Zinc in PDB 5cup: Structure of Rhodopseudomonas Palustris Pdul - Phosphate Bound Form

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

The structure of Structure of Rhodopseudomonas Palustris Pdul - Phosphate Bound Form, PDB code: 5cup 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)	39.23 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.098, 58.763, 136.656, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.8

The binding sites of Zinc atom in the Structure of Rhodopseudomonas Palustris Pdul - Phosphate Bound Form (pdb code 5cup). 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 - Phosphate Bound Form, PDB code: 5cup:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Phosphate 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 - Phosphate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:39.8 occ:1.00 O3 A:PO4303 2.0 41.0 1.0 ND1 A:HIS204 2.0 39.7 1.0 NE2 A:HIS159 2.1 44.2 1.0 NE2 A:HIS157 2.2 37.8 1.0 CE1 A:HIS204 2.9 41.8 1.0 HE1 A:HIS204 3.0 50.2 1.0 CE1 A:HIS159 3.1 43.4 1.0 CE1 A:HIS157 3.1 35.6 1.0 CG A:HIS204 3.1 38.8 1.0 CD2 A:HIS159 3.1 43.4 1.0 HE1 A:HIS157 3.2 42.8 1.0 O A:HOH405 3.2 39.7 1.0 HB2 A:HIS204 3.2 44.1 1.0 HE1 A:HIS159 3.2 52.1 1.0 CD2 A:HIS157 3.3 38.6 1.0 HD2 A:HIS159 3.3 52.0 1.0 P A:PO4303 3.4 38.8 1.0 O A:HOH448 3.4 46.4 1.0 HD2 A:HIS157 3.5 46.3 1.0 CB A:HIS204 3.5 36.7 1.0 O A:HOH402 3.6 42.0 1.0 HB3 A:HIS204 3.6 44.1 1.0 O2 A:PO4303 3.8 37.4 1.0 NE2 A:HIS204 4.0 40.7 1.0 CD2 A:HIS204 4.2 41.1 1.0 ND1 A:HIS159 4.2 45.3 1.0 ND1 A:HIS157 4.2 35.5 1.0 O1 A:PO4303 4.3 44.4 1.0 CG A:HIS159 4.3 43.5 1.0 O4 A:PO4303 4.3 39.7 1.0 CG A:HIS157 4.4 37.4 1.0 HE2 A:HIS204 4.8 48.9 1.0 HG3 A:GLN74 4.9 52.9 1.0 HD1 A:HIS159 5.0 54.4 1.0 HD1 A:HIS157 5.0 42.6 1.0

Zinc binding site 2 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Phosphate 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 - Phosphate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:29.1 occ:1.00 OE1 A:GLU109 2.0 29.6 1.0 O2 A:PO4303 2.1 37.4 1.0 NE2 A:HIS48 2.1 29.1 1.0 NE2 A:HIS50 2.1 29.9 1.0 CD A:GLU109 2.7 30.1 1.0 OE2 A:GLU109 2.9 28.0 1.0 CE1 A:HIS50 3.0 31.8 1.0 CD2 A:HIS48 3.0 28.6 1.0 HE1 A:HIS50 3.1 38.1 1.0 CE1 A:HIS48 3.1 29.7 1.0 P A:PO4303 3.1 38.8 1.0 CD2 A:HIS50 3.2 29.3 1.0 HD2 A:HIS48 3.2 34.3 1.0 O4 A:PO4303 3.2 39.7 1.0 HE1 A:HIS48 3.3 35.6 1.0 HD2 A:HIS50 3.4 35.1 1.0 HD11 A:LEU99 3.5 41.4 1.0 HE21 A:GLN107 3.6 35.8 1.0 O A:HOH405 3.6 39.7 1.0 O1 A:PO4303 3.7 44.4 1.0 CG A:GLU109 4.1 28.1 1.0 HH12 A:ARG103 4.1 46.3 1.0 ND1 A:HIS50 4.1 34.1 1.0 ND1 A:HIS48 4.2 29.4 1.0 HG3 A:GLU109 4.2 33.8 1.0 CG A:HIS48 4.2 27.9 1.0 HE22 A:GLN107 4.2 35.8 1.0 NE2 A:GLN107 4.2 29.8 1.0 HB2 A:GLU109 4.3 31.9 1.0 CG A:HIS50 4.3 32.1 1.0 CD1 A:LEU99 4.4 34.5 1.0 O3 A:PO4303 4.4 41.0 1.0 HH22 A:ARG103 4.4 49.5 1.0 HG A:SER127 4.4 45.2 1.0 HD13 A:LEU99 4.5 41.4 1.0 NH1 A:ARG103 4.7 38.6 1.0 HD12 A:LEU99 4.7 41.4 1.0 OG A:SER127 4.7 37.6 1.0 CB A:GLU109 4.7 26.6 1.0 HG2 A:GLU109 4.7 33.8 1.0 HD1 A:HIS50 4.9 41.0 1.0 NH2 A:ARG103 5.0 41.3 1.0 HD1 A:HIS48 5.0 35.2 1.0 HG A:SER45 5.0 41.7 1.0

