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Calcium in PDB 4b5k: 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: 4b5k 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) 28.92 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.392, 122.000, 125.670, 90.00, 115.48, 90.00
R / Rfree (%) 15.298 / 18.041

Other elements in 4b5k:

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 4b5k). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b5k:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4b5k

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Calcium binding site 1 out of 9 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


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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:Ca1699

b:14.4
occ:0.70
O A:HOH2232 3.0 21.1 1.0
O A:HOH2644 3.0 23.1 1.0
ND1 A:HIS190 3.3 14.3 1.0
N A:SER192 3.4 13.1 1.0
OG A:SER192 3.5 14.0 1.0
CD A:ARG178 3.6 14.8 1.0
N A:ASP191 3.8 14.9 1.0
CB A:SER192 3.8 13.3 1.0
CB A:HIS190 3.8 15.2 1.0
CG A:ARG178 4.0 13.8 1.0
CG A:HIS190 4.0 15.7 1.0
CB A:ARG178 4.0 13.2 1.0
CB A:ASP191 4.1 16.8 1.0
CA A:SER192 4.2 12.7 1.0
CA A:ASP191 4.2 15.0 1.0
C A:ASP191 4.3 14.0 1.0
C A:HIS190 4.3 15.3 1.0
CE1 A:HIS190 4.4 12.2 1.0
O A:HOH2226 4.4 14.0 1.0
CE1 B:TYR412 4.5 16.9 1.0
CA A:HIS190 4.7 15.7 1.0
O A:HOH2247 4.7 30.1 1.0
NH1 A:ARG178 4.8 19.1 1.0
NE A:ARG178 4.9 15.8 1.0
CA A:ARG178 4.9 12.8 1.0
O A:HOH2231 5.0 22.2 1.0

Calcium binding site 2 out of 9 in 4b5k

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Calcium binding site 2 out of 9 in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum


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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:Ca1700

b:17.6
occ:0.50
O A:HOH2645 1.9 25.7 1.0
O A:HOH2648 2.0 34.2 1.0
O A:HOH2401 2.1 22.0 1.0
O A:HOH2398 2.1 23.8 1.0
O A:HOH2647 2.1 36.0 1.0
O A:HOH2646 2.2 25.0 1.0
O A:GLY378 4.2 17.7 1.0
O D:GLY378 4.2 18.4 1.0
O B:GLY378 4.2 17.8 1.0
O C:HOH2253 4.3 24.0 1.0
O B:HOH2352 4.3 24.0 1.0
O A:HOH2399 4.3 25.4 1.0
O C:GLY378 4.3 19.0 1.0
O D:HOH2239 4.4 24.9 1.0
O A:HOH2400 4.5 30.9 1.0
O C:HOH2254 4.5 33.5 1.0
O B:HOH2351 4.6 36.8 1.0
O D:HOH2240 4.6 35.3 1.0
CA D:GLY378 4.7 15.2 1.0
CA A:GLY378 4.8 13.9 1.0
CA B:GLY378 4.8 14.6 1.0
CA C:GLY378 4.8 14.4 1.0
C D:GLY378 4.9 15.6 1.0
C A:GLY378 4.9 15.6 1.0
C B:GLY378 4.9 16.1 1.0
C C:GLY378 5.0 17.1 1.0

Calcium binding site 3 out of 9 in 4b5k

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Calcium binding site 3 out of 9 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:15.2
occ:0.70
O A:HOH2447 3.0 20.6 1.0
O B:HOH2563 3.0 24.8 1.0
ND1 B:HIS190 3.3 15.3 1.0
N B:SER192 3.3 15.2 1.0
OG B:SER192 3.6 13.9 1.0
CD B:ARG178 3.6 14.6 1.0
N B:ASP191 3.7 15.2 1.0
CB B:HIS190 3.7 15.3 1.0
CB B:SER192 3.8 13.3 1.0
CG B:HIS190 3.9 14.4 1.0
CB B:ASP191 4.0 16.4 1.0
CG B:ARG178 4.0 14.8 1.0
CB B:ARG178 4.1 13.6 1.0
CA B:ASP191 4.1 15.3 1.0
C B:ASP191 4.2 15.7 1.0
CA B:SER192 4.2 13.2 1.0
C B:HIS190 4.2 15.7 1.0
CE1 B:HIS190 4.4 14.7 1.0
CA B:HIS190 4.6 15.5 1.0
CE1 A:TYR412 4.6 19.6 1.0
O B:HOH2191 4.6 14.4 1.0
O B:HOH2214 4.7 32.0 1.0
NH1 B:ARG178 4.8 18.9 1.0
NE B:ARG178 4.9 16.4 1.0
CG B:ASP191 4.9 19.4 1.0
O B:HIS190 4.9 15.2 1.0
O B:HOH2213 4.9 26.7 1.0
CA B:ARG178 4.9 13.1 1.0
OD1 B:ASP191 5.0 21.3 1.0
O B:HOH2215 5.0 33.8 1.0

