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Calcium in PDB 5xvz: Catpo Mutant - H246W

Enzymatic activity of Catpo Mutant - H246W

All present enzymatic activity of Catpo Mutant - H246W:
1.11.1.6;

Protein crystallography data

The structure of Catpo Mutant - H246W, PDB code: 5xvz was solved by Y.Yuzugullu Karakus, 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) 100.69 / 1.90
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.338, 120.785, 185.200, 90.00, 102.06, 90.00
R / Rfree (%) 15.8 / 18.7

Other elements in 5xvz:

The structure of Catpo Mutant - H246W also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catpo Mutant - H246W (pdb code 5xvz). 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 - H246W, PDB code: 5xvz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5xvz

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Calcium binding site 1 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:25.9
occ:1.00
 O A:HOH1223 3.1 36.7 1.0
O A:HOH1172 3.2 21.6 1.0
ND1 A:HIS190 3.2 16.1 1.0
N A:SER192 3.3 16.4 1.0
OG A:SER192 3.4 16.6 1.0
CB A:SER192 3.6 16.1 1.0
N A:ASP191 3.6 17.3 1.0
CD A:ARG178 3.7 16.7 1.0
CB A:HIS190 3.8 17.7 1.0
CG A:ARG178 3.9 16.1 1.0
CB A:ARG178 3.9 16.3 1.0
CG A:HIS190 3.9 16.1 1.0
CA A:SER192 4.0 16.2 1.0
CB A:ASP191 4.1 20.6 1.0
CA A:ASP191 4.2 18.6 1.0
C A:ASP191 4.2 18.1 1.0
C A:HIS190 4.2 17.1 1.0
CE1 A:HIS190 4.3 16.9 1.0
O A:HOH949 4.4 15.0 1.0
CE1 B:TYR412 4.6 19.5 1.0
CA A:HIS190 4.6 16.6 1.0
NZ A:LYS489 4.8 38.7 1.0
CA A:ARG178 4.8 16.1 1.0
NE A:ARG178 4.9 16.7 1.0
O A:HIS190 5.0 16.3 1.0
CG A:ASP191 5.0 23.2 1.0

Calcium binding site 2 out of 10 in 5xvz

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Calcium binding site 2 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:42.2
occ:1.00
 O A:HOH1233 3.0 31.3 1.0
NH1 B:ARG449 3.1 21.8 1.0
O A:HOH951 3.2 22.3 1.0
N A:THR437 3.3 22.8 1.0
CA A:PHE436 3.8 23.2 1.0
CD B:ARG449 3.8 23.4 1.0
CB A:THR437 3.9 24.4 1.0
O B:HOH1000 3.9 31.9 1.0
OG1 A:THR437 3.9 24.8 1.0
CB A:PHE436 4.0 22.6 1.0
C A:PHE436 4.0 22.5 1.0
CG B:ARG449 4.2 23.6 1.0
CA A:THR437 4.2 23.9 1.0
O A:HOH1125 4.2 21.4 1.0
CZ B:ARG449 4.2 23.0 1.0
CB B:ARG449 4.4 23.8 1.0
NE B:ARG449 4.5 22.0 1.0
O A:HOH893 4.6 23.4 1.0
O A:THR437 4.6 23.5 1.0
O B:HOH1133 4.8 38.1 1.0
O A:PHE435 4.9 24.6 1.0
C A:THR437 4.9 24.2 1.0
N B:ARG449 5.0 23.7 1.0

Calcium binding site 3 out of 10 in 5xvz

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Calcium binding site 3 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:39.2
occ:1.00
 O B:HOH1233 3.1 23.6 1.0
NH1 A:ARG449 3.2 21.4 1.0
N B:THR437 3.2 19.4 1.0
O B:HOH850 3.3 23.4 1.0
CD A:ARG449 3.7 20.5 1.0
CA B:PHE436 3.7 18.9 1.0
CB B:THR437 3.8 22.0 1.0
O A:HOH1138 3.9 33.8 1.0
OG1 B:THR437 3.9 23.7 1.0
C B:PHE436 4.0 19.1 1.0
CB B:PHE436 4.0 18.2 1.0
CA B:THR437 4.1 21.0 1.0
CG A:ARG449 4.2 20.9 1.0
CZ A:ARG449 4.3 21.3 1.0
O B:HOH1156 4.3 17.2 1.0
NE A:ARG449 4.4 20.4 1.0
O B:THR437 4.6 20.6 1.0
CB A:ARG449 4.6 22.0 1.0
O A:HOH1087 4.8 35.6 1.0
O B:HOH811 4.9 20.3 1.0
C B:THR437 4.9 21.3 1.0
O A:HOH1238 4.9 24.7 1.0
O B:HOH860 4.9 21.7 1.0
O B:PHE435 4.9 19.7 1.0

