Zinc in PDB 5cuo: Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form

All present enzymatic activity of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form:
2.3.1.222;

The structure of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form, PDB code: 5cuo was solved by M.Sutter, O.Erbilgin, C.A.Kerfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.44 / 1.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.740, 56.443, 150.438, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.1

The binding sites of Zinc atom in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form (pdb code 5cuo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form, PDB code: 5cuo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:23.4 occ:1.00 ND1 A:HIS204 2.1 17.9 1.0 NE2 A:HIS157 2.1 17.1 1.0 NE2 A:HIS159 2.2 20.1 1.0 O A:HOH768 2.2 23.0 1.0 O A:HOH759 2.3 18.5 1.0 O A:HOH750 2.5 23.9 1.0 CE1 A:HIS204 2.9 20.6 1.0 HE1 A:HIS204 2.9 24.7 1.0 CE1 A:HIS157 3.0 19.8 1.0 HE1 A:HIS157 3.1 23.7 1.0 CE1 A:HIS159 3.1 24.6 1.0 CD2 A:HIS157 3.2 20.5 1.0 CD2 A:HIS159 3.2 20.7 1.0 CG A:HIS204 3.2 18.9 1.0 HE1 A:HIS159 3.3 29.5 1.0 HD2 A:HIS159 3.4 24.9 1.0 HB2 A:HIS204 3.4 20.2 1.0 HD2 A:HIS157 3.4 24.6 1.0 CB A:HIS204 3.7 16.9 1.0 HB3 A:HIS204 3.8 20.2 1.0 NE2 A:HIS204 4.1 21.7 1.0 ND1 A:HIS157 4.2 22.8 1.0 CD2 A:HIS204 4.2 22.1 1.0 ND1 A:HIS159 4.3 25.4 1.0 CG A:HIS157 4.3 21.6 1.0 CG A:HIS159 4.3 24.2 1.0 HS1 A:COA501 4.3 21.3 1.0 H32 A:COA501 4.4 26.0 1.0 O A:HOH718 4.5 22.9 1.0 O A:HOH746 4.5 25.8 1.0 O A:HOH629 4.6 22.2 1.0 O A:HOH739 4.6 21.2 1.0 S1P A:COA501 4.7 17.8 1.0 HE2 A:HIS204 4.8 26.0 1.0 HD3 A:ARG194 4.9 45.4 1.0 H22 A:COA501 4.9 19.8 1.0 HG3 A:GLN74 4.9 30.9 1.0 HD1 A:HIS157 4.9 27.3 1.0

Zinc binding site 2 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:16.1 occ:1.00 OE2 A:GLU109 1.9 13.2 1.0 HS1 A:COA501 2.0 21.3 1.0 NE2 A:HIS48 2.1 12.7 1.0 NE2 A:HIS50 2.1 11.1 1.0 S1P A:COA501 2.2 17.8 1.0 CD A:GLU109 2.8 16.1 1.0 H21 A:COA501 2.9 19.8 1.0 C2P A:COA501 3.0 16.5 1.0 CD2 A:HIS48 3.0 11.5 1.0 OE1 A:GLU109 3.0 19.4 1.0 CD2 A:HIS50 3.0 14.0 1.0 CE1 A:HIS50 3.1 18.1 1.0 CE1 A:HIS48 3.1 14.7 1.0 HD2 A:HIS48 3.2 13.8 1.0 HD2 A:HIS50 3.2 16.8 1.0 H22 A:COA501 3.3 19.8 1.0 HE1 A:HIS50 3.3 21.7 1.0 HE1 A:HIS48 3.3 17.7 1.0 HD22 A:LEU99 3.6 35.1 1.0 HE21 A:GLN107 3.7 26.1 1.0 HD23 A:LEU99 3.9 35.1 1.0 CG A:GLU109 4.1 16.0 1.0 CD2 A:LEU99 4.2 29.3 1.0 ND1 A:HIS48 4.2 18.7 1.0 CG A:HIS48 4.2 12.1 1.0 ND1 A:HIS50 4.2 19.4 1.0 CG A:HIS50 4.2 12.2 1.0 HB2 A:GLU109 4.2 16.1 1.0 HG3 A:GLU109 4.2 19.2 1.0 O A:HOH746 4.3 25.8 1.0 NE2 A:GLN107 4.4 21.8 1.0 C3P A:COA501 4.4 21.6 1.0 HE22 A:GLN107 4.4 26.1 1.0 O A:HOH718 4.5 22.9 1.0 HH12 A:ARG103 4.6 34.5 1.0 O A:HOH759 4.6 18.5 1.0 H31 A:COA501 4.6 26.0 1.0 HD21 A:LEU99 4.6 35.1 1.0 HH22 A:ARG103 4.7 39.8 1.0 CB A:GLU109 4.7 13.4 1.0 H32 A:COA501 4.7 26.0 1.0 HG2 A:GLU109 4.8 19.2 1.0 HB2 A:LEU99 4.8 28.2 1.0 HD1 A:HIS48 5.0 22.4 1.0 HD1 A:HIS50 5.0 23.3 1.0 O A:HOH733 5.0 19.8 1.0

