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Magnesium in PDB 5rw0: Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446:
1.2.4.2;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446, PDB code: 5rw0 was solved by G.A.Bezerra, W.R.Foster, H.J.Bailey, L.Shrestha, T.Krojer, J.Brandao-Neto, A.Douangamath, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, W.W.Yue, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 85.07 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.130, 147.127, 87.273, 90.00, 102.91, 90.00
R / Rfree (%) 16.1 / 18.7

Other elements in 5rw0:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446 also contains other interesting chemical elements:

Fluorine (F) 5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446 (pdb code 5rw0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446, PDB code: 5rw0:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5rw0

Go back to Magnesium Binding Sites List in 5rw0
Magnesium binding site 1 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1005

b:13.2
occ:1.00
O2A A:TPP1004 2.0 11.3 1.0
O A:LEU368 2.0 15.8 1.0
OD1 A:ASP333 2.1 13.2 1.0
O3B A:TPP1004 2.1 11.7 1.0
OD1 A:ASN366 2.1 13.5 1.0
O A:HOH1240 2.3 11.2 1.0
CG A:ASN366 3.1 14.5 1.0
CG A:ASP333 3.2 13.3 1.0
PA A:TPP1004 3.2 12.0 1.0
PB A:TPP1004 3.2 13.4 1.0
C A:LEU368 3.2 15.8 1.0
O3A A:TPP1004 3.4 12.5 1.0
ND2 A:ASN366 3.5 13.3 1.0
OD2 A:ASP333 3.7 13.8 1.0
O2B A:TPP1004 3.8 14.4 1.0
O7 A:TPP1004 3.9 11.7 1.0
N A:ASP333 4.0 11.9 1.0
N A:LEU368 4.1 17.5 1.0
N A:GLY369 4.1 14.8 1.0
CA A:GLY369 4.1 13.6 1.0
O A:HOH1280 4.2 10.6 1.0
CA A:LEU368 4.3 17.2 1.0
N A:ASN366 4.3 14.5 1.0
CB A:ASP333 4.4 12.0 1.0
O A:VAL364 4.4 13.2 1.0
O1A A:TPP1004 4.4 11.7 1.0
CB A:ASN366 4.5 14.7 1.0
N A:ALA334 4.5 11.8 1.0
O1B A:TPP1004 4.5 12.8 1.0
CA A:ASP333 4.7 11.8 1.0
CA A:ASN366 4.7 15.1 1.0
N A:GLN367 4.7 16.7 1.0
C A:ASN366 4.8 16.0 1.0
CA A:GLY332 4.8 11.6 1.0
C A:GLY332 4.8 12.7 1.0
CB A:LEU368 4.9 18.4 1.0

Magnesium binding site 2 out of 3 in 5rw0

Go back to Magnesium Binding Sites List in 5rw0
Magnesium binding site 2 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:15.9
occ:1.00
O2B B:TPP1003 2.0 15.1 1.0
OD1 B:ASP333 2.1 13.1 1.0
O2A B:TPP1003 2.1 14.7 1.0
O B:LEU368 2.1 17.6 1.0
OD1 B:ASN366 2.1 18.7 1.0
O B:HOH1162 2.2 14.9 1.0
CG B:ASN366 3.1 19.1 1.0
PB B:TPP1003 3.1 15.9 1.0
PA B:TPP1003 3.1 14.5 1.0
CG B:ASP333 3.2 14.5 1.0
O3A B:TPP1003 3.2 15.8 1.0
C B:LEU368 3.3 17.2 1.0
ND2 B:ASN366 3.5 18.4 1.0
O3B B:TPP1003 3.7 16.5 1.0
OD2 B:ASP333 3.7 15.2 1.0
O7 B:TPP1003 3.9 14.2 1.0
N B:ASP333 4.0 13.4 1.0
O B:HOH1195 4.1 16.0 1.0
N B:LEU368 4.1 20.0 1.0
N B:GLY369 4.1 15.8 1.0
CA B:GLY369 4.2 14.4 1.0
CA B:LEU368 4.3 19.6 1.0
N B:ASN366 4.3 18.7 1.0
O B:VAL364 4.4 18.3 1.0
CB B:ASP333 4.4 13.9 1.0
O1B B:TPP1003 4.4 14.8 1.0
O1A B:TPP1003 4.4 13.3 1.0
CB B:ASN366 4.5 18.4 1.0
N B:ALA334 4.5 13.1 1.0
CA B:ASP333 4.7 13.5 1.0
CA B:ASN366 4.7 18.7 1.0
CA B:GLY332 4.8 14.2 1.0
N B:GLN367 4.8 19.5 1.0
C B:ASN366 4.8 19.8 1.0
C B:GLY332 4.8 14.3 1.0
CB B:LEU368 4.9 21.1 1.0

Magnesium binding site 3 out of 3 in 5rw0

Go back to Magnesium Binding Sites List in 5rw0
Magnesium binding site 3 out of 3 in the Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of DHTKD1 in Complex with Z2444997446 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1005

b:10.8
occ:1.00
O B:HOH1478 1.9 9.7 1.0
O A:HOH1545 2.0 8.9 1.0
OE1 B:GLU641 2.1 8.8 1.0
O B:HOH1207 2.2 12.6 1.0
OE1 A:GLU641 2.2 9.5 1.0
O A:HOH1138 2.2 10.2 1.0
CD B:GLU641 3.1 10.7 1.0
CD A:GLU641 3.2 12.4 1.0
OE2 B:GLU641 3.4 12.8 1.0
OE2 A:GLU641 3.6 13.7 1.0
O B:HOH1311 4.2 12.4 1.0
O B:GLY671 4.3 11.4 1.0
O A:HOH1445 4.3 8.3 1.0
O A:GLY671 4.3 10.3 1.0
CG B:GLU641 4.4 7.9 1.0
CG A:GLU641 4.4 11.0 1.0
CB B:GLU641 4.5 9.5 1.0
OE2 A:GLU344 4.5 12.3 1.0
CB A:GLU641 4.6 10.3 1.0
OE2 B:GLU344 4.6 14.0 1.0
O B:HOH1490 4.7 11.6 1.0
O A:HOH1537 4.8 9.3 1.0
O B:HOH1135 5.0 7.6 1.0

Reference:

G.A.Bezerra, W.R.Foster, H.J.Bailey, L.Shrestha, T.Krojer, J.Brandao-Neto, A.Douangamath, N.Burgess-Brown, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, W.W.Yue. Pandda Analysis Group Deposition To Be Published.
Page generated: Tue Aug 12 18:47:19 2025

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