Sodium in PDB 8iq8: Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii

The structure of Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii, PDB code: 8iq8 was solved by P.Chitnumsub, S.Maenpuen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.04 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	93.433, 62.84, 135.952, 90, 90.09, 90
R / Rfree (%)	22.5 / 25.5

The binding sites of Sodium atom in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii (pdb code 8iq8). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii, PDB code: 8iq8:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:12.1 occ:1.00 OG A:SER269 2.9 3.8 1.0 O A:HOH582 2.9 29.9 1.0 OG A:SER15 3.2 4.8 1.0 OG A:SER270 3.4 3.5 1.0 CB A:SER15 3.7 4.7 1.0 CB A:VAL13 3.9 4.1 1.0 CB A:SER270 3.9 3.4 1.0 N A:SER15 3.9 4.6 1.0 CB A:SER269 4.0 3.7 1.0 CD A:PRO14 4.0 4.4 1.0 C A:SER269 4.2 3.5 1.0 CA A:SER15 4.4 4.8 1.0 N A:SER270 4.4 3.4 1.0 O A:SER269 4.4 3.6 1.0 CG1 A:VAL13 4.5 4.2 1.0 N A:PRO14 4.5 4.4 1.0 CG2 A:VAL13 4.5 4.1 1.0 CA A:SER269 4.6 3.6 1.0 CA A:VAL13 4.8 4.2 1.0 SD A:MET197 4.8 18.5 1.0 CA A:SER270 4.8 3.3 1.0 C A:VAL13 4.9 4.2 1.0 CG A:PRO14 4.9 4.7 1.0 NH2 A:ARG29 4.9 7.6 1.0 C A:PRO14 5.0 4.5 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:11.4 occ:1.00 O B:HOH580 2.9 24.5 1.0 O B:HOH576 2.9 25.1 1.0 OG B:SER269 2.9 3.9 1.0 OG B:SER15 3.3 5.1 1.0 OG B:SER270 3.3 3.0 1.0 CB B:SER15 3.7 4.9 1.0 CB B:VAL13 3.9 3.5 1.0 N B:SER15 3.9 4.5 1.0 CD B:PRO14 3.9 4.2 1.0 CB B:SER270 4.0 2.9 1.0 CB B:SER269 4.0 3.6 1.0 C B:SER269 4.3 3.2 1.0 N B:PRO14 4.4 4.0 1.0 CA B:SER15 4.4 4.9 1.0 CG1 B:VAL13 4.4 3.5 1.0 N B:SER270 4.4 3.0 1.0 O B:SER269 4.5 3.2 1.0 CG B:MET197 4.5 21.0 1.0 CG2 B:VAL13 4.5 3.5 1.0 O B:HOH591 4.5 29.2 1.0 CA B:SER269 4.6 3.4 1.0 CG B:PRO14 4.6 4.3 1.0 CA B:VAL13 4.8 3.5 1.0 C B:VAL13 4.8 3.7 1.0 C B:PRO14 4.8 4.4 1.0 CA B:SER270 4.9 2.9 1.0 SD B:MET197 4.9 24.0 1.0 CA B:PRO14 5.0 4.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:12.0 occ:1.00 OG C:SER269 2.9 3.4 1.0 OG C:SER15 3.1 4.7 1.0 OG C:SER270 3.4 3.1 1.0 CB C:SER15 3.6 4.6 1.0 CB C:SER270 3.9 3.0 1.0 N C:SER15 3.9 4.4 1.0 CB C:VAL13 3.9 3.9 1.0 CB C:SER269 4.0 3.3 1.0 CD C:PRO14 4.1 4.1 1.0 C C:SER269 4.2 3.1 1.0 CA C:SER15 4.3 4.6 1.0 CG1 C:VAL13 4.4 4.0 1.0 N C:SER270 4.4 3.0 1.0 O C:SER269 4.5 3.2 1.0 CG2 C:VAL13 4.5 3.9 1.0 N C:PRO14 4.6 4.2 1.0 CA C:SER269 4.6 3.2 1.0 SD C:MET197 4.7 19.9 1.0 CA C:SER270 4.8 2.9 1.0 NH2 C:ARG29 4.8 6.5 1.0 CA C:VAL13 4.9 4.0 1.0 CG C:PRO14 4.9 4.4 1.0 C C:VAL13 4.9 4.0 1.0 C C:PRO14 5.0 4.3 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase (Dhpao) From Acinetobacter Baumannii within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:11.4 occ:1.00 OG D:SER269 2.8 3.9 1.0 O D:HOH587 3.1 25.2 1.0 OG D:SER15 3.3 4.8 1.0 OG D:SER270 3.3 3.1 1.0 CB D:SER15 3.7 4.7 1.0 CB D:VAL13 3.8 3.7 1.0 N D:SER15 3.9 4.3 1.0 CB D:SER270 3.9 3.0 1.0 CB D:SER269 3.9 3.7 1.0 CD D:PRO14 4.0 4.0 1.0 C D:SER269 4.2 3.3 1.0 CG1 D:VAL13 4.4 3.7 1.0 O D:SER269 4.4 3.2 1.0 N D:SER270 4.4 3.1 1.0 CA D:SER15 4.4 4.6 1.0 CG2 D:VAL13 4.4 3.7 1.0 N D:PRO14 4.4 3.9 1.0 CA D:SER269 4.5 3.5 1.0 CA D:VAL13 4.8 3.7 1.0 CG D:PRO14 4.8 4.1 1.0 C D:VAL13 4.8 3.7 1.0 CA D:SER270 4.8 3.0 1.0 C D:PRO14 4.9 4.2 1.0 SD D:MET197 4.9 22.7 1.0 NH2 D:ARG29 4.9 7.5 1.0

P.Pimviriyakul, S.Buttranon, S.Soithongcharoen, C.Supawatkon, K.Disayabootr, P.Watthaisong, R.Tinikul, A.Jaruwat, P.Chaiyen, P.Chitnumsub, S.Maenpuen. Structure and Biochemical Characterization of An Extradiol 3,4-Dihydroxyphenylacetate 2,3-Dioxygenase From Acinetobacter Baumannii. Arch.Biochem.Biophys. V. 747 09768 2023.
ISSN: ESSN 1096-0384
PubMed: 37769893
DOI: 10.1016/J.ABB.2023.109768