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Sodium in PDB 4qnk: The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate

Enzymatic activity of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate

All present enzymatic activity of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate:
4.2.1.19;

Protein crystallography data

The structure of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate, PDB code: 4qnk was solved by C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 1.75
Space group I 2 3 1
Cell size a, b, c (Å), α, β, γ (°) 225.130, 225.130, 225.130, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 17.9

Other elements in 4qnk:

The structure of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate also contains other interesting chemical elements:

Manganese (Mn) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate (pdb code 4qnk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate, PDB code: 4qnk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4qnk

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Sodium binding site 1 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:19.9
occ:1.00
 O A:HOH548 2.2 25.7 1.0
O A:HOH479 2.3 27.6 1.0
OG A:SER189 2.4 19.9 1.0
O A:ASP190 2.5 14.6 1.0
O A:ARG193 2.6 23.2 1.0
O A:GLY96 2.6 14.7 1.0
C A:ASP190 3.4 14.7 1.0
C A:GLY96 3.5 10.9 1.0
N A:ASP190 3.6 11.9 1.0
CB A:SER189 3.7 20.4 1.0
CA A:GLY96 3.7 14.3 1.0
C A:ARG193 3.7 27.9 1.0
CA A:ASP190 4.1 13.7 1.0
CA A:SER189 4.1 14.7 1.0
C A:SER189 4.1 13.4 1.0
N A:ARG193 4.3 13.5 1.0
CA A:ARG193 4.4 12.2 1.0
O A:HOH509 4.4 34.9 1.0
N A:PRO191 4.4 12.4 1.0
CB A:ARG193 4.5 15.9 1.0
CB A:ASP190 4.6 13.9 1.0
CA A:PRO191 4.6 20.8 1.0
N A:ILE97 4.8 11.7 1.0
C A:PRO191 4.9 18.8 1.0
O A:SER189 5.0 14.1 1.0

Sodium binding site 2 out of 8 in 4qnk

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Sodium binding site 2 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:21.2
occ:1.00
 O B:HOH556 2.2 27.6 1.0
O B:HOH487 2.3 25.4 1.0
OG B:SER189 2.4 20.2 1.0
O B:ASP190 2.4 14.0 1.0
O B:ARG193 2.5 21.2 1.0
O B:GLY96 2.6 13.5 1.0
C B:ASP190 3.4 12.8 1.0
C B:GLY96 3.6 13.9 1.0
N B:ASP190 3.6 11.3 1.0
CB B:SER189 3.7 15.6 1.0
C B:ARG193 3.7 27.2 1.0
CA B:GLY96 3.8 14.7 1.0
CA B:ASP190 4.1 9.3 1.0
CA B:SER189 4.1 12.0 1.0
C B:SER189 4.1 14.1 1.0
N B:ARG193 4.3 14.6 1.0
CA B:ARG193 4.4 12.2 1.0
O B:HOH509 4.4 34.0 1.0
N B:PRO191 4.4 13.7 1.0
CB B:ARG193 4.5 13.7 1.0
CB B:ASP190 4.6 16.1 1.0
CA B:PRO191 4.6 17.2 1.0
N B:ILE97 4.8 11.8 1.0
C B:PRO191 4.8 18.8 1.0
O B:SER189 5.0 17.4 1.0

Sodium binding site 3 out of 8 in 4qnk

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Sodium binding site 3 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na305

b:20.7
occ:1.00
 O C:HOH462 2.2 23.5 1.0
O C:HOH498 2.3 28.4 1.0
O C:ASP190 2.4 15.5 1.0
OG C:SER189 2.4 21.7 1.0
O C:ARG193 2.5 22.4 1.0
O C:GLY96 2.6 15.5 1.0
C C:ASP190 3.4 16.4 1.0
N C:ASP190 3.5 10.2 1.0
C C:GLY96 3.6 16.8 1.0
CB C:SER189 3.7 18.4 1.0
C C:ARG193 3.8 25.9 1.0
CA C:GLY96 3.8 14.7 1.0
CA C:SER189 4.0 15.3 1.0
C C:SER189 4.0 14.6 1.0
CA C:ASP190 4.0 13.4 1.0
N C:ARG193 4.4 13.9 1.0
N C:PRO191 4.4 13.5 1.0
CA C:ARG193 4.4 15.4 1.0
CA C:PRO191 4.5 19.3 1.0
CB C:ARG193 4.6 17.9 1.0
CB C:ASP190 4.6 12.4 1.0
O C:HOH562 4.8 50.8 1.0
N C:ILE97 4.8 13.3 1.0
C C:PRO191 4.9 19.9 1.0
O C:SER189 5.0 18.4 1.0

