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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: Mon Jul 15 15:57:54 2024

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