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Calcium in PDB 5xy4: Catpo Mutant - V536W

Enzymatic activity of Catpo Mutant - V536W

All present enzymatic activity of Catpo Mutant - V536W:
1.11.1.6;

Protein crystallography data

The structure of Catpo Mutant - V536W, PDB code: 5xy4 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) 90.46 / 1.80
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.420, 120.743, 184.653, 90.00, 102.05, 90.00
R / Rfree (%) 15.8 / 19.3

Other elements in 5xy4:

The structure of Catpo Mutant - V536W also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catpo Mutant - V536W (pdb code 5xy4). 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 - V536W, PDB code: 5xy4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5xy4

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Calcium binding site 1 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:24.9
occ:1.00
 O A:HOH1750 3.1 36.7 1.0
ND1 A:HIS190 3.1 18.7 1.0
N A:SER192 3.2 17.7 1.0
O B:HOH1163 3.3 28.6 1.0
OG A:SER192 3.5 17.9 1.0
CB A:SER192 3.6 17.4 1.0
CD A:ARG178 3.7 18.8 1.0
N A:ASP191 3.7 19.2 1.0
CB A:HIS190 3.8 18.9 1.0
CG A:HIS190 3.9 17.8 1.0
CG A:ARG178 3.9 18.5 1.0
CB A:ARG178 3.9 18.2 1.0
CA A:SER192 4.0 17.7 1.0
CB A:ASP191 4.1 21.1 1.0
CE1 A:HIS190 4.2 19.1 1.0
C A:ASP191 4.2 18.9 1.0
CA A:ASP191 4.2 20.5 1.0
C A:HIS190 4.2 18.5 1.0
O A:HOH1566 4.5 18.9 1.0
CA A:HIS190 4.6 18.2 1.0
CE1 B:TYR412 4.7 20.9 1.0
NZ A:LYS489 4.8 36.7 1.0
CA A:ARG178 4.8 17.5 1.0
NE A:ARG178 4.9 20.1 1.0
NH1 A:ARG178 4.9 21.3 1.0
O A:HIS190 4.9 20.1 1.0
O A:HOH1698 5.0 27.3 1.0

Calcium binding site 2 out of 10 in 5xy4

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Calcium binding site 2 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:38.5
occ:1.00
 O A:HOH1774 3.1 28.8 1.0
NH1 B:ARG449 3.1 20.3 1.0
O A:HOH1368 3.3 25.0 1.0
N A:THR437 3.3 25.4 1.0
O B:HOH992 3.6 35.6 1.0
CD B:ARG449 3.8 21.6 1.0
CA A:PHE436 3.8 25.3 1.0
CB A:THR437 3.9 26.0 1.0
OG1 A:THR437 4.0 24.2 1.0
C A:PHE436 4.1 24.6 1.0
CG B:ARG449 4.1 22.6 1.0
CB A:PHE436 4.1 25.8 1.0
CA A:THR437 4.2 25.5 1.0
O A:HOH1642 4.2 25.9 1.0
CZ B:ARG449 4.2 21.5 1.0
CB B:ARG449 4.4 23.5 1.0
NE B:ARG449 4.4 19.9 1.0
O A:HOH1471 4.5 26.9 1.0
O A:THR437 4.5 26.9 1.0
N B:ARG449 4.8 24.5 1.0
O B:HOH868 4.9 38.6 1.0
C A:THR437 4.9 25.7 1.0
O A:PHE435 5.0 26.3 1.0
CD1 D:LEU49 5.0 23.0 1.0

Calcium binding site 3 out of 10 in 5xy4

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Calcium binding site 3 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:36.4
occ:1.00
 O B:HOH1271 3.1 23.3 1.0
NH1 A:ARG449 3.1 22.5 1.0
O B:HOH892 3.3 27.9 1.0
N B:THR437 3.4 23.7 1.0
CD A:ARG449 3.6 21.9 1.0
CB B:THR437 3.8 24.2 1.0
O A:HOH1684 3.9 36.5 1.0
OG1 B:THR437 3.9 24.5 1.0
CA B:PHE436 3.9 21.9 1.0
CG A:ARG449 4.0 23.0 1.0
CZ A:ARG449 4.2 21.8 1.0
CB B:PHE436 4.2 21.7 1.0
C B:PHE436 4.2 22.8 1.0
CA B:THR437 4.2 24.4 1.0
NE A:ARG449 4.3 20.8 1.0
O B:HOH1097 4.3 22.3 1.0
CB A:ARG449 4.3 24.4 1.0
O B:THR437 4.6 24.0 1.0
O A:HOH1571 4.7 38.4 1.0
O B:HOH816 4.7 24.8 1.0
N A:ARG449 4.8 24.8 1.0
O C:HOH1314 4.9 27.7 1.0
C B:THR437 5.0 24.8 1.0
CD1 C:LEU49 5.0 20.3 1.0