Zinc binding site 3 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:18.8 occ:1.00 NE2 B:HIS157 2.1 16.4 1.0 NE2 B:HIS159 2.2 12.5 1.0 O B:HOH737 2.2 20.0 1.0 ND1 B:HIS204 2.2 14.0 1.0 O B:HOH786 2.2 16.2 1.0 O B:HOH795 2.3 21.8 1.0 CE1 B:HIS204 3.0 15.7 1.0 HE1 B:HIS204 3.1 18.8 1.0 CE1 B:HIS157 3.1 16.7 1.0 CE1 B:HIS159 3.1 17.8 1.0 CD2 B:HIS157 3.2 14.2 1.0 CD2 B:HIS159 3.2 15.3 1.0 HE1 B:HIS159 3.2 21.3 1.0 HE1 B:HIS157 3.2 20.0 1.0 CG B:HIS204 3.3 13.7 1.0 HD2 B:HIS157 3.4 17.0 1.0 HD2 B:HIS159 3.4 18.4 1.0 HB2 B:HIS204 3.4 13.8 1.0 CB B:HIS204 3.7 11.5 1.0 HB3 B:HIS204 3.8 13.8 1.0 O B:HOH830 4.1 33.5 1.0 H22 B:COA501 4.1 18.6 1.0 HS1 B:COA501 4.2 15.8 1.0 NE2 B:HIS204 4.2 16.6 1.0 ND1 B:HIS157 4.2 14.7 1.0 ND1 B:HIS159 4.2 17.9 1.0 CG B:HIS157 4.3 12.4 1.0 CG B:HIS159 4.3 16.3 1.0 CD2 B:HIS204 4.3 15.6 1.0 O B:HOH844 4.4 35.6 1.0 O B:HOH744 4.5 21.3 1.0 O B:HOH783 4.6 20.6 1.0 O B:HOH629 4.6 19.2 1.0 S1P B:COA501 4.6 13.2 1.0 O B:HOH753 4.6 26.5 1.0 H32 B:COA501 4.7 18.8 1.0 C2P B:COA501 4.8 15.5 1.0 HG3 B:GLN74 4.8 19.8 1.0 HD3 B:ARG194 4.8 29.2 1.0 HE2 B:HIS204 4.9 19.9 1.0 HD1 B:HIS157 5.0 17.7 1.0 HD1 B:HIS159 5.0 21.5 1.0

Zinc binding site 4 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Rhodopseudomonas Palustris Pdul - Coa Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn503 b:13.5 occ:1.00 OE2 B:GLU109 1.9 13.1 1.0 NE2 B:HIS48 2.0 10.1 1.0 NE2 B:HIS50 2.0 11.9 1.0 HS1 B:COA501 2.2 15.8 1.0 S1P B:COA501 2.2 13.2 1.0 CD B:GLU109 2.8 13.1 1.0 CD2 B:HIS48 3.0 11.5 1.0 CE1 B:HIS50 3.0 13.2 1.0 H21 B:COA501 3.0 18.6 1.0 CE1 B:HIS48 3.1 12.5 1.0 CD2 B:HIS50 3.1 11.5 1.0 OE1 B:GLU109 3.1 16.8 1.0 HD2 B:HIS48 3.1 13.8 1.0 HE1 B:HIS50 3.1 15.9 1.0 C2P B:COA501 3.2 15.5 1.0 HD2 B:HIS50 3.3 13.8 1.0 HE1 B:HIS48 3.3 15.0 1.0 HD22 B:LEU99 3.5 28.2 1.0 HE21 B:GLN107 3.7 18.7 1.0 H22 B:COA501 3.7 18.6 1.0 CG B:GLU109 4.1 15.0 1.0 ND1 B:HIS50 4.1 13.7 1.0 CG B:HIS48 4.1 13.4 1.0 ND1 B:HIS48 4.2 11.9 1.0 HG3 B:GLU109 4.2 18.0 1.0 CG B:HIS50 4.2 12.9 1.0 HB2 B:GLU109 4.3 11.1 1.0 H31 B:COA501 4.4 18.8 1.0 CD2 B:LEU99 4.4 23.5 1.0 HD23 B:LEU99 4.4 28.2 1.0 NE2 B:GLN107 4.4 15.6 1.0 C3P B:COA501 4.4 15.7 1.0 O B:HOH744 4.5 21.3 1.0 HE22 B:GLN107 4.5 18.7 1.0 O B:HOH753 4.5 26.5 1.0 HH22 B:ARG103 4.6 29.3 1.0 O B:HOH786 4.7 16.2 1.0 O B:HOH613 4.7 16.9 1.0 CB B:GLU109 4.8 9.2 1.0 HG2 B:GLU109 4.8 18.0 1.0 HB2 B:LEU99 4.8 16.2 1.0 HD21 B:LEU99 4.8 28.2 1.0 O B:HOH787 4.8 27.6 1.0 H32 B:COA501 4.9 18.8 1.0 HD1 B:HIS50 4.9 16.5 1.0 HH12 B:ARG103 4.9 32.7 1.0 HD1 B:HIS48 4.9 14.2 1.0

O.Erbilgin, M.Sutter, C.A.Kerfeld. The Structural Basis of Coenzyme A Recycling in A Bacterial Organelle. Plos Biol. V. 14 02399 2016.
ISSN: ESSN 1545-7885
PubMed: 26959993
DOI: 10.1371/JOURNAL.PBIO.1002399