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Calcium in PDB 4b40: 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: 4b40 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) 29.41 / 1.93
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.726, 121.814, 125.435, 90.00, 115.10, 90.00
R / Rfree (%) 16.576 / 19.929

Other elements in 4b40:

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 4b40). 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: 4b40:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4b40

Go back to Calcium Binding Sites List in 4b40
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:Ca1700

b:17.6
occ:0.70
 O A:HOH2517 2.8 27.4 1.0
O A:HOH2204 3.0 21.4 1.0
ND1 A:HIS190 3.2 18.6 1.0
N A:SER192 3.3 17.0 1.0
CD A:ARG178 3.6 17.6 1.0
OG A:SER192 3.6 16.3 1.0
N A:ASP191 3.7 17.7 1.0
CB A:SER192 3.8 15.9 1.0
CB A:HIS190 3.8 19.2 1.0
CG A:HIS190 4.0 19.2 1.0
CG A:ARG178 4.0 16.3 1.0
CB A:ASP191 4.1 19.7 1.0
CB A:ARG178 4.1 15.7 1.0
CA A:ASP191 4.1 17.9 1.0
CA A:SER192 4.2 16.4 1.0
C A:ASP191 4.2 17.7 1.0
C A:HIS190 4.3 18.6 1.0
CE1 A:HIS190 4.3 18.6 1.0
O A:HOH2195 4.5 14.7 1.0
CE1 B:TYR412 4.5 19.4 1.0
CA A:HIS190 4.6 18.7 1.0
O A:HOH2213 4.7 34.1 1.0
NE A:ARG178 4.8 17.9 1.0
O A:HOH2212 4.9 27.0 1.0
O A:HOH2202 4.9 24.8 1.0
NH1 A:ARG178 4.9 20.4 1.0
CA A:ARG178 5.0 15.2 1.0
O A:HIS190 5.0 19.1 1.0
CG A:ASP191 5.0 22.6 1.0
OD1 A:ASP191 5.0 22.9 1.0

Calcium binding site 2 out of 5 in 4b40

Go back to Calcium Binding Sites List in 4b40
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:Ca1701

b:21.1
occ:0.50
 O A:HOH2521 1.9 34.6 1.0
O A:HOH2518 2.0 25.2 1.0
O A:HOH2335 2.1 24.7 1.0
O A:HOH2336 2.1 24.6 1.0
O A:HOH2520 2.2 33.2 1.0
O A:HOH2519 2.2 29.9 1.0
O B:GLY378 4.2 23.2 1.0
O A:GLY378 4.2 19.7 1.0
O D:GLY378 4.2 23.0 1.0
O B:HOH2322 4.2 42.1 1.0
O C:HOH2220 4.2 34.0 1.0
O C:GLY378 4.3 25.1 1.0
O C:HOH2221 4.3 44.7 1.0
O B:HOH2314 4.3 40.6 1.0
O A:HOH2338 4.3 39.1 1.0
O D:HOH2212 4.4 32.4 1.0
O A:HOH2337 4.5 33.4 1.0
CA B:GLY378 4.7 18.8 1.0
CA D:GLY378 4.7 19.1 1.0
CA C:GLY378 4.8 18.1 1.0
CA A:GLY378 4.8 17.1 1.0
C B:GLY378 4.9 21.0 1.0
C D:GLY378 4.9 20.9 1.0
C A:GLY378 4.9 18.0 1.0

Calcium binding site 3 out of 5 in 4b40

Go back to Calcium Binding Sites List in 4b40
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:Ca1700

b:18.4
occ:0.70
 O B:HOH2485 3.0 29.8 1.0
O A:HOH2381 3.1 19.2 1.0
ND1 B:HIS190 3.2 18.8 1.0
N B:SER192 3.3 18.1 1.0
OG B:SER192 3.5 17.3 1.0
CD B:ARG178 3.7 17.3 1.0
N B:ASP191 3.7 17.8 1.0
CB B:SER192 3.8 15.6 1.0
CB B:HIS190 3.8 18.0 1.0
CG B:ARG178 3.9 16.6 1.0
CG B:HIS190 3.9 18.0 1.0
CB B:ARG178 3.9 15.5 1.0
CB B:ASP191 4.0 20.8 1.0
CA B:SER192 4.1 16.7 1.0
CA B:ASP191 4.2 19.2 1.0
C B:ASP191 4.2 19.2 1.0
C B:HIS190 4.3 18.7 1.0
CE1 B:HIS190 4.3 17.7 1.0
O B:HOH2188 4.5 19.9 1.0
CE1 A:TYR412 4.6 20.0 1.0
CA B:HIS190 4.7 18.3 1.0
CA B:ARG178 4.8 15.4 1.0
NE B:ARG178 4.9 17.3 1.0
NH1 B:ARG178 4.9 18.3 1.0
CG B:ASP191 5.0 23.5 1.0
O B:HIS190 5.0 20.1 1.0

Calcium binding site 4 out of 5 in 4b40

Go back to Calcium Binding Sites List in 4b40
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:Ca1700

b:22.4
occ:1.00
 O C:HOH2349 2.9 36.5 1.0
O C:HOH2115 3.0 22.3 1.0
ND1 C:HIS190 3.3 17.9 1.0
N C:SER192 3.4 15.7 1.0
OG C:SER192 3.6 15.1 1.0
CD C:ARG178 3.7 17.8 1.0
N C:ASP191 3.7 15.7 1.0
CB C:SER192 3.7 15.1 1.0
CB C:HIS190 3.8 16.6 1.0
CG C:HIS190 4.0 17.2 1.0
CG C:ARG178 4.0 16.7 1.0
CB C:ASP191 4.1 18.2 1.0
CB C:ARG178 4.1 15.4 1.0
CA C:ASP191 4.2 16.3 1.0
CA C:SER192 4.2 15.1 1.0
C C:ASP191 4.2 16.0 1.0
C C:HIS190 4.3 15.9 1.0
CE1 C:HIS190 4.4 18.3 1.0
O C:HOH2122 4.5 37.4 1.0
CE1 D:TYR412 4.5 16.9 1.0
O C:HOH2109 4.6 17.3 1.0
CA C:HIS190 4.7 15.9 1.0
CA C:ARG178 4.9 14.0 1.0
NE C:ARG178 4.9 18.8 1.0
NH1 C:ARG178 4.9 20.0 1.0
O C:HIS190 4.9 16.1 1.0
O C:HOH2114 5.0 25.2 1.0
OD1 C:ASP191 5.0 21.7 1.0
CG C:ASP191 5.0 20.0 1.0

Calcium binding site 5 out of 5 in 4b40

Go back to Calcium Binding Sites List in 4b40
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:Ca1700

b:15.8
occ:0.70
 O D:HOH2327 2.8 28.0 1.0
O C:HOH2238 3.0 22.9 1.0
ND1 D:HIS190 3.3 15.7 1.0
N D:SER192 3.3 16.5 1.0
OG D:SER192 3.6 15.6 1.0
N D:ASP191 3.7 16.0 1.0
CD D:ARG178 3.7 18.3 1.0
CB D:HIS190 3.8 15.9 1.0
CB D:SER192 3.8 15.7 1.0
CG D:HIS190 4.0 15.7 1.0
CB D:ASP191 4.0 20.6 1.0
CB D:ARG178 4.0 16.6 1.0
CG D:ARG178 4.1 17.0 1.0
CA D:ASP191 4.1 17.7 1.0
CA D:SER192 4.2 16.3 1.0
C D:ASP191 4.2 17.3 1.0
C D:HIS190 4.3 15.7 1.0
CE1 D:HIS190 4.4 16.6 1.0
CE1 C:TYR412 4.4 18.0 1.0
O D:HOH2116 4.4 34.9 1.0
O D:HOH2108 4.6 19.7 1.0
CA D:HIS190 4.6 16.0 1.0
NH1 D:ARG178 4.8 21.0 1.0
CG D:ASP191 4.9 23.2 1.0
OD1 D:ASP191 4.9 27.2 1.0
NE D:ARG178 4.9 18.8 1.0
CA D:ARG178 4.9 16.1 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 22:32:55 2024

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