Calcium binding site 4 out of 10 in 5xy4

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Calcium binding site 4 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:48.5
occ:1.00
 O D:HOH824 2.1 26.1 1.0
O C:HOH860 2.1 28.1 1.0
O C:HOH1317 2.1 39.1 1.0
O D:HOH1244 2.2 29.7 1.0
O B:HOH1257 2.3 28.4 1.0
O B:HOH1297 2.4 47.9 1.0
O D:GLY378 4.1 23.5 1.0
O A:GLY378 4.1 26.6 1.0
O C:GLY378 4.2 24.4 1.0
O B:GLY378 4.2 23.5 1.0
O A:HOH1634 4.2 28.6 1.0
O C:HOH993 4.3 28.7 1.0
O B:HOH1231 4.3 39.3 1.0
O B:HOH1057 4.3 34.4 1.0
O A:HOH1637 4.4 38.9 1.0
O D:HOH990 4.4 26.6 1.0
O C:HOH1243 4.4 33.4 1.0
O D:HOH1194 4.6 40.6 1.0
CA D:GLY378 4.7 22.9 1.0
CA A:GLY378 4.7 22.3 1.0
CA C:GLY378 4.8 22.3 1.0
CA B:GLY378 4.8 21.6 1.0
C D:GLY378 4.8 22.6 1.0
C A:GLY378 4.9 25.3 1.0
C C:GLY378 4.9 23.6 1.0
C B:GLY378 4.9 23.6 1.0

Calcium binding site 5 out of 10 in 5xy4

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Calcium binding site 5 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:26.7
occ:1.00
 O B:HOH1264 2.9 32.6 1.0
O A:HOH1714 3.1 28.8 1.0
ND1 B:HIS190 3.1 18.1 1.0
N B:SER192 3.2 19.2 1.0
OG B:SER192 3.4 17.7 1.0
CB B:SER192 3.6 17.7 1.0
N B:ASP191 3.7 21.1 1.0
CD B:ARG178 3.7 21.8 1.0
CB B:HIS190 3.8 19.7 1.0
CG B:HIS190 3.9 18.6 1.0
CG B:ARG178 3.9 20.9 1.0
CB B:ARG178 4.0 21.4 1.0
CA B:SER192 4.0 19.2 1.0
CB B:ASP191 4.0 23.1 1.0
CA B:ASP191 4.2 22.1 1.0
C B:ASP191 4.2 19.8 1.0
CE1 B:HIS190 4.2 17.8 1.0
C B:HIS190 4.3 20.5 1.0
O B:HOH968 4.4 21.6 1.0
CE1 A:TYR412 4.5 24.3 1.0
CA B:HIS190 4.6 20.4 1.0
O B:HOH1202 4.7 38.6 1.0
CA B:ARG178 4.9 19.5 1.0
CG B:ASP191 5.0 27.7 1.0
NE B:ARG178 5.0 21.5 1.0
O B:HIS190 5.0 21.5 1.0

Calcium binding site 6 out of 10 in 5xy4

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Calcium binding site 6 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:43.9
occ:1.00
 O B:HOH1158 2.9 27.3 1.0
OG B:SER255 3.0 28.6 1.0
O B:HOH960 3.4 31.6 1.0
CA B:GLY213 3.7 23.1 1.0
CD2 B:PHE476 3.8 29.3 1.0
CB B:SER255 3.9 25.7 1.0
N B:GLY213 4.0 22.9 1.0
O B:HOH1070 4.2 27.2 1.0
CE2 B:PHE476 4.3 30.5 1.0
CG B:GLU473 4.4 36.0 1.0
CG2 B:VAL539 4.4 55.5 1.0
OE2 B:GLU473 4.6 36.2 1.0
NH1 B:ARG689 4.7 31.4 1.0
O B:LEU256 4.8 25.5 1.0
CG B:PHE476 4.9 27.9 1.0
CB B:ILE538 4.9 38.1 1.0
CD1 B:ILE538 4.9 36.2 1.0
CG2 B:ILE538 4.9 38.5 1.0
C B:GLY213 4.9 22.1 1.0
CB B:PHE476 5.0 26.9 1.0