Calcium binding site 4 out of 10 in 5xvz

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Calcium binding site 4 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:27.5
occ:1.00
 O B:HOH1218 3.0 31.4 1.0
O B:HOH1192 3.1 22.5 1.0
ND1 B:HIS190 3.2 16.4 1.0
N B:SER192 3.3 19.4 1.0
OG B:SER192 3.4 18.2 1.0
CB B:SER192 3.6 18.9 1.0
N B:ASP191 3.6 19.8 1.0
CD B:ARG178 3.7 18.8 1.0
CB B:HIS190 3.8 18.5 1.0
CB B:ARG178 3.9 19.0 1.0
CG B:HIS190 4.0 17.1 1.0
CG B:ARG178 4.0 18.5 1.0
CB B:ASP191 4.0 23.4 1.0
CA B:SER192 4.0 19.0 1.0
CA B:ASP191 4.1 21.3 1.0
C B:ASP191 4.2 20.2 1.0
C B:HIS190 4.2 19.0 1.0
CE1 B:HIS190 4.3 16.4 1.0
O B:HOH990 4.4 18.9 1.0
CE1 A:TYR412 4.5 23.6 1.0
CA B:HIS190 4.6 18.7 1.0
NZ B:LYS489 4.7 44.1 1.0
CA B:ARG178 4.9 18.2 1.0
NE B:ARG178 4.9 19.1 1.0
O B:HIS190 4.9 19.2 1.0
CG B:ASP191 4.9 27.9 1.0
NH1 B:ARG178 5.0 19.7 1.0

Calcium binding site 5 out of 10 in 5xvz

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Calcium binding site 5 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:45.4
occ:1.00
 O B:HOH1117 2.8 24.6 1.0
OG B:SER255 3.1 32.5 1.0
O B:HOH1111 3.2 28.4 1.0
CA B:GLY213 3.7 21.3 1.0
CD2 B:PHE476 3.7 28.8 1.0
CB B:SER255 3.9 28.8 1.0
N B:GLY213 4.0 21.4 1.0
O B:HOH1087 4.1 24.2 1.0
CE2 B:PHE476 4.2 30.1 1.0
CG2 B:VAL539 4.5 51.5 1.0
CG B:GLU473 4.5 32.9 1.0
OE2 B:GLU473 4.7 32.5 1.0
O B:LEU256 4.7 23.8 1.0
NH1 B:ARG689 4.8 35.0 1.0
CG B:PHE476 4.8 26.9 1.0
CD1 B:ILE538 4.8 34.0 1.0
C B:GLY213 4.9 21.5 1.0
CB B:ILE538 4.9 33.5 1.0
CB B:PHE476 5.0 26.0 1.0
O B:HOH944 5.0 32.4 1.0

Calcium binding site 6 out of 10 in 5xvz

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Calcium binding site 6 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:52.8
occ:1.00
 O C:HOH861 2.0 27.6 1.0
O C:HOH1270 2.0 37.9 1.0
O D:HOH866 2.2 25.9 1.0
O C:HOH1244 2.3 31.4 1.0
O B:HOH1256 2.5 41.5 1.0
O B:HOH1227 2.6 30.6 1.0
O D:HOH1066 4.0 42.0 1.0
O C:HOH1200 4.0 35.8 1.0
O C:GLY378 4.1 24.1 1.0
O B:GLY378 4.1 23.4 1.0
O D:GLY378 4.2 24.5 1.0
O A:GLY378 4.3 23.5 1.0
O B:HOH1080 4.4 29.2 1.0
O C:HOH1180 4.4 33.9 1.0
O D:HOH987 4.5 31.7 1.0
O B:HOH1178 4.6 38.7 1.0
CA D:GLY378 4.7 21.0 1.0
CA B:GLY378 4.7 19.7 1.0
CA C:GLY378 4.7 20.8 1.0
C C:GLY378 4.8 22.2 1.0
C B:GLY378 4.8 21.9 1.0
CA A:GLY378 4.9 19.7 1.0
C D:GLY378 4.9 22.9 1.0

Calcium binding site 7 out of 10 in 5xvz

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Calcium binding site 7 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:31.3
occ:1.00
 O D:HOH1165 3.0 27.9 1.0
N C:SER192 3.2 20.8 1.0
ND1 C:HIS190 3.2 19.6 1.0
OG C:SER192 3.5 19.4 1.0
CB C:SER192 3.6 19.9 1.0
N C:ASP191 3.7 21.6 1.0
CB C:HIS190 3.8 21.0 1.0
CD C:ARG178 3.8 21.1 1.0
CG C:HIS190 3.9 19.9 1.0
CA C:SER192 4.0 20.1 1.0
CB C:ASP191 4.0 22.9 1.0
CB C:ARG178 4.0 19.3 1.0
CG C:ARG178 4.0 19.6 1.0
C C:ASP191 4.1 21.7 1.0
CA C:ASP191 4.1 22.0 1.0
C C:HIS190 4.2 21.5 1.0
CE1 C:HIS190 4.3 19.7 1.0
CE1 D:TYR412 4.6 21.6 1.0
O C:HOH1032 4.6 20.1 1.0
CA C:HIS190 4.6 21.2 1.0
NZ C:LYS489 4.8 39.7 1.0
CG C:ASP191 4.9 24.8 1.0
CA C:ARG178 4.9 18.9 1.0
O C:HIS190 4.9 20.4 1.0
NE C:ARG178 4.9 21.2 1.0
O C:HOH903 5.0 35.2 1.0
OD1 C:ASP191 5.0 25.5 1.0
NH1 C:ARG178 5.0 22.6 1.0

