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Calcium in PDB 5y17: Catpo Mutant - E316F

Enzymatic activity of Catpo Mutant - E316F

All present enzymatic activity of Catpo Mutant - E316F:
1.11.1.6;

Protein crystallography data

The structure of Catpo Mutant - E316F, PDB code: 5y17 was solved by Y.Karakus Yuzugullu, G.Goc, S.Balci, A.R.Pearson, B.Yorke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.51 / 2.30
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.733, 120.870, 183.804, 90.00, 101.97, 90.00
R / Rfree (%) 17.8 / 22

Other elements in 5y17:

The structure of Catpo Mutant - E316F also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catpo Mutant - E316F (pdb code 5y17). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Catpo Mutant - E316F, PDB code: 5y17:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5y17

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Calcium binding site 1 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:31.8
occ:1.00
 ND1 A:HIS190 3.1 21.8 1.0
O A:HOH1022 3.2 27.7 1.0
N A:SER192 3.4 23.7 1.0
OG A:SER192 3.5 21.3 1.0
CB A:SER192 3.6 22.1 1.0
CD A:ARG178 3.6 26.8 1.0
N A:ASP191 3.7 25.4 1.0
CB A:HIS190 3.8 22.6 1.0
CG A:ARG178 3.9 27.3 1.0
CG A:HIS190 3.9 21.4 1.0
CB A:ARG178 3.9 25.6 1.0
CA A:SER192 4.1 23.1 1.0
CB A:ASP191 4.1 28.6 1.0
CE1 A:HIS190 4.2 20.9 1.0
CA A:ASP191 4.2 26.4 1.0
C A:HIS190 4.3 25.1 1.0
C A:ASP191 4.3 25.0 1.0
O A:HOH960 4.5 17.0 1.0
CE1 B:TYR412 4.5 25.9 1.0
CA A:HIS190 4.6 24.1 1.0
CA A:ARG178 4.7 24.4 1.0
O A:HOH1014 4.8 35.4 1.0
NE A:ARG178 4.9 26.7 1.0
N A:ARG178 4.9 24.5 1.0
NH1 A:ARG178 5.0 26.3 1.0
O A:HIS190 5.0 26.2 1.0

Calcium binding site 2 out of 10 in 5y17

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Calcium binding site 2 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:41.8
occ:1.00
 O A:HOH815 2.8 31.1 1.0
NH1 B:ARG449 3.3 28.8 1.0
N A:THR437 3.3 27.3 1.0
CD B:ARG449 3.8 30.4 1.0
CB A:THR437 3.8 28.1 1.0
CA A:PHE436 3.9 29.0 1.0
OG1 A:THR437 4.0 27.8 1.0
O B:HOH906 4.1 27.1 1.0
CB A:PHE436 4.1 30.1 1.0
CA A:THR437 4.1 28.1 1.0
C A:PHE436 4.1 28.6 1.0
CG B:ARG449 4.2 31.9 1.0
O A:HOH890 4.3 27.4 1.0
CZ B:ARG449 4.3 28.0 1.0
O A:THR437 4.4 28.2 1.0
NE B:ARG449 4.5 28.6 1.0
CB B:ARG449 4.5 32.8 1.0
O A:HOH871 4.6 21.4 1.0
C A:THR437 4.8 27.9 1.0
CD1 D:LEU49 4.8 29.0 1.0
N B:ARG449 4.9 34.8 1.0

Calcium binding site 3 out of 10 in 5y17

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Calcium binding site 3 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:43.8
occ:1.00
 NH1 A:ARG449 3.2 28.9 1.0
N B:THR437 3.4 28.4 1.0
CD A:ARG449 3.5 30.1 1.0
CG A:ARG449 3.8 31.2 1.0
CB B:THR437 3.9 30.2 1.0
CA B:PHE436 3.9 28.1 1.0
CB B:PHE436 4.1 29.3 1.0
OG1 B:THR437 4.2 31.7 1.0
C B:PHE436 4.2 28.2 1.0
CZ A:ARG449 4.2 28.3 1.0
CA B:THR437 4.2 29.8 1.0
CB A:ARG449 4.2 33.6 1.0
NE A:ARG449 4.3 29.4 1.0
O B:HOH988 4.3 18.3 1.0
O B:THR437 4.6 30.7 1.0
O B:HOH977 4.7 28.6 1.0
N A:ARG449 4.8 33.8 1.0
CD1 C:LEU49 4.8 33.8 1.0
C B:THR437 4.9 31.8 1.0

Calcium binding site 4 out of 10 in 5y17

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Calcium binding site 4 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:55.4
occ:1.00
 O B:HOH818 2.0 23.0 1.0
O A:HOH811 2.3 23.1 1.0
O D:HOH1040 2.4 26.1 1.0
O A:HOH1040 2.5 28.4 1.0
O B:GLY378 4.0 21.5 1.0
O C:GLY378 4.0 28.9 1.0
O D:GLY378 4.2 23.9 1.0
O A:GLY378 4.2 26.5 1.0
CA B:GLY378 4.5 21.2 1.0
C B:GLY378 4.7 22.1 1.0
CA C:GLY378 4.7 24.6 1.0
CA D:GLY378 4.7 23.7 1.0
CA A:GLY378 4.8 25.5 1.0
C C:GLY378 4.8 26.3 1.0
C A:GLY378 4.9 25.9 1.0
C D:GLY378 4.9 24.2 1.0

Calcium binding site 5 out of 10 in 5y17

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Calcium binding site 5 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:29.6
occ:1.00
 O A:HOH1033 3.1 30.7 1.0
ND1 B:HIS190 3.2 20.7 1.0
N B:SER192 3.3 21.3 1.0
OG B:SER192 3.5 20.9 1.0
N B:ASP191 3.6 22.8 1.0
CB B:SER192 3.6 22.1 1.0
CD B:ARG178 3.7 27.8 1.0
CB B:HIS190 3.8 22.4 1.0
CG B:HIS190 3.9 21.2 1.0
CG B:ARG178 3.9 26.8 1.0
CB B:ASP191 4.0 25.6 1.0
CB B:ARG178 4.1 25.2 1.0
CA B:SER192 4.1 21.9 1.0
CA B:ASP191 4.2 22.9 1.0
C B:HIS190 4.2 22.7 1.0
C B:ASP191 4.2 21.8 1.0
CE1 B:HIS190 4.3 19.7 1.0
O B:HOH838 4.5 19.1 1.0
CE1 A:TYR412 4.6 24.4 1.0
CA B:HIS190 4.6 22.8 1.0
OD1 B:ASP191 4.9 29.6 1.0
O B:HOH996 4.9 28.2 1.0
CA B:ARG178 4.9 24.1 1.0
CG B:ASP191 4.9 27.7 1.0
NH1 B:ARG178 4.9 24.1 1.0
NE B:ARG178 4.9 28.3 1.0
O B:HIS190 4.9 21.2 1.0
O B:HOH989 5.0 22.9 1.0

Calcium binding site 6 out of 10 in 5y17

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Calcium binding site 6 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:48.6
occ:1.00
 OG B:SER255 2.8 33.3 1.0
O B:HOH973 3.2 28.6 1.0
CB B:SER255 3.8 32.5 1.0
CA B:GLY213 3.8 27.3 1.0
CD2 B:PHE476 3.8 35.1 1.0
N B:GLY213 4.2 27.8 1.0
CG2 B:VAL539 4.2 49.1 1.0
CE2 B:PHE476 4.3 36.4 1.0
O B:LEU256 4.6 29.9 1.0
CB B:ILE538 4.8 38.0 1.0
NH1 B:ARG689 4.8 39.8 1.0
CG B:GLU473 4.8 42.4 1.0
OE2 B:GLU473 4.8 46.5 1.0
CD1 B:ILE538 4.9 37.2 1.0
CG2 B:ILE538 4.9 38.2 1.0
CG B:PHE476 4.9 34.5 1.0

Calcium binding site 7 out of 10 in 5y17

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Calcium binding site 7 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:40.9
occ:1.00
 ND1 C:HIS190 3.1 31.3 1.0
N C:SER192 3.3 31.4 1.0
OG C:SER192 3.5 27.8 1.0
CB C:SER192 3.6 30.5 1.0
N C:ASP191 3.6 31.0 1.0
CB C:HIS190 3.8 30.8 1.0
CD C:ARG178 3.8 31.6 1.0
CG C:HIS190 3.9 30.7 1.0
CA C:SER192 4.0 32.4 1.0
CB C:ASP191 4.0 33.7 1.0
CG C:ARG178 4.1 31.4 1.0
CA C:ASP191 4.1 33.2 1.0
CB C:ARG178 4.1 30.1 1.0
CE1 C:HIS190 4.2 32.1 1.0
C C:ASP191 4.2 33.5 1.0
C C:HIS190 4.2 32.0 1.0
O C:HOH921 4.4 36.1 1.0
CE1 D:TYR412 4.6 31.9 1.0
CA C:HIS190 4.6 31.4 1.0
CA C:ARG178 4.9 29.5 1.0
O C:HIS190 4.9 31.6 1.0
OD1 C:ASP191 5.0 34.4 1.0
CG C:ASP191 5.0 34.8 1.0

Calcium binding site 8 out of 10 in 5y17

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Calcium binding site 8 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:51.7
occ:1.00
 OG C:SER255 2.8 26.6 1.0
O C:HOH970 3.0 27.3 1.0
O C:HOH911 3.0 28.9 1.0
O C:HOH877 3.3 36.5 1.0
CB C:SER255 3.8 27.3 1.0
CA C:GLY213 3.9 28.0 1.0
CD2 C:PHE476 3.9 36.0 1.0
CG2 C:VAL539 4.1 43.6 1.0
N C:GLY213 4.2 29.2 1.0
CE2 C:PHE476 4.4 35.5 1.0
O C:HOH1002 4.4 26.8 1.0
CG C:GLU473 4.7 36.1 1.0
O C:LEU256 4.7 28.8 1.0
NH1 C:ARG689 4.7 38.7 1.0
OE2 C:GLU473 4.8 37.7 1.0
CB C:ILE538 4.8 39.2 1.0
CG2 C:ILE538 4.8 38.3 1.0
O C:HOH941 4.9 21.4 1.0
CD1 C:ILE538 4.9 40.0 1.0

Calcium binding site 9 out of 10 in 5y17

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Calcium binding site 9 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:38.3
occ:1.00
 O D:HOH1000 2.9 25.6 1.0
ND1 D:HIS190 3.3 30.3 1.0
N D:SER192 3.4 30.2 1.0
CD D:ARG178 3.5 26.9 1.0
OG D:SER192 3.6 29.4 1.0
N D:ASP191 3.7 30.8 1.0
CB D:SER192 3.7 28.8 1.0
CG D:ARG178 3.8 26.7 1.0
CB D:HIS190 3.9 30.6 1.0
CB D:ARG178 4.0 25.8 1.0
CG D:HIS190 4.0 30.1 1.0
CB D:ASP191 4.1 32.9 1.0
CA D:SER192 4.1 29.7 1.0
CA D:ASP191 4.2 31.4 1.0
C D:ASP191 4.3 31.0 1.0
C D:HIS190 4.3 30.6 1.0
CE1 D:HIS190 4.3 30.5 1.0
CE1 C:TYR412 4.5 36.1 1.0
CA D:HIS190 4.7 30.8 1.0
NE D:ARG178 4.7 27.8 1.0
O D:HOH887 4.7 42.2 1.0
CA D:ARG178 4.8 25.4 1.0
NH1 D:ARG178 4.8 27.7 1.0
OD1 D:ASP191 5.0 35.1 1.0

Calcium binding site 10 out of 10 in 5y17

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Calcium binding site 10 out of 10 in the Catpo Mutant - E316F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Catpo Mutant - E316F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:49.0
occ:1.00
 O D:HOH913 2.9 21.7 1.0
OG D:SER255 3.0 31.7 1.0
O D:HOH933 3.5 28.4 1.0
CA D:GLY213 3.7 28.8 1.0
CD2 D:PHE476 3.8 34.1 1.0
CB D:SER255 3.9 29.6 1.0
N D:GLY213 4.1 28.7 1.0
CG2 D:VAL539 4.2 50.9 1.0
CE2 D:PHE476 4.3 33.6 1.0
CG D:GLU473 4.6 40.0 1.0
OE2 D:GLU473 4.6 42.6 1.0
O D:HOH985 4.7 35.3 1.0
CB D:ILE538 4.8 37.8 1.0
CG D:PHE476 4.9 34.0 1.0
O D:LEU256 4.9 28.8 1.0
CD1 D:ILE538 4.9 33.6 1.0
CG2 D:ILE538 4.9 37.6 1.0
NH1 D:ARG689 5.0 37.4 1.0
C D:GLY213 5.0 28.0 1.0

Reference:

Y.Yuzugullu Karakus, G.Goc, S.Balci, B.A.Yorke, C.H.Trinh, M.J.Mcpherson, A.R.Pearson. Identification of the Site of Oxidase Substrate Binding in Scytalidium Thermophilum Catalase. Acta Crystallogr D Struct V. 74 979 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 30289408
DOI: 10.1107/S2059798318010628
Page generated: Mon Jul 15 15:13:12 2024

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