Calcium binding site 4 out of 9 in 4b5k

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Calcium binding site 4 out of 9 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
B:Ca1700

b:27.9
occ:0.70
OG B:SER255 2.9 25.0 1.0
O B:HOH2223 3.0 25.0 1.0
O B:HOH2556 3.1 33.6 1.0
O B:HOH2258 3.4 24.8 1.0
CD2 B:PHE476 3.7 23.3 1.0
CA B:GLY213 3.9 16.2 1.0
CB B:SER255 3.9 22.1 1.0
CG2 B:VAL539 4.1 37.7 1.0
CE2 B:PHE476 4.2 23.8 1.0
N B:GLY213 4.3 17.6 1.0
O B:HOH2224 4.4 21.8 1.0
NH1 B:ARG689 4.5 23.3 1.0
OE2 B:GLU473 4.7 34.9 1.0
CG B:GLU473 4.8 30.9 1.0
O B:LEU256 4.8 19.4 1.0
CB B:ILE538 4.8 28.4 1.0
CG2 B:ILE538 4.8 26.9 1.0
CG B:PHE476 4.9 22.1 1.0
CD1 B:ILE538 4.9 29.7 1.0

Calcium binding site 5 out of 9 in 4b5k

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Calcium binding site 5 out of 9 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
B:Ca1701

b:22.9
occ:0.70
O A:HOH2484 2.7 36.6 1.0
O B:HOH2564 3.0 23.1 1.0
O B:HOH2420 3.1 25.4 1.0
N B:THR437 3.2 16.7 1.0
NH1 A:ARG449 3.3 15.0 1.0
CA B:PHE436 3.8 16.4 1.0
CD A:ARG449 3.8 15.3 1.0
CB B:THR437 3.9 17.0 1.0
OG1 B:THR437 4.0 15.9 1.0
C B:PHE436 4.0 15.4 1.0
CB B:PHE436 4.0 15.7 1.0
O B:HOH2414 4.1 19.4 1.0
CA B:THR437 4.1 15.3 1.0
CG A:ARG449 4.2 14.9 1.0
O A:HOH2485 4.3 29.0 1.0
CZ A:ARG449 4.3 14.6 1.0
O B:HOH2417 4.4 24.1 1.0
O B:THR437 4.5 19.0 1.0
CB A:ARG449 4.5 15.5 1.0
NE A:ARG449 4.5 15.0 1.0
O A:HOH2483 4.8 35.9 1.0
C B:THR437 4.8 16.8 1.0
O B:HOH2186 4.9 33.3 1.0
O B:PHE435 4.9 17.2 1.0

Calcium binding site 6 out of 9 in 4b5k

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Calcium binding site 6 out of 9 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 6 of Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1699

b:11.1
occ:0.70
O C:HOH2123 3.0 20.0 1.0
O C:HOH2423 3.0 28.3 1.0
ND1 C:HIS190 3.3 12.5 1.0
N C:SER192 3.3 11.2 1.0
OG C:SER192 3.5 12.0 1.0
CD C:ARG178 3.6 11.4 1.0
N C:ASP191 3.7 11.9 1.0
CB C:SER192 3.8 11.2 1.0
CB C:HIS190 3.9 11.8 1.0
CB C:ARG178 3.9 10.7 1.0
CG C:ARG178 4.0 10.8 1.0
CG C:HIS190 4.0 11.8 1.0
CB C:ASP191 4.1 13.4 1.0
CA C:SER192 4.1 10.8 1.0
CA C:ASP191 4.2 12.2 1.0
C C:ASP191 4.2 11.8 1.0
C C:HIS190 4.3 10.8 1.0
CE1 C:HIS190 4.4 12.2 1.0
CE1 D:TYR412 4.4 13.8 1.0
O C:HOH2115 4.5 14.8 1.0
O C:HOH2137 4.6 26.6 1.0
CA C:HIS190 4.7 11.5 1.0
CA C:ARG178 4.8 10.5 1.0
NE C:ARG178 4.8 12.9 1.0
NH1 C:ARG178 4.9 14.9 1.0

