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Calcium in PDB 4b31: 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: 4b31 was solved by Y.Yuzugullu, 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) 113.27 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.045, 121.310, 125.589, 90.00, 115.58, 90.00
R / Rfree (%) 15.15 / 20.845

Other elements in 4b31:

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 4b31). 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: 4b31:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4b31

Go back to Calcium Binding Sites List in 4b31
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:Ca1698

b:5.5
occ:0.60
 O A:HOH2473 2.9 30.0 1.0
O A:HOH2194 2.9 13.1 1.0
ND1 A:HIS190 3.2 13.8 1.0
N A:SER192 3.4 11.3 1.0
CD A:ARG178 3.6 8.9 1.0
OG A:SER192 3.6 9.4 1.0
N A:ASP191 3.7 11.8 1.0
CB A:SER192 3.7 9.5 1.0
CB A:HIS190 4.0 12.4 1.0
CB A:ARG178 4.0 7.9 1.0
CG A:ARG178 4.0 8.3 1.0
CG A:HIS190 4.0 13.4 1.0
CB A:ASP191 4.1 14.4 1.0
CA A:SER192 4.2 10.9 1.0
CA A:ASP191 4.2 12.1 1.0
CE1 A:HIS190 4.3 13.3 1.0
C A:ASP191 4.3 11.2 1.0
C A:HIS190 4.3 10.8 1.0
CE1 B:TYR412 4.5 8.3 1.0
O A:HOH2186 4.5 6.1 1.0
O A:HOH2202 4.7 29.2 1.0
CA A:HIS190 4.7 11.8 1.0
NH1 A:ARG178 4.7 10.6 1.0
NE A:ARG178 4.8 9.8 1.0
O A:HOH2193 4.8 20.9 1.0
CA A:ARG178 4.9 8.1 1.0

Calcium binding site 2 out of 5 in 4b31

Go back to Calcium Binding Sites List in 4b31
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
A:Ca1699

b:24.8
occ:0.50
 O A:HOH3002 1.7 36.0 1.0
O A:HOH3001 2.0 28.8 1.0
O A:HOH2315 2.1 14.5 1.0
O A:HOH2314 2.1 30.5 1.0
O B:HOH2270 2.2 10.9 1.0
O D:HOH2171 2.2 29.4 1.0
O C:HOH2176 4.1 26.7 1.0
O B:GLY378 4.1 13.0 1.0
O C:GLY378 4.2 10.8 1.0
O D:HOH2166 4.2 24.3 1.0
O A:HOH2316 4.2 26.8 1.0
O A:GLY378 4.2 14.7 1.0
O A:HOH2317 4.3 26.5 1.0
O D:GLY378 4.3 12.1 1.0
CA B:GLY378 4.5 10.6 1.0
O D:HOH2172 4.6 25.7 1.0
CA D:GLY378 4.7 9.4 1.0
C B:GLY378 4.8 11.6 1.0
O B:HOH2260 4.8 17.9 1.0
CA C:GLY378 4.9 8.7 1.0
C C:GLY378 5.0 10.2 1.0
C D:GLY378 5.0 10.7 1.0

Calcium binding site 3 out of 5 in 4b31

Go back to Calcium Binding Sites List in 4b31
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:Ca1699

b:22.6
occ:1.00
 O B:HOH2384 2.8 14.7 1.0
O A:HOH2359 3.0 22.2 1.0
N B:SER192 3.3 10.3 1.0
ND1 B:HIS190 3.3 10.0 1.0
CD B:ARG178 3.6 8.5 1.0
N B:ASP191 3.6 11.7 1.0
OG B:SER192 3.7 10.9 1.0
CB B:HIS190 3.7 10.8 1.0
CB B:ASP191 3.9 14.4 1.0
CG B:ARG178 3.9 8.3 1.0
CB B:SER192 3.9 10.0 1.0
CG B:HIS190 3.9 9.9 1.0
CA B:ASP191 4.0 12.6 1.0
CB B:ARG178 4.0 8.1 1.0
C B:ASP191 4.1 12.2 1.0
CA B:SER192 4.2 10.2 1.0
C B:HIS190 4.2 11.5 1.0
CE1 B:HIS190 4.4 10.2 1.0
O B:HOH2167 4.6 33.0 1.0
CA B:HIS190 4.6 10.9 1.0
O B:HOH2152 4.6 11.7 1.0
CE1 A:TYR412 4.6 10.4 1.0
NE B:ARG178 4.8 8.4 1.0
NH1 B:ARG178 4.8 9.3 1.0
CG B:ASP191 4.8 18.3 1.0
O B:HOH2166 4.8 26.0 1.0
O B:HOH2157 4.9 15.3 1.0
OD1 B:ASP191 4.9 20.7 1.0
O B:HIS190 4.9 11.9 1.0
CA B:ARG178 4.9 8.4 1.0