Sodium binding site 4 out of 8 in 4qnk

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Sodium binding site 4 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na304

b:21.5
occ:1.00
 O D:HOH532 2.2 29.1 1.0
O D:HOH520 2.3 26.2 1.0
O D:ASP190 2.4 15.4 1.0
OG D:SER189 2.5 21.8 1.0
O D:ARG193 2.5 24.0 1.0
O D:GLY96 2.6 17.2 1.0
C D:ASP190 3.4 11.4 1.0
C D:GLY96 3.5 14.1 1.0
N D:ASP190 3.6 13.5 1.0
CB D:SER189 3.7 17.1 1.0
C D:ARG193 3.7 23.1 1.0
CA D:GLY96 3.8 15.9 1.0
C D:SER189 4.0 12.9 1.0
CA D:SER189 4.0 10.4 1.0
CA D:ASP190 4.0 11.0 1.0
N D:ARG193 4.3 15.5 1.0
O D:HOH488 4.4 32.2 1.0
CA D:ARG193 4.4 16.3 1.0
N D:PRO191 4.4 14.4 1.0
CB D:ARG193 4.5 12.7 1.0
CA D:PRO191 4.5 14.5 1.0
CB D:ASP190 4.6 11.2 1.0
N D:ILE97 4.8 12.7 1.0
C D:PRO191 4.9 16.2 1.0
O D:SER189 4.9 14.9 1.0

Sodium binding site 5 out of 8 in 4qnk

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Sodium binding site 5 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na305

b:20.6
occ:1.00
 O E:HOH405 2.3 25.4 1.0
O E:HOH500 2.3 23.7 1.0
OG E:SER189 2.5 24.6 1.0
O E:ASP190 2.5 16.3 1.0
O E:ARG193 2.5 26.9 1.0
O E:GLY96 2.6 14.3 1.0
C E:ASP190 3.4 13.3 1.0
N E:ASP190 3.5 12.4 1.0
C E:GLY96 3.6 16.1 1.0
CB E:SER189 3.6 18.0 1.0
C E:ARG193 3.7 23.8 1.0
CA E:GLY96 3.8 15.7 1.0
CA E:SER189 4.0 14.0 1.0
C E:SER189 4.0 11.3 1.0
CA E:ASP190 4.1 11.9 1.0
N E:ARG193 4.3 13.5 1.0
CA E:ARG193 4.4 15.7 1.0
N E:PRO191 4.4 12.2 1.0
O E:HOH493 4.5 32.2 1.0
CB E:ARG193 4.6 18.3 1.0
CA E:PRO191 4.6 18.3 1.0
CB E:ASP190 4.7 12.8 1.0
N E:ILE97 4.8 12.0 1.0
C E:PRO191 4.9 20.3 1.0
O E:SER189 4.9 13.6 1.0

Sodium binding site 6 out of 8 in 4qnk

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Sodium binding site 6 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na304

b:22.5
occ:1.00
 O F:HOH546 2.2 32.0 1.0
O F:HOH540 2.2 28.8 1.0
OG F:SER189 2.4 21.5 1.0
O F:ASP190 2.5 15.8 1.0
O F:ARG193 2.5 24.3 1.0
O F:GLY96 2.6 16.1 1.0
C F:ASP190 3.4 13.6 1.0
N F:ASP190 3.5 16.2 1.0
C F:GLY96 3.6 19.5 1.0
CB F:SER189 3.7 18.2 1.0
C F:ARG193 3.7 27.6 1.0
CA F:GLY96 3.8 17.1 1.0
C F:SER189 4.0 13.5 1.0
CA F:ASP190 4.0 11.8 1.0
CA F:SER189 4.1 11.8 1.0
N F:ARG193 4.3 18.9 1.0
CA F:ARG193 4.4 16.6 1.0
N F:PRO191 4.4 12.8 1.0
CB F:ARG193 4.5 17.1 1.0
CB F:ASP190 4.6 15.3 1.0
O F:HOH502 4.6 32.4 1.0
CA F:PRO191 4.6 18.0 1.0
N F:ILE97 4.8 13.6 1.0
C F:PRO191 4.9 20.3 1.0
O F:SER189 4.9 13.3 1.0

Sodium binding site 7 out of 8 in 4qnk

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Sodium binding site 7 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na305

b:22.7
occ:1.00
 O G:HOH525 2.2 24.7 1.0
O G:HOH538 2.3 26.7 1.0
O G:ASP190 2.5 15.7 1.0
OG G:SER189 2.5 25.5 1.0
O G:ARG193 2.5 25.1 1.0
O G:GLY96 2.6 15.5 1.0
C G:ASP190 3.4 18.3 1.0
C G:GLY96 3.5 19.2 1.0
N G:ASP190 3.5 12.6 1.0
CB G:SER189 3.6 19.1 1.0
C G:ARG193 3.7 29.5 1.0
CA G:GLY96 3.7 17.5 1.0
C G:SER189 4.0 12.3 1.0
CA G:SER189 4.0 15.7 1.0
CA G:ASP190 4.0 12.7 1.0
N G:ARG193 4.3 15.8 1.0
CA G:ARG193 4.3 17.0 1.0
N G:PRO191 4.4 15.8 1.0
CB G:ARG193 4.5 16.1 1.0
O G:HOH513 4.5 40.4 1.0
CA G:PRO191 4.6 18.7 1.0
O G:HOH548 4.6 45.0 1.0
CB G:ASP190 4.6 16.3 1.0
N G:ILE97 4.8 12.0 1.0
C G:PRO191 4.8 20.9 1.0
O G:SER189 4.9 11.4 1.0

Sodium binding site 8 out of 8 in 4qnk

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Sodium binding site 8 out of 8 in the The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of The Structure of Wt A. Thaliana IGPD2 in Complex with MN2+ and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na304

b:20.8
occ:1.00
 O H:HOH504 2.2 30.3 1.0
O H:HOH531 2.3 24.3 1.0
O H:ASP190 2.5 17.1 1.0
OG H:SER189 2.5 19.4 1.0
O H:ARG193 2.5 26.1 1.0
O H:GLY96 2.6 14.8 1.0
C H:ASP190 3.4 17.0 1.0
N H:ASP190 3.6 14.9 1.0
C H:GLY96 3.6 13.3 1.0
C H:ARG193 3.7 19.5 1.0
CB H:SER189 3.7 16.4 1.0
CA H:GLY96 3.8 15.5 1.0
CA H:ASP190 4.1 12.3 1.0
CA H:SER189 4.1 11.4 1.0
C H:SER189 4.1 10.8 1.0
N H:ARG193 4.3 12.1 1.0
CA H:ARG193 4.4 12.2 1.0
N H:PRO191 4.4 12.8 1.0
O H:HOH475 4.5 31.6 1.0
CB H:ARG193 4.5 15.0 1.0
CB H:ASP190 4.6 10.8 1.0
CA H:PRO191 4.6 17.1 1.0
N H:ILE97 4.8 12.1 1.0
C H:PRO191 4.9 18.7 1.0

Reference:

C.Bisson, K.L.Britton, S.E.Sedelnikova, H.F.Rodgers, T.C.Eadsforth, R.C.Viner, T.R.Hawkes, P.J.Baker, D.W.Rice. Crystal Structures Reveal That the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled By Switching Mn(II) Coordination. Structure V. 23 1236 2015.
ISSN: ISSN 0969-2126
PubMed: 26095028
DOI: 10.1016/J.STR.2015.05.012
Page generated: Mon Oct 7 18:01:19 2024

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