Sodium in PDB 7u34: The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus

All present enzymatic activity of The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus:
5.3.1.9;

The structure of The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus, PDB code: 7u34 was solved by K.Yan, B.Kowalski, W.Fang, D.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	58.01 / 1.56
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	84.452, 84.452, 232.024, 90, 90, 90
R / Rfree (%)	15.7 / 18.3

The structure of The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus (pdb code 7u34). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus, PDB code: 7u34:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus


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 Phosphoglucose Isomerase From Aspergillus Fumigatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na607 b:19.9 occ:1.00 HG A:SER482 2.0 20.4 1.0 H A:SER482 2.4 18.0 1.0 O A:HOH1092 2.8 32.6 1.0 OG A:SER482 2.8 17.0 1.0 HB A:THR480 2.8 22.0 1.0 OE1 A:GLN300 2.8 31.0 1.0 HD2 A:PRO481 2.9 23.7 1.0 HB3 A:ASP52 3.0 23.5 1.0 HB3 A:SER482 3.1 19.5 1.0 HB3 A:GLN300 3.1 25.0 1.0 HG13 A:VAL51 3.2 22.3 1.0 N A:SER482 3.2 14.9 1.0 CB A:SER482 3.4 16.2 1.0 OG1 A:THR480 3.5 15.2 1.0 HG1 A:THR480 3.5 18.3 1.0 CB A:THR480 3.6 18.3 1.0 HB2 A:PRO481 3.6 17.2 1.0 CD A:PRO481 3.7 19.7 1.0 N A:PRO481 3.8 15.4 1.0 CA A:SER482 3.9 12.3 1.0 CD A:GLN300 3.9 34.3 1.0 CB A:GLN300 4.0 20.8 1.0 CB A:ASP52 4.0 19.6 1.0 CG1 A:VAL51 4.1 18.6 1.0 HB2 A:GLN300 4.2 25.0 1.0 C A:PRO481 4.2 15.0 1.0 HG21 A:THR480 4.2 20.3 1.0 HB2 A:SER482 4.2 19.5 1.0 CB A:PRO481 4.3 14.3 1.0 O A:HOH1001 4.3 34.2 1.0 H A:THR483 4.3 15.1 1.0 HB2 A:ASP52 4.3 23.5 1.0 HG12 A:VAL51 4.3 22.3 1.0 CA A:PRO481 4.3 14.2 1.0 HG2 A:PRO481 4.4 22.7 1.0 CG A:GLN300 4.4 22.8 1.0 CG A:PRO481 4.4 18.9 1.0 C A:THR480 4.4 14.6 1.0 HG2 A:GLN300 4.4 27.4 1.0 HD3 A:PRO481 4.5 23.7 1.0 CG2 A:THR480 4.5 16.9 1.0 HA A:SER482 4.5 14.8 1.0 OD2 A:ASP52 4.6 16.2 1.0 HG11 A:VAL51 4.6 22.3 1.0 CA A:THR480 4.6 12.9 1.0 HB A:VAL51 4.7 18.6 1.0 HA A:ASP52 4.7 25.6 1.0 CG A:ASP52 4.7 18.8 1.0 CA A:ASP52 4.8 21.3 1.0 N A:ASP52 4.8 18.5 1.0 O A:HOH925 4.8 33.5 1.0 N A:THR483 4.9 12.6 1.0 HG22 A:THR480 4.9 20.3 1.0 C A:SER482 4.9 11.9 1.0 H A:ASP52 4.9 22.3 1.0 HD21 A:ASN49 4.9 19.1 1.0 HA A:THR480 5.0 15.5 1.0

Sodium binding site 2 out of 4 in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus


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 Phosphoglucose Isomerase From Aspergillus Fumigatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na608 b:19.9 occ:1.00 O A:HOH859 2.6 13.7 1.0 HD2 A:PHE465 2.7 16.2 1.0 HA A:LEU441 2.7 15.2 1.0 O A:ALA440 2.8 10.1 1.0 ND1 A:HIS401 2.8 11.1 1.0 HB3 A:PHE465 2.8 13.5 1.0 HA2 A:GLY444 3.2 15.4 1.0 HD21 A:LEU441 3.3 13.9 1.0 C A:ALA440 3.4 11.8 1.0 CD2 A:PHE465 3.5 13.5 1.0 CA A:LEU441 3.6 12.7 1.0 HA2 A:GLY467 3.6 14.2 1.0 CE1 A:HIS401 3.6 13.5 1.0 HE1 A:HIS401 3.6 16.2 1.0 HB3 A:HIS401 3.6 14.2 1.0 CB A:PHE465 3.7 11.2 1.0 H A:GLY467 3.8 14.6 1.0 N A:LEU441 3.8 11.0 1.0 HA A:HIS401 3.8 10.8 1.0 CG A:HIS401 3.8 11.0 1.0 HB1 A:ALA440 3.8 14.6 1.0 H A:GLY444 4.0 15.3 1.0 CG A:PHE465 4.0 10.9 1.0 CA A:GLY444 4.1 12.8 1.0 CB A:HIS401 4.1 11.8 1.0 HB2 A:PHE465 4.1 13.5 1.0 C A:LEU441 4.2 12.1 1.0 CD2 A:LEU441 4.3 11.6 1.0 O A:LEU441 4.3 12.0 1.0 HD2 A:ARG469 4.3 21.1 1.0 O A:HIS401 4.3 11.7 1.0 CA A:GLY467 4.4 11.9 1.0 N A:GLY467 4.4 12.1 1.0 CA A:HIS401 4.4 9.0 1.0 HA3 A:GLY444 4.4 15.4 1.0 CE2 A:PHE465 4.5 13.3 1.0 N A:GLY444 4.5 12.7 1.0 H A:LEU441 4.5 13.2 1.0 HG A:LEU441 4.5 13.3 1.0 CA A:ALA440 4.5 9.6 1.0 HE2 A:PHE465 4.5 15.9 1.0 CB A:ALA440 4.5 12.2 1.0 CB A:LEU441 4.7 11.9 1.0 HA A:ALA440 4.7 11.5 1.0 HD22 A:LEU441 4.7 13.9 1.0 CG A:LEU441 4.7 11.1 1.0 HD23 A:LEU441 4.7 13.9 1.0 HB3 A:ALA440 4.8 14.6 1.0 HA3 A:GLY467 4.8 14.2 1.0 NE2 A:HIS401 4.8 12.6 1.0 CA A:PHE465 4.8 10.8 1.0 HA A:PHE465 4.8 12.9 1.0 C A:HIS401 4.9 11.5 1.0 CD2 A:HIS401 4.9 12.5 1.0

Sodium binding site 3 out of 4 in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus


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 Phosphoglucose Isomerase From Aspergillus Fumigatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na609 b:16.8 occ:1.00 HA2 A:GLY366 2.8 11.7 1.0 OG1 A:THR380 3.0 9.9 1.0 O A:GLY381 3.1 10.6 1.0 HG1 A:THR380 3.1 11.9 1.0 H A:GLY381 3.1 14.1 1.0 N A:GLY381 3.4 11.7 1.0 H A:LYS367 3.7 11.2 1.0 CA A:GLY366 3.7 9.7 1.0 H A:THR380 3.8 13.7 1.0 C A:THR380 3.8 11.3 1.0 C A:GLY381 3.9 10.5 1.0 O A:ASN365 3.9 9.9 1.0 CA A:GLY381 4.0 12.0 1.0 HA3 A:GLY381 4.0 14.4 1.0 HA3 A:GLY366 4.1 11.7 1.0 CB A:THR380 4.1 11.6 1.0 N A:LYS367 4.2 9.3 1.0 C A:GLY366 4.3 10.1 1.0 CA A:THR380 4.3 10.3 1.0 HB A:THR380 4.4 14.0 1.0 N A:THR380 4.4 11.4 1.0 O A:THR380 4.4 12.5 1.0 O A:LYS367 4.6 12.2 1.0 N A:GLY366 4.6 11.5 1.0 C A:ASN365 4.7 10.9 1.0 HA2 A:GLY381 4.9 14.4 1.0

Sodium binding site 4 out of 4 in the The Structure of Phosphoglucose Isomerase From Aspergillus Fumigatus


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 Phosphoglucose Isomerase From Aspergillus Fumigatus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na610 b:44.1 occ:1.00 O A:HOH1146 2.8 30.9 1.0 O A:HOH1075 4.6 47.2 1.0 O A:HOH849 4.8 28.8 1.0 O A:HOH724 4.9 31.8 1.0

Y.Zhou, K.Yan, Q.Qin, O.G.Raimi, C.Du, B.Wang, C.S.Ahamefule, B.Kowalski, C.Jin, D.M.F.Van Aalten, W.Fang. Phosphoglucose Isomerase Is Important For Aspergillus Fumigatus Cell Wall Biogenesis. Mbio V. 13 42622 2022.
ISSN: ESSN 2150-7511
PubMed: 35913157
DOI: 10.1128/MBIO.01426-22