Calcium binding site 4 out of 5 in 4b31

Go back to Calcium Binding Sites List in 4b31
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:Ca1698

b:19.4
occ:1.00
 O C:HOH2089 3.0 17.3 1.0
O C:HOH2091 3.1 18.7 1.0
ND1 C:HIS190 3.3 8.2 1.0
N C:SER192 3.4 7.0 1.0
CD C:ARG178 3.6 6.5 1.0
N C:ASP191 3.6 8.1 1.0
OG C:SER192 3.7 6.2 1.0
CB C:HIS190 3.7 7.7 1.0
CB C:ASP191 3.9 10.5 1.0
CB C:SER192 3.9 6.1 1.0
CG C:HIS190 3.9 7.7 1.0
CG C:ARG178 3.9 6.3 1.0
CA C:ASP191 4.1 8.9 1.0
CB C:ARG178 4.1 5.9 1.0
C C:HIS190 4.2 7.4 1.0
C C:ASP191 4.2 7.8 1.0
CA C:SER192 4.3 6.4 1.0
O C:HOH2096 4.3 27.2 1.0
CE1 C:HIS190 4.4 9.0 1.0
O C:HOH2083 4.5 3.5 1.0
CA C:HIS190 4.6 7.2 1.0
CE1 D:TYR412 4.7 5.9 1.0
NE C:ARG178 4.8 6.7 1.0
CG C:ASP191 4.8 13.2 1.0
NH1 C:ARG178 4.8 6.5 1.0
OD1 C:ASP191 4.9 15.2 1.0
CA C:ARG178 4.9 6.0 1.0
O C:HOH2088 4.9 15.9 1.0
O C:HIS190 4.9 7.5 1.0
O C:HOH2095 5.0 22.9 1.0

Calcium binding site 5 out of 5 in 4b31

Go back to Calcium Binding Sites List in 4b31
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:Ca1699

b:22.3
occ:1.00
 O D:HOH2247 2.7 29.0 1.0
O C:HOH2188 3.0 22.0 1.0
ND1 D:HIS190 3.4 9.1 1.0
N D:SER192 3.4 9.9 1.0
CD D:ARG178 3.5 8.4 1.0
N D:ASP191 3.7 9.6 1.0
OG D:SER192 3.7 8.5 1.0
CB D:HIS190 3.8 9.6 1.0
CB D:SER192 3.9 9.0 1.0
CB D:ASP191 4.0 13.7 1.0
CG D:ARG178 4.0 8.2 1.0
CB D:ARG178 4.0 8.4 1.0
CG D:HIS190 4.0 9.0 1.0
CA D:ASP191 4.1 11.2 1.0
CA D:SER192 4.3 9.3 1.0
C D:ASP191 4.3 10.7 1.0
C D:HIS190 4.3 9.6 1.0
CE1 D:HIS190 4.5 9.2 1.0
O D:HOH2087 4.6 11.2 1.0
CE1 C:TYR412 4.6 9.2 1.0
CA D:HIS190 4.7 9.3 1.0
NH1 D:ARG178 4.7 9.0 1.0
NE D:ARG178 4.7 8.7 1.0
OD1 D:ASP191 4.8 18.0 1.0
O D:HOH2093 4.8 22.3 1.0
CG D:ASP191 4.8 16.9 1.0
CA D:ARG178 4.9 8.1 1.0

Reference:

Y.Yuzugullu, C.H.Trinh, L.Fairhurst, Z.B.Ogel, M.J.Mcpherson, A.R.Pearson. Investigating the Active Centre of the Scytalidium Thermophilum Catalase Acta Crystallogr.,Sect.F V. 69 369 2013.
ISSN: ISSN 1744-3091
PubMed: 23545640
DOI: 10.1107/S1744309113004211
Page generated: Sat Jul 13 22:31:59 2024

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