Zinc binding site 3 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Phosphate 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 - Phosphate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:30.5 occ:1.00 ND1 B:HIS204 2.0 28.2 1.0 O3 B:PO4303 2.0 33.1 1.0 NE2 B:HIS157 2.2 26.8 1.0 NE2 B:HIS159 2.2 28.5 1.0 O B:HOH417 2.7 27.9 1.0 CE1 B:HIS204 2.9 28.9 1.0 HE1 B:HIS204 3.0 34.6 1.0 CG B:HIS204 3.1 27.0 1.0 CE1 B:HIS157 3.1 27.2 1.0 HB2 B:HIS204 3.1 31.1 1.0 CE1 B:HIS159 3.2 28.8 1.0 CD2 B:HIS159 3.2 28.4 1.0 CD2 B:HIS157 3.2 26.0 1.0 HE1 B:HIS157 3.2 32.7 1.0 HE1 B:HIS159 3.3 34.5 1.0 HD2 B:HIS159 3.3 34.0 1.0 P B:PO4303 3.4 34.3 1.0 HD2 B:HIS157 3.4 31.2 1.0 CB B:HIS204 3.5 25.9 1.0 HB3 B:HIS204 3.6 31.1 1.0 O B:HOH466 3.6 31.4 1.0 O1 B:PO4303 3.7 28.5 1.0 O B:HOH496 3.7 31.1 1.0 NE2 B:HIS204 4.1 27.2 1.0 CD2 B:HIS204 4.2 28.3 1.0 ND1 B:HIS157 4.2 25.5 1.0 O2 B:PO4303 4.2 34.6 1.0 ND1 B:HIS159 4.3 30.3 1.0 CG B:HIS157 4.3 24.1 1.0 CG B:HIS159 4.3 28.8 1.0 O4 B:PO4303 4.4 36.6 1.0 HE2 B:HIS204 4.8 32.7 1.0 O B:HOH446 4.8 30.3 1.0 HG3 B:GLN74 4.9 35.9 1.0 O B:HOH524 4.9 26.6 1.0 CA B:HIS204 5.0 25.1 1.0 HD1 B:HIS157 5.0 30.6 1.0

Zinc binding site 4 out of 4 in the Structure of Rhodopseudomonas Palustris Pdul - Phosphate 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 - Phosphate Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn302 b:27.3 occ:1.00 OE1 B:GLU109 2.0 23.8 1.0 NE2 B:HIS48 2.1 24.2 1.0 NE2 B:HIS50 2.1 25.5 1.0 O1 B:PO4303 2.1 28.5 1.0 CD B:GLU109 2.8 26.1 1.0 CE1 B:HIS48 3.0 23.4 1.0 CE1 B:HIS50 3.0 26.8 1.0 OE2 B:GLU109 3.0 24.3 1.0 HE1 B:HIS48 3.1 28.1 1.0 P B:PO4303 3.1 34.3 1.0 HE1 B:HIS50 3.1 32.1 1.0 CD2 B:HIS48 3.1 23.3 1.0 CD2 B:HIS50 3.2 26.5 1.0 O2 B:PO4303 3.3 34.6 1.0 HD2 B:HIS48 3.4 27.9 1.0 HD2 B:HIS50 3.4 31.8 1.0 O4 B:PO4303 3.6 36.6 1.0 HE22 B:GLN107 3.7 30.6 1.0 HD22 B:LEU99 4.0 34.2 1.0 HH12 B:ARG103 4.1 39.6 1.0 CG B:GLU109 4.1 25.4 1.0 ND1 B:HIS48 4.1 23.3 1.0 ND1 B:HIS50 4.2 29.0 1.0 HE21 B:GLN107 4.2 30.6 1.0 O B:HOH417 4.2 27.9 1.0 CG B:HIS48 4.2 22.6 1.0 HG3 B:GLU109 4.2 30.5 1.0 NE2 B:GLN107 4.2 25.5 1.0 CG B:HIS50 4.3 27.1 1.0 HB2 B:GLU109 4.3 27.0 1.0 HD23 B:LEU99 4.4 34.2 1.0 O3 B:PO4303 4.4 33.1 1.0 O B:HOH446 4.5 30.3 1.0 CD2 B:LEU99 4.6 28.5 1.0 NH1 B:ARG103 4.6 33.0 1.0 HH22 B:ARG103 4.6 40.3 1.0 CB B:GLU109 4.8 22.5 1.0 HG2 B:GLU109 4.8 30.5 1.0 HD1 B:HIS48 4.9 27.9 1.0 HD1 B:HIS50 4.9 34.8 1.0 HG B:SER45 5.0 38.0 1.0 HH11 B:ARG103 5.0 39.6 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