4.3 11.1 1.0
O A:HIS124 4.4 12.3 1.0
O A:GLY97 4.4 9.3 1.0
N A:PRO126 4.6 9.8 1.0
CB A:PRO126 4.6 10.5 1.0
HG3 A:GLU101 4.7 11.4 1.0
CG A:PRO126 4.7 15.1 1.0
HA A:GLU101 4.7 10.2 1.0
O A:HOH438 4.8 15.0 1.0
HA A:ARG98 4.8 11.4 1.0
H A:ASP127 4.8 16.1 1.0
CA A:GLU101 4.9 8.5 1.0
O A:PHE125 4.9 13.8 1.0
HD3 A:PRO126 4.9 10.9 1.0
C A:PHE125 4.9 11.1 1.0
HB2 A:HIS124 5.0 16.2 1.0

Magnesium binding site 3 out of 4 in 6cw7

Go back to Magnesium Binding Sites List in 6cw7
Magnesium binding site 3 out of 4 in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:32.6
occ:1.00
 O A:HOH436 2.2 32.1 1.0
O A:HOH429 2.2 30.8 1.0
O A:HOH431 2.2 30.0 1.0
NE2 A:HIS160 2.3 22.7 1.0
O A:HOH489 2.4 35.9 1.0
O A:HOH319 2.6 37.9 1.0
CD2 A:HIS160 3.1 16.5 1.0
HD2 A:HIS160 3.2 19.9 1.0
CE1 A:HIS160 3.3 20.7 1.0
HE1 A:HIS160 3.6 24.8 1.0
O A:ASP131 4.3 19.5 1.0
CG A:HIS160 4.3 16.4 1.0
ND1 A:HIS160 4.4 18.0 1.0
HB3 A:ARG159 4.7 15.8 1.0
HB2 A:ARG159 4.7 15.8 1.0
O A:HOH491 4.9 22.3 1.0

Magnesium binding site 4 out of 4 in 6cw7

Go back to Magnesium Binding Sites List in 6cw7
Magnesium binding site 4 out of 4 in the E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of E. Coli Dhfr Product Complex with (6S)-5,6,7,8-Tetrahydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:28.5
occ:1.00
 O A:HOH405 1.9 48.5 1.0
OD2 A:ASP70 2.2 24.2 1.0
O A:HOH441 2.4 43.6 1.0
O A:HOH316 3.0 36.2 1.0
CG A:ASP70 3.1 17.2 1.0
O A:HOH305 3.3 36.7 1.0
OD1 A:ASP70 3.5 26.6 1.0
O A:HOH463 4.1 30.9 1.0
O A:THR68 4.1 18.5 0.5
HA A:ASP70 4.2 13.7 1.0
CB A:ASP70 4.4 13.6 1.0
HB3 A:ASP70 4.6 16.3 1.0
CA A:ASP70 4.8 11.4 1.0

Reference:

H.Cao, M.Gao, H.Zhou, J.Skolnick. The Crystal Structure of A Tetrahydrofolate-Bound Dihydrofolate Reductase Reveals the Origin of Slow Product Release. Commun Biol V. 1 226 2018.
ISSN: ESSN 2399-3642
PubMed: 30564747
DOI: 10.1038/S42003-018-0236-Y
Page generated: Mon Sep 30 22:47:03 2024

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