Calcium in PDB 5zz1: Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum

Enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum

All present enzymatic activity of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum:
1.11.1.6;

Protein crystallography data

The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 5zz1 was solved by Y.Yuzugullu Karakus, C.H.Trinh, A.R.Pearson, Z.B.Ogel, M.J.Mcpherson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.40 / 1.91
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.528, 121.677, 185.454, 90.00, 102.16, 90.00
R / Rfree (%) 14.2 / 17.4

Other elements in 5zz1:

The structure of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum (pdb code 5zz1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 5zz1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 5zz1

Go back to Calcium Binding Sites List in 5zz1
Calcium binding site 1 out of 5 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:19.1
occ:1.00
 ND1 A:HIS190 3.1 11.8 1.0
O B:HOH2114 3.2 20.6 1.0
N A:SER192 3.3 11.4 1.0
OG A:SER192 3.4 11.3 1.0
N A:ASP191 3.7 12.4 1.0
CB A:SER192 3.7 11.1 1.0
CB A:HIS190 3.7 11.9 1.0
CD A:ARG178 3.8 13.0 1.0
CG A:HIS190 3.9 11.6 1.0
CG A:ARG178 4.0 11.9 1.0
CB A:ARG178 4.0 11.0 1.0
CA A:SER192 4.1 11.2 1.0
CE1 A:HIS190 4.2 12.2 1.0
C A:ASP191 4.2 12.3 1.0
CB A:ASP191 4.2 14.9 1.0
CA A:ASP191 4.2 13.2 1.0
C A:HIS190 4.2 11.9 1.0
O A:HOH969 4.5 11.3 1.0
CE1 B:TYR412 4.5 13.7 1.0
CA A:HIS190 4.6 12.0 1.0
CA A:ARG178 4.8 10.3 1.0
O A:HIS190 4.9 11.4 1.0
NE A:ARG178 4.9 13.6 1.0

Calcium binding site 2 out of 5 in 5zz1

Go back to Calcium Binding Sites List in 5zz1
Calcium binding site 2 out of 5 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1701

b:44.1
occ:1.00
 O B:HOH1896 2.0 18.0 1.0
O D:HOH821 2.1 24.8 1.0
O B:HOH2194 2.3 27.9 1.0
O D:HOH1178 2.3 26.5 1.0
O D:GLY378 4.2 22.1 1.0
O B:GLY378 4.2 20.5 1.0
O C:GLY378 4.2 20.9 1.0
O A:GLY378 4.3 22.1 1.0
O C:HOH1092 4.4 20.8 1.0
O A:HOH1005 4.5 25.1 1.0
O D:HOH1028 4.5 23.2 1.0
CA B:GLY378 4.7 16.6 1.0
CA C:GLY378 4.7 16.0 1.0
CA D:GLY378 4.7 17.3 1.0
O B:HOH2191 4.8 25.6 1.0
CA A:GLY378 4.9 16.7 1.0
C C:GLY378 4.9 16.9 1.0
O A:HOH1190 4.9 33.4 1.0
C B:GLY378 4.9 18.3 1.0
C D:GLY378 4.9 18.7 1.0

Calcium binding site 3 out of 5 in 5zz1

Go back to Calcium Binding Sites List in 5zz1
Calcium binding site 3 out of 5 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1705

b:23.2
occ:1.00
 ND1 B:HIS190 3.1 14.3 1.0
O B:HOH2156 3.2 23.0 1.0
N B:SER192 3.2 15.1 1.0
OG B:SER192 3.4 15.1 1.0
CB B:SER192 3.6 14.7 1.0
N B:ASP191 3.7 16.0 1.0
CB B:HIS190 3.8 15.4 1.0
CD B:ARG178 3.8 15.9 1.0
CG B:HIS190 3.9 14.3 1.0
CB B:ARG178 4.0 14.6 1.0
CA B:SER192 4.0 15.1 1.0
CG B:ARG178 4.0 15.2 1.0
CB B:ASP191 4.1 19.2 1.0
C B:ASP191 4.2 15.9 1.0
CA B:ASP191 4.2 17.1 1.0
CE1 B:HIS190 4.2 14.5 1.0
C B:HIS190 4.2 15.4 1.0
O B:HOH2014 4.4 18.1 1.0
CE1 A:TYR412 4.5 20.1 1.0
CA B:HIS190 4.6 15.8 1.0
CA B:ARG178 4.9 13.9 1.0
O B:HIS190 4.9 14.5 1.0
OD1 B:ASP191 5.0 25.5 1.0
O B:HOH2180 5.0 22.2 1.0

