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Magnesium in PDB 6cxk: E. Coli Dhfr Substrate Complex with Dihydrofolate

Enzymatic activity of E. Coli Dhfr Substrate Complex with Dihydrofolate

All present enzymatic activity of E. Coli Dhfr Substrate Complex with Dihydrofolate:
1.5.1.3;

Protein crystallography data

The structure of E. Coli Dhfr Substrate Complex with Dihydrofolate, PDB code: 6cxk 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) 30.95 / 1.11
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 33.698, 51.525, 77.421, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 19.6

Other elements in 6cxk:

The structure of E. Coli Dhfr Substrate Complex with Dihydrofolate also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 6cxk

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Magnesium binding site 1 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


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 Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:14.7
occ:1.00
 O A:HOH384 2.1 14.3 1.0
OE1 A:GLU101 2.1 10.4 1.0
O A:HOH340 2.2 14.7 1.0
CD A:GLU101 3.1 9.3 1.0
OE2 A:GLU101 3.4 10.5 1.0
HB2 A:ASP127 3.5 24.5 1.0
O A:HOH391 3.9 15.6 1.0
H A:ASP127 3.9 18.2 1.0
HB3 A:PRO126 4.2 14.8 1.0
HB3 A:HIS165 4.3 47.0 1.0
HD2 A:HIS165 4.4 49.1 1.0
O A:ASP127 4.4 16.6 1.0
CB A:ASP127 4.4 20.4 1.0
CD2 A:HIS165 4.4 41.0 1.0
O A:HIS164 4.5 23.9 1.0
CG A:GLU101 4.5 8.9 1.0
N A:ASP127 4.5 15.2 1.0
HG3 A:GLU101 4.6 10.7 1.0
CG A:HIS165 4.7 34.7 1.0
HG2 A:GLU101 4.9 10.7 1.0
OD1 A:ASP127 4.9 42.2 1.0
NE2 A:HIS165 4.9 48.8 1.0
HA A:PRO126 4.9 14.6 1.0
CA A:ASP127 4.9 17.0 1.0
CG A:ASP127 4.9 31.1 1.0
CB A:PRO126 5.0 12.4 1.0
HB3 A:ASP127 5.0 24.5 1.0
HB3 A:HIS164 5.0 44.4 1.0

Magnesium binding site 2 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 2 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


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 Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:12.2
occ:1.00
 O A:HOH386 2.3 11.1 1.0
OE2 A:GLU101 2.4 10.5 1.0
O A:HOH448 2.6 19.7 1.0
HB2 A:GLU101 3.0 11.8 1.0
CD A:GLU101 3.3 9.3 1.0
HA A:PRO126 3.3 14.6 1.0
HG2 A:GLU101 3.6 10.7 1.0
CG A:GLU101 3.8 8.9 1.0
CB A:GLU101 3.8 9.8 1.0
O A:HOH340 3.9 14.7 1.0
HB3 A:PRO126 4.2 14.8 1.0
CA A:PRO126 4.2 12.1 1.0
OE1 A:GLU101 4.3 10.4 1.0
HB3 A:GLU101 4.3 11.8 1.0
O A:GLY97 4.5 10.1 1.0
HG3 A:PRO126 4.5 20.3 1.0
O A:HIS124 4.6 12.3 1.0
CB A:PRO126 4.7 12.4 1.0
N A:PRO126 4.7 11.3 1.0
H A:ASP127 4.7 18.2 1.0
HG3 A:GLU101 4.7 10.7 1.0
HB2 A:HIS124 4.8 13.7 1.0
O A:HOH436 4.8 15.2 1.0
HA A:GLU101 4.8 11.1 1.0
HH22 A:ARG12 4.9 45.2 1.0
HA A:ARG98 4.9 12.0 1.0
O A:PHE125 4.9 13.1 1.0
HD3 A:PRO126 4.9 11.8 1.0
CA A:GLU101 4.9 9.3 1.0
C A:PHE125 5.0 11.7 1.0
CG A:PRO126 5.0 16.9 1.0

Magnesium binding site 3 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 3 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


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 Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:34.6
occ:1.00
 O A:HOH467 2.0 37.7 1.0
O A:HOH326 2.1 26.2 1.0
O A:HOH342 2.3 23.9 1.0
NE2 A:HIS124 2.4 21.2 1.0
O A:HOH325 3.2 42.0 1.0
CD2 A:HIS124 3.3 17.3 1.0
CE1 A:HIS124 3.4 18.6 1.0
HD2 A:HIS124 3.4 20.7 1.0
HE1 A:HIS124 3.5 22.4 1.0
HA A:ASP122 4.0 17.2 1.0
OD1 A:ASP122 4.2 23.1 1.0
O A:HOH329 4.3 36.6 1.0
O A:ASP122 4.3 15.7 1.0
HB3 A:ASP122 4.4 21.2 1.0
CG A:HIS124 4.4 12.7 1.0
ND1 A:HIS124 4.4 15.5 1.0
CA A:ASP122 4.7 14.3 1.0
C A:ASP122 4.8 13.6 1.0
CB A:ASP122 4.9 17.7 1.0
OD2 A:ASP11 4.9 21.4 0.6
CG A:ASP122 5.0 21.6 1.0

Magnesium binding site 4 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 4 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


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 Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg204

b:23.7
occ:1.00
 O A:HOH429 2.0 24.3 1.0
O A:HOH328 2.1 27.1 1.0
O A:HOH378 2.1 28.4 1.0
NE2 A:HIS160 2.3 20.7 1.0
CD2 A:HIS160 3.1 15.7 1.0
HD2 A:HIS160 3.1 18.8 1.0
CE1 A:HIS160 3.4 20.2 1.0
HE1 A:HIS160 3.6 24.2 1.0
O A:ASP131 4.2 19.7 1.0
O A:HOH311 4.3 34.1 1.0
CG A:HIS160 4.3 16.8 1.0
ND1 A:HIS160 4.4 18.6 1.0
HB3 A:ARG159 4.4 14.6 1.0
HB2 A:ARG159 4.5 14.6 1.0
OD1 A:ASP131 4.7 42.5 1.0
O A:HOH483 4.8 24.7 1.0
CB A:ARG159 4.9 12.2 1.0
OD2 A:ASP131 4.9 36.8 1.0

Magnesium binding site 5 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 5 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of E. Coli Dhfr Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg205

b:30.1
occ:1.00
 OD2 A:ASP142 2.0 35.7 1.0
CG A:ASP142 3.2 26.8 1.0
O A:HOH339 3.6 36.0 1.0
OD1 A:ASP142 3.9 26.6 1.0
CB A:ASP142 4.3 15.4 1.0
HB3 A:ASP142 4.4 18.5 1.0
HB2 A:ASP142 4.5 18.5 1.0

Magnesium binding site 6 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 6 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of E. Coli Dhfr Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg206

b:32.8
occ:1.00
 OD2 A:ASP70 2.0 23.5 1.0
O A:HOH462 2.3 39.4 1.0
O A:HOH324 2.4 35.6 1.0
CG A:ASP70 3.0 19.0 1.0
O A:HOH305 3.0 33.7 1.0
OD1 A:ASP70 3.4 25.9 1.0
O A:THR68 3.9 27.0 1.0
HA A:ASP70 3.9 17.7 1.0
CB A:ASP70 4.2 16.6 1.0
HB3 A:ASP70 4.5 20.0 1.0
CA A:ASP70 4.5 14.7 1.0
O A:HOH338 4.6 28.4 1.0
HA A:THR68 4.9 26.7 1.0
C A:THR68 5.0 18.1 1.0
HB2 A:ASP70 5.0 20.0 1.0

Magnesium binding site 7 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 7 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of E. Coli Dhfr Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg207

b:43.5
occ:1.00
 O A:HOH426 2.2 52.3 1.0
OD1 A:ASP87 2.3 44.9 1.0
O A:HOH419 2.4 35.4 1.0
O A:HOH331 2.5 34.2 1.0
CG A:ASP87 3.5 54.1 1.0
OD2 A:ASP87 4.0 67.6 1.0
HA A:ASP87 4.1 27.8 1.0
O A:VAL88 4.2 14.6 1.0
O A:HOH352 4.3 27.1 1.0
HA A:PRO89 4.4 15.1 1.0
C A:VAL88 4.6 13.7 1.0
CB A:ASP87 4.6 30.8 1.0
CA A:ASP87 4.7 23.2 1.0
C A:ASP87 4.7 31.5 1.0
N A:VAL88 4.8 16.3 1.0
H A:VAL88 4.9 19.5 1.0

Magnesium binding site 8 out of 8 in 6cxk

Go back to Magnesium Binding Sites List in 6cxk
Magnesium binding site 8 out of 8 in the E. Coli Dhfr Substrate Complex with Dihydrofolate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of E. Coli Dhfr Substrate Complex with Dihydrofolate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg208

b:19.6
occ:0.48
 O A:HOH346 2.0 35.7 1.0
O A:HOH316 2.1 38.6 1.0
O A:HOH358 2.2 31.2 1.0
OE2 A:GLU120 3.6 22.4 0.5
OD2 A:ASP122 4.1 24.9 1.0
HA2 A:GLY121 4.1 19.3 1.0
OE1 A:GLU120 4.2 29.3 0.5
CD A:GLU120 4.2 26.0 0.5
O A:GLU120 4.3 20.8 0.5
HG2 A:GLU120 4.4 25.2 0.5
O A:GLU120 4.4 21.4 0.5
O A:HOH312 4.5 37.1 1.0
O A:HOH446 4.6 39.7 1.0
O A:HOH302 4.6 24.3 1.0
HG3 A:GLU120 4.7 25.2 0.5
H A:ASP122 5.0 16.2 1.0
HB2 A:ASP122 5.0 21.2 1.0
HB2 A:GLU120 5.0 20.3 0.5
CG A:GLU120 5.0 21.0 0.5

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 22:48:16 2024

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