Calcium binding site 8 out of 10 in 5xvz

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Calcium binding site 8 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:41.2
occ:1.00
 O C:HOH1169 2.9 24.4 1.0
OG C:SER255 3.0 24.2 1.0
O C:HOH1107 3.3 24.1 1.0
O C:HOH1056 3.4 36.7 1.0
CD2 C:PHE476 3.8 25.3 1.0
CA C:GLY213 3.8 20.1 1.0
CB C:SER255 3.9 22.3 1.0
N C:GLY213 4.2 20.4 1.0
O C:HOH1106 4.2 26.8 1.0
CE2 C:PHE476 4.3 26.3 1.0
CG2 C:VAL539 4.3 43.9 1.0
CG C:GLU473 4.5 33.9 1.0
OE2 C:GLU473 4.6 33.6 1.0
CB C:ILE538 4.7 28.4 1.0
NH1 C:ARG689 4.8 31.2 1.0
CD1 C:ILE538 4.8 30.1 1.0
CG2 C:ILE538 4.8 27.7 1.0
O C:LEU256 4.9 22.7 1.0
CG C:PHE476 4.9 25.3 1.0

Calcium binding site 9 out of 10 in 5xvz

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Calcium binding site 9 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:28.4
occ:1.00
 O D:HOH1140 2.9 26.8 1.0
O D:HOH1203 3.0 31.0 1.0
N D:SER192 3.3 20.6 1.0
ND1 D:HIS190 3.3 19.0 1.0
OG D:SER192 3.5 18.1 1.0
CB D:SER192 3.6 18.4 1.0
CD D:ARG178 3.7 21.0 1.0
N D:ASP191 3.7 21.3 1.0
CB D:HIS190 3.8 20.2 1.0
CG D:ARG178 3.9 20.4 1.0
CG D:HIS190 4.0 18.6 1.0
CB D:ARG178 4.0 19.6 1.0
CA D:SER192 4.0 19.0 1.0
CB D:ASP191 4.1 23.4 1.0
CA D:ASP191 4.2 22.1 1.0
C D:ASP191 4.2 21.2 1.0
C D:HIS190 4.2 21.1 1.0
CE1 D:HIS190 4.4 18.0 1.0
CE1 C:TYR412 4.6 23.4 1.0
CA D:HIS190 4.6 20.4 1.0
O D:HOH1102 4.6 20.5 1.0
NZ D:LYS489 4.7 45.4 1.0
NE D:ARG178 4.8 22.5 1.0
NH1 D:ARG178 4.9 24.2 1.0
CA D:ARG178 4.9 18.1 1.0
O D:HOH879 4.9 38.6 1.0
CG D:ASP191 4.9 27.2 1.0
O D:HOH1062 5.0 26.1 1.0
O D:HIS190 5.0 20.4 1.0
OD1 D:ASP191 5.0 27.6 1.0

Calcium binding site 10 out of 10 in 5xvz

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Calcium binding site 10 out of 10 in the Catpo Mutant - H246W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Catpo Mutant - H246W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:48.2
occ:1.00
 OG D:SER255 2.9 28.0 1.0
O D:HOH1129 3.0 26.3 1.0
O D:HOH1126 3.1 38.2 1.0
O D:HOH969 3.4 25.4 1.0
CD2 D:PHE476 3.8 26.3 1.0
CA D:GLY213 3.9 21.4 1.0
CB D:SER255 3.9 25.9 1.0
CE2 D:PHE476 4.2 27.3 1.0
N D:GLY213 4.3 20.9 1.0
O D:HOH1071 4.3 23.6 1.0
CG2 D:VAL539 4.4 43.1 1.0
CG D:GLU473 4.6 31.9 1.0
NH1 D:ARG689 4.6 35.4 1.0
OE2 D:GLU473 4.7 34.5 1.0
CB D:ILE538 4.8 31.7 1.0
O D:LEU256 4.8 22.6 1.0
CG2 D:ILE538 4.8 31.3 1.0
CD1 D:ILE538 4.8 31.0 1.0
O D:HOH1118 4.9 27.4 1.0
CG D:PHE476 4.9 25.4 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 15:10:37 2024

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