Calcium binding site 4 out of 5 in 5zz1

Go back to Calcium Binding Sites List in 5zz1
Calcium binding site 4 out of 5 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:24.8
occ:1.00
 ND1 C:HIS190 3.1 14.0 1.0
O D:HOH995 3.2 24.3 1.0
N C:SER192 3.2 14.6 1.0
OG C:SER192 3.5 14.6 1.0
N C:ASP191 3.7 16.5 1.0
CB C:SER192 3.7 14.4 1.0
CD C:ARG178 3.7 17.8 1.0
CB C:HIS190 3.8 15.6 1.0
CG C:HIS190 3.9 14.8 1.0
CG C:ARG178 4.0 16.5 1.0
CB C:ARG178 4.0 15.8 1.0
CA C:SER192 4.0 14.6 1.0
CB C:ASP191 4.1 18.6 1.0
C C:ASP191 4.1 15.7 1.0
CA C:ASP191 4.2 17.1 1.0
CE1 C:HIS190 4.2 14.5 1.0
C C:HIS190 4.2 16.2 1.0
CE1 D:TYR412 4.5 17.8 1.0
O C:HOH965 4.5 14.1 1.0
CA C:HIS190 4.6 16.2 1.0
O C:HOH835 4.9 34.0 1.0
CA C:ARG178 4.9 14.7 1.0
NE C:ARG178 4.9 18.4 1.0
O C:HIS190 5.0 16.0 1.0

Calcium binding site 5 out of 5 in 5zz1

Go back to Calcium Binding Sites List in 5zz1
Calcium binding site 5 out of 5 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:24.2
occ:1.00
 O C:HOH1088 3.0 23.7 1.0
ND1 D:HIS190 3.2 14.8 1.0
N D:SER192 3.3 16.6 1.0
OG D:SER192 3.5 16.1 1.0
CB D:SER192 3.6 15.8 1.0
N D:ASP191 3.7 17.3 1.0
CD D:ARG178 3.7 16.7 1.0
CB D:HIS190 3.8 15.9 1.0
CG D:HIS190 3.9 14.9 1.0
CG D:ARG178 3.9 15.4 1.0
CB D:ARG178 4.0 14.6 1.0
CA D:SER192 4.0 16.0 1.0
CB D:ASP191 4.1 20.0 1.0
CA D:ASP191 4.2 18.5 1.0
C D:ASP191 4.2 17.4 1.0
C D:HIS190 4.3 16.8 1.0
CE1 D:HIS190 4.3 14.5 1.0
O D:HOH1001 4.4 18.2 1.0
CE1 C:TYR412 4.5 18.4 1.0
CA D:HIS190 4.6 16.1 1.0
NE D:ARG178 4.9 17.4 1.0
CA D:ARG178 4.9 13.6 1.0
O D:HIS190 4.9 15.6 1.0
NH1 D:ARG178 4.9 18.8 1.0
CG D:ASP191 5.0 23.3 1.0

Reference:

Y.Yuzugullu Karakus, G.Goc, S.Balci, B.A.Yorke, C.H.Trinh, M.J.Mcpherson, A.R.Pearson. Identification of the Site of Oxidase Substrate Binding in Scytalidium Thermophilum Catalase. Acta Crystallogr D Struct V. 74 979 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289408
DOI: 10.1107/S2059798318010628
Page generated: Sat Dec 12 05:56:18 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy