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Calcium in PDB 4b2y: 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: 4b2y 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) 29.01 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.323, 121.205, 124.965, 90.00, 115.54, 90.00
R / Rfree (%) 15 / 18.1

Other elements in 4b2y:

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 4b2y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Probing the Active Center of Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4b2y:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4b2y

Go back to Calcium Binding Sites List in 4b2y
Calcium binding site 1 out of 6 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:Ca1699

b:21.2
occ:1.00
 O A:HOH2222 3.0 17.7 1.0
O A:HOH2582 3.0 26.4 1.0
ND1 A:HIS190 3.2 13.1 1.0
N A:SER192 3.3 12.7 1.0
OG A:SER192 3.6 12.7 1.0
CB A:SER192 3.7 12.4 1.0
CD A:ARG178 3.7 13.2 1.0
N A:ASP191 3.8 13.1 1.0
CB A:HIS190 3.8 13.3 1.0
CG A:HIS190 3.9 13.1 1.0
CG A:ARG178 4.0 12.1 1.0
CB A:ARG178 4.0 11.4 1.0
CA A:SER192 4.1 12.7 1.0
CB A:ASP191 4.1 14.8 1.0
CA A:ASP191 4.2 13.8 1.0
C A:ASP191 4.2 13.2 1.0
C A:HIS190 4.2 13.2 1.0
CE1 A:HIS190 4.3 13.4 1.0
O A:HOH2215 4.4 12.2 1.0
CE1 B:TYR412 4.6 14.3 1.0
CA A:HIS190 4.6 13.5 1.0
O A:HOH2240 4.8 28.5 1.0
NH1 A:ARG178 4.9 15.8 1.0
CA A:ARG178 4.9 11.3 1.0
O A:HIS190 4.9 13.0 1.0
NE A:ARG178 4.9 13.9 1.0

Calcium binding site 2 out of 6 in 4b2y

Go back to Calcium Binding Sites List in 4b2y
Calcium binding site 2 out of 6 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:Ca1700

b:22.4
occ:0.50
 O A:HOH2585 2.0 32.9 1.0
O B:HOH2334 2.1 20.3 1.0
O A:HOH2584 2.1 35.1 1.0
O A:HOH2583 2.1 29.9 1.0
O A:HOH2378 2.1 18.0 1.0
O A:HOH2377 2.1 29.5 1.0
O B:HOH2333 4.0 41.3 1.0
O A:HOH2379 4.2 39.2 1.0
O C:GLY378 4.2 17.7 1.0
O B:GLY378 4.2 19.8 1.0
O A:GLY378 4.3 20.0 1.0
O A:HOH2038 4.3 40.5 1.0
O D:GLY378 4.3 18.1 1.0
O C:HOH2240 4.3 23.7 1.0
O B:HOH2332 4.4 28.8 1.0
O D:HOH2217 4.4 22.9 1.0
O A:HOH2380 4.5 21.9 1.0
O B:HOH2322 4.6 35.8 1.0
CA B:GLY378 4.7 16.2 1.0
O D:HOH2212 4.7 37.0 1.0
CA C:GLY378 4.8 14.9 1.0
CA D:GLY378 4.8 14.8 1.0
CA A:GLY378 4.9 15.3 1.0
C B:GLY378 4.9 17.9 1.0
C C:GLY378 4.9 16.3 1.0

Calcium binding site 3 out of 6 in 4b2y

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Calcium binding site 3 out of 6 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:9.8
occ:0.60
 O A:HOH2425 3.0 21.4 1.0
O B:HOH2515 3.2 24.4 1.0
CD B:ARG178 3.4 13.7 1.0
ND1 B:HIS190 3.4 13.4 1.0
N B:SER192 3.5 13.6 1.0
OG B:SER192 3.5 13.0 1.0
CG B:ARG178 3.6 13.6 1.0
CB B:ARG178 3.6 12.2 1.0
CB B:SER192 3.8 13.1 1.0
CB B:HIS190 4.0 13.4 1.0
N B:ASP191 4.0 14.6 1.0
CG B:HIS190 4.1 13.1 1.0
CA B:SER192 4.3 12.9 1.0
CB B:ASP191 4.3 17.3 1.0
O B:HOH2191 4.3 15.8 1.0
CE1 A:TYR412 4.4 18.4 1.0
CE1 B:HIS190 4.4 13.5 1.0
CA B:ASP191 4.4 15.3 1.0
C B:ASP191 4.4 15.0 1.0
CA B:ARG178 4.5 12.1 1.0
C B:HIS190 4.6 14.7 1.0
NE B:ARG178 4.6 14.6 1.0
NH1 B:ARG178 4.7 17.0 1.0
N B:ARG178 4.8 11.8 1.0
O B:HOH2195 4.8 20.5 1.0
O B:HOH2208 4.9 36.6 1.0
CA B:HIS190 4.9 14.5 1.0
O B:ILE183 5.0 11.6 1.0

