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Calcium in PDB 4b7a: 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: 4b7a 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) 113.30 / 1.95
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 200.865, 121.677, 125.528, 90.00, 115.50, 90.00
R / Rfree (%) 15.095 / 18.618

Other elements in 4b7a:

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 4b7a). 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: 4b7a:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4b7a

Go back to Calcium Binding Sites List in 4b7a
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:17.9
occ:0.70
 O A:HOH2199 3.0 41.0 1.0
O A:HOH2192 3.1 22.6 1.0
N A:SER192 3.2 14.6 1.0
ND1 A:HIS190 3.2 14.2 1.0
OG A:SER192 3.5 18.4 1.0
CB A:SER192 3.7 16.6 1.0
N A:ASP191 3.7 16.8 1.0
CD A:ARG178 3.7 17.5 1.0
CB A:HIS190 3.8 16.4 1.0
CG A:HIS190 4.0 16.4 1.0
CG A:ARG178 4.0 15.3 1.0
CB A:ASP191 4.0 19.7 1.0
CA A:SER192 4.0 15.6 1.0
CB A:ARG178 4.0 15.4 1.0
C A:ASP191 4.2 15.7 1.0
CA A:ASP191 4.2 18.8 1.0
C A:HIS190 4.2 18.5 1.0
CE1 A:HIS190 4.4 15.2 1.0
O A:HOH2184 4.5 17.3 1.0
CE1 B:TYR412 4.5 20.7 1.0
CA A:HIS190 4.7 17.2 1.0
O A:HOH2204 4.8 37.9 1.0
O A:HOH2203 4.9 40.0 1.0
O A:HIS190 4.9 16.9 1.0
NE A:ARG178 4.9 19.5 1.0
CA A:ARG178 4.9 14.6 1.0
O A:HOH2191 4.9 26.8 1.0
NH1 A:ARG178 5.0 23.9 1.0

Calcium binding site 2 out of 5 in 4b7a

Go back to Calcium Binding Sites List in 4b7a
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:28.2
occ:0.50
 O B:HOH2293 2.1 26.9 1.0
O A:HOH2321 2.1 21.9 1.0
O A:HOH2489 2.2 44.7 1.0
O D:HOH2202 2.2 31.9 1.0
O A:HOH2488 2.2 32.6 1.0
O B:GLY378 4.1 25.1 1.0
O C:GLY378 4.3 24.7 1.0
O D:HOH2204 4.3 30.1 1.0
O D:GLY378 4.4 24.5 1.0
O C:HOH2199 4.4 27.8 1.0
O B:HOH2292 4.4 45.2 1.0
O A:GLY378 4.4 24.3 1.0
O B:HOH2291 4.5 29.3 1.0
O C:HOH2200 4.5 34.8 1.0
O A:HOH2322 4.6 31.0 1.0
O A:HOH2323 4.6 29.0 1.0
CA C:GLY378 4.7 18.6 1.0
CA B:GLY378 4.8 19.6 1.0
O D:HOH2203 4.8 31.1 1.0
CA D:GLY378 4.9 18.8 1.0
C B:GLY378 4.9 21.7 1.0
C C:GLY378 4.9 23.1 1.0
CA A:GLY378 4.9 18.9 1.0

Calcium binding site 3 out of 5 in 4b7a

Go back to Calcium Binding Sites List in 4b7a
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:Ca1701

b:16.6
occ:0.70
 O A:HOH2365 3.0 28.6 1.0
O B:HOH2437 3.1 32.5 1.0
N B:SER192 3.2 16.1 1.0
ND1 B:HIS190 3.3 15.8 1.0
OG B:SER192 3.4 17.7 1.0
CD B:ARG178 3.7 16.0 1.0
N B:ASP191 3.7 16.3 1.0
CB B:SER192 3.7 15.4 1.0
CB B:HIS190 3.8 19.7 1.0
CG B:ARG178 3.9 15.7 1.0
CG B:HIS190 4.0 14.7 1.0
CB B:ASP191 4.0 21.8 1.0
CB B:ARG178 4.0 15.2 1.0
CA B:SER192 4.1 15.0 1.0
CA B:ASP191 4.1 18.4 1.0
C B:ASP191 4.1 17.2 1.0
C B:HIS190 4.2 16.4 1.0
CE1 B:HIS190 4.4 14.5 1.0
O B:HOH2164 4.5 19.9 1.0
CE1 A:TYR412 4.5 19.1 1.0
CA B:HIS190 4.6 14.4 1.0
O B:HOH2177 4.7 37.7 1.0
NH1 B:ARG178 4.9 18.9 1.0
O B:HIS190 4.9 16.4 1.0
NE B:ARG178 4.9 17.8 1.0
CA B:ARG178 4.9 14.9 1.0
O B:HOH2179 4.9 38.4 1.0
O B:HOH2178 5.0 38.8 1.0

Calcium binding site 4 out of 5 in 4b7a

Go back to Calcium Binding Sites List in 4b7a
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:15.3
occ:0.70
 O C:HOH2103 2.8 35.4 1.0
O C:HOH2100 3.0 21.3 1.0
ND1 C:HIS190 3.3 13.2 1.0
N C:SER192 3.4 12.7 1.0
OG C:SER192 3.6 14.4 1.0
CD C:ARG178 3.6 13.8 1.0
N C:ASP191 3.7 14.2 1.0
CB C:HIS190 3.8 13.7 1.0
CB C:SER192 3.9 12.6 1.0
CG C:HIS190 3.9 13.5 1.0
CG C:ARG178 4.0 12.9 1.0
CB C:ARG178 4.0 11.5 1.0
CB C:ASP191 4.1 18.4 1.0
CA C:ASP191 4.2 15.1 1.0
CA C:SER192 4.2 12.6 1.0
C C:HIS190 4.2 13.0 1.0
C C:ASP191 4.2 13.7 1.0
CE1 C:HIS190 4.4 14.8 1.0
CE1 D:TYR412 4.5 13.2 1.0
O C:HOH2109 4.5 44.0 1.0
CA C:HIS190 4.6 12.9 1.0
O C:HOH2093 4.7 14.0 1.0
O C:HOH2099 4.8 23.7 1.0
NE C:ARG178 4.9 15.6 1.0
NH1 C:ARG178 4.9 18.1 1.0
CG C:ASP191 4.9 22.8 1.0
CA C:ARG178 4.9 11.4 1.0
OD1 C:ASP191 4.9 25.7 1.0
O C:HOH2108 4.9 41.5 1.0
O C:HIS190 5.0 12.1 1.0

Calcium binding site 5 out of 5 in 4b7a

Go back to Calcium Binding Sites List in 4b7a
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:16.9
occ:0.70
 O D:HOH2296 2.8 37.6 1.0
O C:HOH2214 3.1 27.3 1.0
N D:SER192 3.3 14.9 1.0
ND1 D:HIS190 3.5 15.5 1.0
OG D:SER192 3.6 16.2 1.0
CD D:ARG178 3.6 16.7 1.0
N D:ASP191 3.7 14.4 1.0
CB D:SER192 3.8 15.1 1.0
CB D:ASP191 3.9 19.6 1.0
CB D:HIS190 3.9 15.7 1.0
CB D:ARG178 4.0 15.1 1.0
CG D:ARG178 4.0 14.8 1.0
CA D:ASP191 4.1 16.2 1.0
CG D:HIS190 4.2 14.6 1.0
CA D:SER192 4.2 15.2 1.0
C D:ASP191 4.2 15.7 1.0
C D:HIS190 4.3 14.8 1.0
CE1 C:TYR412 4.4 18.8 1.0
O D:HOH2111 4.4 33.0 1.0
CE1 D:HIS190 4.6 15.8 1.0
O D:HOH2105 4.7 19.7 1.0
NH1 D:ARG178 4.7 20.6 1.0
CA D:HIS190 4.7 15.5 1.0
CG D:ASP191 4.8 24.5 1.0
NE D:ARG178 4.9 17.1 1.0
O D:HOH2110 4.9 32.3 1.0
OD1 D:ASP191 4.9 26.1 1.0
OH C:TYR412 4.9 22.4 1.0
CA D:ARG178 5.0 14.4 1.0
NZ D:LYS489 5.0 25.8 0.5

Reference:

Y.Yuzugullu, C.H.Trinh, A.R.Pearson, Z.B.Ogel, M.J.Mcpherson. Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum To Be Published.
Page generated: Sat Jul 13 22:36:10 2024

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