Calcium binding site 7 out of 9 in 4b5k

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Calcium binding site 7 out of 9 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 7 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:21.2
occ:0.70
OG C:SER255 2.9 21.4 1.0
O C:HOH2149 3.0 18.4 1.0
O C:HOH2183 3.3 20.3 1.0
O C:HOH2182 3.3 31.8 1.0
CD2 C:PHE476 3.7 22.1 1.0
CA C:GLY213 3.8 13.5 1.0
CB C:SER255 3.9 17.1 1.0
CE2 C:PHE476 4.1 22.8 1.0
CG2 C:VAL539 4.2 31.8 1.0
N C:GLY213 4.2 12.9 1.0
O C:HOH2148 4.4 16.0 1.0
OE2 C:GLU473 4.7 24.6 1.0
CG C:GLU473 4.7 24.8 1.0
NH1 C:ARG689 4.7 24.1 1.0
CG2 C:ILE538 4.8 20.5 1.0
O C:LEU256 4.8 15.9 1.0
CB C:ILE538 4.8 20.5 1.0
CD1 C:ILE538 4.8 21.3 1.0
CG C:PHE476 4.9 20.5 1.0

Calcium binding site 8 out of 9 in 4b5k

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Calcium binding site 8 out of 9 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 8 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:15.7
occ:0.70
O D:HOH2384 2.8 27.7 1.0
O C:HOH2272 3.0 22.9 1.0
ND1 D:HIS190 3.3 15.2 1.0
N D:SER192 3.4 15.1 1.0
OG D:SER192 3.6 15.4 1.0
N D:ASP191 3.6 15.2 1.0
CD D:ARG178 3.7 16.2 1.0
CB D:HIS190 3.7 15.4 1.0
CB D:SER192 3.9 14.7 1.0
CG D:HIS190 3.9 14.5 1.0
CB D:ASP191 4.0 17.7 1.0
CG D:ARG178 4.0 13.8 1.0
CB D:ARG178 4.1 13.9 1.0
CA D:ASP191 4.1 15.7 1.0
CA D:SER192 4.2 14.7 1.0
C D:ASP191 4.2 16.3 1.0
C D:HIS190 4.3 14.3 1.0
CE1 D:HIS190 4.4 14.2 1.0
O D:HOH2127 4.5 33.0 1.0
CE1 C:TYR412 4.5 19.9 1.0
O D:HOH2114 4.6 18.0 1.0
CA D:HIS190 4.6 15.0 1.0
NH1 D:ARG178 4.8 19.8 1.0
O D:HOH2126 4.9 36.3 1.0
NE D:ARG178 4.9 16.1 1.0
O D:HOH2118 4.9 23.1 1.0
CA D:ARG178 4.9 13.3 1.0
CG D:ASP191 5.0 20.5 1.0
OD1 D:ASP191 5.0 22.2 1.0

Calcium binding site 9 out of 9 in 4b5k

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Calcium binding site 9 out of 9 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 9 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:26.5
occ:0.70
O D:HOH2137 2.9 22.7 1.0
OG D:SER255 3.0 27.4 1.0
O D:HOH2175 3.3 25.8 1.0
CD2 D:PHE476 3.6 25.1 1.0
CA D:GLY213 3.7 16.8 1.0
CB D:SER255 4.0 21.9 1.0
N D:GLY213 4.1 17.1 1.0
CE2 D:PHE476 4.1 27.4 1.0
O D:HOH2136 4.2 22.9 1.0
CG2 D:VAL539 4.2 36.8 1.0
CG D:GLU473 4.3 27.4 1.0
O D:LEU256 4.7 18.6 1.0
CG D:PHE476 4.7 23.2 1.0
OE2 D:GLU473 4.7 30.7 1.0
NH1 D:ARG689 4.7 25.8 1.0
CG2 D:ILE538 4.9 25.3 1.0
CB D:PHE476 4.9 22.0 1.0
CB D:ILE538 5.0 25.6 1.0
CD1 D:ILE538 5.0 26.5 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 Dec 12 04:40:36 2020

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