Calcium binding site 4 out of 6 in 4b2y

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Calcium binding site 4 out of 6 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:Ca1699

b:18.6
occ:1.00
 O C:HOH2124 3.0 19.7 1.0
O C:HOH2128 3.0 27.4 1.0
ND1 C:HIS190 3.2 11.3 1.0
N C:SER192 3.3 11.9 1.0
OG C:SER192 3.5 12.1 1.0
N C:ASP191 3.7 11.7 1.0
CD C:ARG178 3.7 12.8 1.0
CB C:SER192 3.7 12.0 1.0
CB C:HIS190 3.8 11.6 1.0
CG C:HIS190 3.9 11.1 1.0
CB C:ARG178 4.0 11.1 1.0
CB C:ASP191 4.0 14.2 1.0
CG C:ARG178 4.1 12.3 1.0
CA C:SER192 4.1 11.3 1.0
CA C:ASP191 4.2 13.2 1.0
C C:ASP191 4.2 12.4 1.0
C C:HIS190 4.3 11.6 1.0
CE1 C:HIS190 4.3 11.5 1.0
O C:HOH2118 4.5 12.0 1.0
CE1 D:TYR412 4.5 13.9 1.0
CA C:HIS190 4.7 11.3 1.0
NZ C:LYS489 4.8 24.3 1.0
CA C:ARG178 4.9 10.8 1.0
NE C:ARG178 4.9 13.1 1.0
NH1 C:ARG178 4.9 14.3 1.0
CG C:ASP191 5.0 16.7 1.0
O C:HIS190 5.0 10.7 1.0
OD1 C:ASP191 5.0 18.5 1.0

Calcium binding site 5 out of 6 in 4b2y

Go back to Calcium Binding Sites List in 4b2y
Calcium binding site 5 out of 6 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
C:Ca1700

b:16.8
occ:0.60
 OG C:SER255 2.9 15.1 1.0
O C:HOH2142 3.0 18.7 1.0
O C:HOH2176 3.2 17.9 1.0
O C:HOH2175 3.3 28.7 1.0
CD2 C:PHE476 3.7 16.7 1.0
CA C:GLY213 3.8 12.4 1.0
CB C:SER255 3.9 13.7 1.0
CE2 C:PHE476 4.1 17.2 1.0
CG2 C:VAL539 4.2 31.0 1.0
N C:GLY213 4.2 12.0 1.0
CG C:GLU473 4.3 22.5 1.0
O C:HOH2143 4.5 16.5 1.0
NH1 C:ARG689 4.6 20.2 1.0
OE2 C:GLU473 4.7 23.8 1.0
O C:LEU256 4.8 14.5 1.0
CG C:PHE476 4.9 16.3 1.0
CG2 C:ILE538 4.9 19.4 1.0
CB C:ILE538 4.9 20.3 1.0
CD1 C:ILE538 5.0 21.1 1.0

Calcium binding site 6 out of 6 in 4b2y

Go back to Calcium Binding Sites List in 4b2y
Calcium binding site 6 out of 6 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
D:Ca1699

b:7.9
occ:0.60
 O D:HOH2334 3.0 22.3 1.0
O C:HOH2256 3.2 19.6 1.0
ND1 D:HIS190 3.2 12.4 1.0
N D:SER192 3.3 12.8 1.0
OG D:SER192 3.5 12.8 1.0
CB D:SER192 3.7 12.8 1.0
N D:ASP191 3.7 12.6 1.0
CD D:ARG178 3.7 12.8 1.0
CB D:HIS190 3.8 12.4 1.0
CG D:ARG178 3.9 12.5 1.0
CB D:ARG178 3.9 12.3 1.0
CG D:HIS190 3.9 11.7 1.0
CA D:SER192 4.1 13.3 1.0
CB D:ASP191 4.1 14.4 1.0
CA D:ASP191 4.1 13.5 1.0
C D:ASP191 4.2 13.5 1.0
C D:HIS190 4.2 12.8 1.0
CE1 D:HIS190 4.3 12.0 1.0
O D:HOH2114 4.4 16.7 1.0
CE1 C:TYR412 4.5 13.9 1.0
CA D:HIS190 4.6 12.6 1.0
CA D:ARG178 4.8 12.2 1.0
O D:HIS190 4.9 12.2 1.0
NE D:ARG178 5.0 13.2 1.0
NH1 D:ARG178 5.0 14.9 1.0
CG D:ASP191 5.0 16.0 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: ESSN 1744-3091
PubMed: 23545640
DOI: 10.1107/S1744309113004211
Page generated: Sat Jul 13 22:31:58 2024

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