Atomistry » Zinc » PDB 5cqh-5d56 » 5cuo
Atomistry »
  Zinc »
    PDB 5cqh-5d56 »
      5cuo »

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

Enzymatic activity of 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;

Protein crystallography data

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

Zinc Binding Sites:

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 5cuo

Go back to Zinc Binding Sites List in 5cuo
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 5cuo

Go back to Zinc Binding Sites List in 5cuo
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 5cuo

Go back to Zinc Binding Sites List in 5cuo
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 5cuo

Go back to Zinc Binding Sites List in 5cuo
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

Reference:

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
Page generated: Wed Dec 16 06:07:24 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy