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Calcium in PDB 4aum: Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum

Enzymatic activity of Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum

All present enzymatic activity of Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum:
1.11.1.6;

Protein crystallography data

The structure of Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4aum was solved by Y.Yuzugullu, C.H.Trinh, M.A.Smith, A.R.Pearson, S.E.V.Phillips, D.Sutay Kocabas, U.Bakir, 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) 113.00 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 201.420, 121.447, 125.208, 90.00, 115.51, 90.00
R / Rfree (%) 11.812 / 14.55

Other elements in 4aum:

The structure of Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum (pdb code 4aum). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum, PDB code: 4aum:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 4aum

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Calcium binding site 1 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca910

b:11.7
occ:0.50
 O A:HOH2474 2.0 19.4 1.0
O B:HOH2419 2.0 18.5 1.0
O A:HOH2769 2.0 27.0 1.0
O A:HOH2768 2.1 28.1 1.0
O A:HOH2473 2.1 20.4 1.0
O D:HOH2286 2.1 20.7 1.0
O A:GLY378 4.2 16.3 1.0
O B:GLY378 4.2 14.7 1.0
O B:HOH2048 4.2 30.1 1.0
O D:GLY378 4.2 15.7 1.0
O C:GLY378 4.2 15.1 1.0
O C:HOH2308 4.3 20.5 1.0
O A:HOH2475 4.4 20.5 1.0
O D:HOH2287 4.4 19.9 1.0
O B:HOH2420 4.4 18.6 1.0
O A:HOH2476 4.4 24.4 1.0
O A:HOH2044 4.5 31.2 1.0
O B:HOH2418 4.5 25.0 1.0
O C:HOH2309 4.6 25.8 1.0
O D:HOH2288 4.6 26.0 1.0
CA B:GLY378 4.7 9.4 1.0
CA D:GLY378 4.7 9.0 1.0
CA C:GLY378 4.7 9.1 1.0
CA A:GLY378 4.8 9.1 1.0
C B:GLY378 4.9 10.6 1.0
C D:GLY378 4.9 10.4 1.0
C A:GLY378 4.9 10.6 1.0
C C:GLY378 4.9 11.3 1.0

Calcium binding site 2 out of 10 in 4aum

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Calcium binding site 2 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1699

b:10.0
occ:0.80
 O A:HOH2771 3.1 19.5 1.0
ND1 A:HIS190 3.1 7.5 1.0
O A:HOH2272 3.2 15.5 1.0
N A:SER192 3.3 7.9 1.0
OG A:SER192 3.4 7.6 1.0
CB A:SER192 3.7 8.1 1.0
N A:ASP191 3.7 8.6 1.0
CD A:ARG178 3.7 8.0 1.0
CB A:HIS190 3.8 7.7 1.0
CG A:HIS190 3.9 7.1 1.0
CG A:ARG178 4.0 7.8 1.0
CB A:ARG178 4.0 7.4 1.0
CA A:SER192 4.1 7.2 1.0
CB A:ASP191 4.1 10.0 1.0
CA A:ASP191 4.2 8.2 1.0
C A:ASP191 4.2 7.9 1.0
C A:HIS190 4.2 8.6 1.0
CE1 A:HIS190 4.3 7.5 1.0
O A:HOH2261 4.4 9.4 1.0
CE1 B:TYR412 4.5 9.4 1.0
CA A:HIS190 4.6 8.6 1.0
O A:HOH2292 4.8 25.7 1.0
CA A:ARG178 4.9 6.3 1.0
O A:HIS190 4.9 8.6 1.0
NE A:ARG178 5.0 8.0 1.0

Calcium binding site 3 out of 10 in 4aum

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Calcium binding site 3 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1700

b:12.0
occ:0.50
 O A:HOH2772 2.9 18.6 1.0
NH1 B:ARG449 3.1 10.0 1.0
O A:HOH2557 3.2 17.6 1.0
N A:THR437 3.3 9.1 1.0
CD B:ARG449 3.7 9.0 1.0
O B:HOH2502 3.8 26.6 1.0
CA A:PHE436 3.9 8.6 1.0
CB A:THR437 3.9 9.1 1.0
OG1 A:THR437 4.0 10.3 1.0
CB A:PHE436 4.1 9.4 1.0
C A:PHE436 4.1 8.5 1.0
CG B:ARG449 4.1 8.5 1.0
O A:HOH2549 4.1 15.2 1.0
CA A:THR437 4.2 8.8 1.0
CZ B:ARG449 4.2 9.7 1.0
NE B:ARG449 4.4 9.1 1.0
CB B:ARG449 4.4 9.5 1.0
O A:HOH2553 4.5 16.8 1.0
O A:THR437 4.6 10.7 1.0
O B:HOH2501 4.7 25.5 1.0
O A:HOH2253 4.9 24.6 1.0
O A:PHE435 4.9 10.0 1.0
N B:ARG449 4.9 9.6 1.0
C A:THR437 5.0 9.8 1.0

Calcium binding site 4 out of 10 in 4aum

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Calcium binding site 4 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1699

b:9.5
occ:0.70
 O B:HOH2693 3.1 22.9 1.0
O A:HOH2524 3.1 15.5 1.0
ND1 B:HIS190 3.2 8.8 1.0
N B:SER192 3.3 8.6 1.0
OG B:SER192 3.4 8.9 1.0
CB B:SER192 3.7 8.3 1.0
N B:ASP191 3.7 8.9 1.0
CD B:ARG178 3.7 9.2 1.0
CB B:HIS190 3.8 8.4 1.0
CG B:HIS190 3.9 8.1 1.0
CG B:ARG178 4.0 8.4 1.0
CB B:ARG178 4.0 7.9 1.0
CA B:SER192 4.1 8.7 1.0
CB B:ASP191 4.1 11.0 1.0
CA B:ASP191 4.2 8.8 1.0
C B:ASP191 4.2 9.1 1.0
C B:HIS190 4.2 9.5 1.0
CE1 B:HIS190 4.3 8.6 1.0
O B:HOH2228 4.4 10.1 1.0
CE1 A:TYR412 4.5 11.1 1.0
CA B:HIS190 4.6 9.3 1.0
O B:HOH2253 4.7 25.9 1.0
CA B:ARG178 4.9 7.5 1.0
O B:HIS190 4.9 9.5 1.0
NH1 B:ARG178 5.0 13.6 1.0
NE B:ARG178 5.0 10.2 1.0

Calcium binding site 5 out of 10 in 4aum

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Calcium binding site 5 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1700

b:15.6
occ:0.60
 OG B:SER255 3.0 17.0 1.0
O B:HOH2267 3.0 15.1 1.0
O B:HOH2310 3.2 31.5 1.0
O B:HOH2311 3.2 17.1 1.0
CD2 B:PHE476 3.7 16.1 1.0
CA B:GLY213 3.8 9.5 1.0
CB B:SER255 3.8 12.9 1.0
N B:GLY213 4.1 9.2 1.0
CG2 B:VAL539 4.2 28.8 1.0
CE2 B:PHE476 4.2 18.5 1.0
O B:HOH2268 4.4 14.4 1.0
NH1 B:ARG689 4.6 16.1 1.0
OE2 B:GLU473 4.7 21.7 1.0
CG B:GLU473 4.7 21.7 1.0
O B:LEU256 4.8 12.8 1.0
CG2 B:ILE538 4.8 18.3 1.0
CG B:PHE476 4.8 13.2 1.0
CB B:ILE538 4.8 17.2 1.0
CD1 B:ILE538 5.0 18.9 1.0

Calcium binding site 6 out of 10 in 4aum

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Calcium binding site 6 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1701

b:14.0
occ:0.60
 O A:HOH2569 2.7 33.3 1.0
O B:HOH2694 3.0 18.4 1.0
NH1 A:ARG449 3.1 10.7 1.0
O B:HOH2491 3.2 17.9 1.0
N B:THR437 3.3 9.5 1.0
CD A:ARG449 3.7 8.8 1.0
CA B:PHE436 3.8 10.4 1.0
CB B:THR437 3.9 9.7 1.0
O A:HOH2570 4.0 26.5 1.0
OG1 B:THR437 4.0 10.9 1.0
C B:PHE436 4.0 9.8 1.0
CG A:ARG449 4.1 9.1 1.0
CB B:PHE436 4.1 10.3 1.0
CA B:THR437 4.2 9.8 1.0
CZ A:ARG449 4.2 8.9 1.0
O B:HOH2484 4.2 14.4 1.0
NE A:ARG449 4.4 9.6 1.0
CB A:ARG449 4.4 9.5 1.0
O B:HOH2487 4.5 14.7 1.0
O B:THR437 4.6 11.7 1.0
O A:HOH2568 4.8 25.9 1.0
O B:HOH2222 4.9 26.4 1.0
O B:PHE435 4.9 10.4 1.0
C B:THR437 4.9 10.1 1.0
N A:ARG449 4.9 9.1 1.0
CD1 C:LEU49 5.0 8.8 1.0

Calcium binding site 7 out of 10 in 4aum

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Calcium binding site 7 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1698

b:7.4
occ:0.70
 O C:HOH2152 3.1 20.2 1.0
ND1 C:HIS190 3.1 6.5 1.0
O C:HOH2524 3.2 24.5 1.0
N C:SER192 3.2 5.8 1.0
OG C:SER192 3.4 6.9 1.0
CB C:SER192 3.6 6.6 1.0
N C:ASP191 3.7 6.8 1.0
CD C:ARG178 3.7 6.9 1.0
CB C:HIS190 3.8 6.6 1.0
CG C:HIS190 3.9 6.1 1.0
CG C:ARG178 4.0 6.6 1.0
CB C:ARG178 4.0 6.7 1.0
CA C:SER192 4.0 6.2 1.0
CB C:ASP191 4.1 7.8 1.0
C C:ASP191 4.2 6.4 1.0
CA C:ASP191 4.2 6.7 1.0
CE1 C:HIS190 4.2 6.6 1.0
C C:HIS190 4.3 6.7 1.0
O C:HOH2142 4.4 8.9 1.0
CE1 D:TYR412 4.5 9.6 1.0
CA C:HIS190 4.6 6.9 1.0
O C:HOH2169 4.7 23.8 1.0
CA C:ARG178 4.8 6.0 1.0
O C:HIS190 4.9 7.3 1.0
NE C:ARG178 5.0 7.9 1.0
NH1 C:ARG178 5.0 12.2 1.0

Calcium binding site 8 out of 10 in 4aum

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Calcium binding site 8 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1699

b:13.2
occ:0.60
 O C:HOH2189 3.0 13.8 1.0
OG C:SER255 3.0 14.2 1.0
O C:HOH2226 3.2 26.2 1.0
O C:HOH2227 3.3 15.6 1.0
CD2 C:PHE476 3.8 14.1 1.0
CA C:GLY213 3.8 8.4 1.0
CB C:SER255 3.9 11.1 1.0
CG2 C:VAL539 4.0 21.0 1.0
N C:GLY213 4.2 8.2 1.0
CE2 C:PHE476 4.2 17.5 1.0
O C:HOH2188 4.4 12.8 1.0
OE2 C:GLU473 4.7 17.4 1.0
NH1 C:ARG689 4.7 16.6 1.0
CG2 C:ILE538 4.7 14.3 1.0
CB C:ILE538 4.7 13.6 1.0
CG C:GLU473 4.7 17.5 1.0
O C:LEU256 4.8 11.6 1.0
CD1 C:ILE538 4.9 14.9 1.0
CG C:PHE476 4.9 11.9 1.0

Calcium binding site 9 out of 10 in 4aum

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Calcium binding site 9 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1698

b:11.0
occ:0.80
 O D:HOH2473 3.1 23.4 1.0
ND1 D:HIS190 3.2 9.2 1.0
O C:HOH2328 3.2 17.3 1.0
N D:SER192 3.3 7.9 1.0
OG D:SER192 3.4 8.9 1.0
CB D:SER192 3.6 8.4 1.0
N D:ASP191 3.7 9.2 1.0
CD D:ARG178 3.7 10.3 1.0
CB D:HIS190 3.8 9.4 1.0
CG D:HIS190 3.9 8.4 1.0
CG D:ARG178 4.0 8.5 1.0
CB D:ARG178 4.0 8.2 1.0
CA D:SER192 4.0 8.0 1.0
CB D:ASP191 4.1 11.7 1.0
CA D:ASP191 4.1 9.7 1.0
C D:ASP191 4.2 8.4 1.0
C D:HIS190 4.3 9.2 1.0
CE1 D:HIS190 4.3 9.3 1.0
O D:HOH2138 4.4 10.2 1.0
CE1 C:TYR412 4.5 11.6 1.0
CA D:HIS190 4.6 9.6 1.0
O D:HOH2156 4.7 27.3 1.0
CA D:ARG178 4.8 7.4 1.0
O D:HIS190 4.9 9.2 1.0
NE D:ARG178 4.9 10.5 1.0

Calcium binding site 10 out of 10 in 4aum

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Calcium binding site 10 out of 10 in the Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional 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 10 of Crystal Structure, Recombinant Expression and Mutagenesis Studies of the Bifunctional Catalase-Phenol Oxidase From Scytalidium Thermophilum within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1699

b:17.5
occ:0.60
 O D:HOH2168 2.9 16.3 1.0
OG D:SER255 2.9 17.7 1.0
O D:HOH2213 3.2 32.7 1.0
O D:HOH2214 3.3 18.2 1.0
CD2 D:PHE476 3.8 17.6 1.0
CA D:GLY213 3.8 10.2 1.0
CB D:SER255 3.8 14.2 1.0
CG2 D:VAL539 4.1 27.6 1.0
N D:GLY213 4.1 11.3 1.0
CE2 D:PHE476 4.3 19.4 1.0
O D:HOH2167 4.4 14.4 1.0
CG D:GLU473 4.6 23.3 1.0
NH1 D:ARG689 4.7 19.6 1.0
OE2 D:GLU473 4.7 23.1 1.0
O D:LEU256 4.8 13.3 1.0
CG2 D:ILE538 4.8 19.7 1.0
CB D:ILE538 4.8 17.1 1.0
CG D:PHE476 4.9 14.6 1.0
CD1 D:ILE538 4.9 18.6 1.0

Reference:

Y.Yuzugullu, C.H.Trinh, M.A.Smith, A.R.Pearson, S.E.V.Phillips, D.Sutay Kocabas, U.Bakir, Z.B.Ogel, M.J.Mcpherson. Structure, Recombinant Expression and Mutagenesis Studies of the Catalase with Oxidase Activity From Scytalidium Thermophilum Acta Crystallogr.,Sect.D V. 69 398 2013.
ISSN: ISSN 0907-4449
PubMed: 23519415
DOI: 10.1107/S0907444912049001
Page generated: Sat Jul 13 22:19:09 2024

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