Calcium binding site 7 out of 10 in 5xy4

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Calcium binding site 7 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:32.3
occ:1.00
 O D:HOH1214 3.0 27.0 1.0
ND1 C:HIS190 3.1 24.1 1.0
N C:SER192 3.3 21.6 1.0
O C:HOH1253 3.4 51.3 1.0
OG C:SER192 3.5 20.4 1.0
CB C:SER192 3.6 21.6 1.0
N C:ASP191 3.7 23.9 1.0
CD C:ARG178 3.7 23.7 1.0
CB C:HIS190 3.8 23.5 1.0
CG C:HIS190 3.9 23.1 1.0
CG C:ARG178 3.9 22.5 1.0
CB C:ARG178 4.0 21.5 1.0
CA C:SER192 4.0 21.9 1.0
CB C:ASP191 4.0 27.3 1.0
CA C:ASP191 4.2 24.8 1.0
C C:ASP191 4.2 22.7 1.0
CE1 C:HIS190 4.2 24.1 1.0
C C:HIS190 4.2 23.7 1.0
O C:HOH1077 4.5 18.6 1.0
CE1 D:TYR412 4.5 26.5 1.0
CA C:HIS190 4.6 24.1 1.0
O C:HOH1244 4.7 38.9 1.0
CA C:ARG178 4.9 21.2 1.0
NE C:ARG178 4.9 24.6 1.0
O C:HIS190 5.0 23.4 1.0
CG C:ASP191 5.0 30.1 1.0
NH1 C:ARG178 5.0 25.6 1.0
OD1 C:ASP191 5.0 32.1 1.0

Calcium binding site 8 out of 10 in 5xy4

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Calcium binding site 8 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:41.6
occ:1.00
 O C:HOH1182 2.9 25.5 1.0
OG C:SER255 2.9 24.5 1.0
O C:HOH1204 3.3 40.6 1.0
O C:HOH1009 3.3 28.3 1.0
CA C:GLY213 3.6 23.4 1.0
CB C:SER255 3.8 25.1 1.0
CD2 C:PHE476 3.8 27.5 1.0
N C:GLY213 4.0 23.8 1.0
O C:HOH1170 4.1 28.0 1.0
CE2 C:PHE476 4.3 28.9 1.0
CG2 C:VAL539 4.4 52.3 1.0
CG C:GLU473 4.5 35.7 1.0
O C:LEU256 4.6 25.3 1.0
NH1 C:ARG689 4.7 30.0 1.0
OE2 C:GLU473 4.7 36.6 1.0
CB C:ILE538 4.8 35.5 1.0
CD1 C:ILE538 4.9 37.4 1.0
CG C:PHE476 4.9 28.1 1.0
CG2 C:ILE538 4.9 36.7 1.0
C C:GLY213 4.9 23.0 1.0
O C:HOH1190 5.0 28.7 1.0

Calcium binding site 9 out of 10 in 5xy4

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Calcium binding site 9 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:30.3
occ:1.00
 O C:HOH1206 3.0 28.7 1.0
ND1 D:HIS190 3.2 23.3 1.0
O D:HOH1254 3.2 31.5 1.0
N D:SER192 3.2 22.9 1.0
OG D:SER192 3.5 21.8 1.0
CB D:SER192 3.5 22.2 1.0
CD D:ARG178 3.7 22.9 1.0
N D:ASP191 3.7 23.2 1.0
CB D:HIS190 3.8 23.3 1.0
CG D:ARG178 3.9 23.3 1.0
CG D:HIS190 3.9 21.7 1.0
CA D:SER192 4.0 23.1 1.0
CB D:ARG178 4.0 22.0 1.0
CB D:ASP191 4.1 27.4 1.0
C D:ASP191 4.1 25.3 1.0
CA D:ASP191 4.2 25.6 1.0
CE1 D:HIS190 4.2 23.5 1.0
C D:HIS190 4.2 24.4 1.0
O D:HOH1112 4.4 24.3 1.0
CE1 C:TYR412 4.6 25.1 1.0
CA D:HIS190 4.6 24.4 1.0
CA D:ARG178 4.9 21.7 1.0
NE D:ARG178 4.9 22.4 1.0
NH1 D:ARG178 4.9 24.9 1.0
O D:HIS190 4.9 24.8 1.0
CG D:ASP191 5.0 29.9 1.0

Calcium binding site 10 out of 10 in 5xy4

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Calcium binding site 10 out of 10 in the Catpo Mutant - V536W


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Catpo Mutant - V536W within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca703

b:43.7
occ:1.00
 OG D:SER255 2.8 27.0 1.0
O D:HOH1181 2.9 30.3 1.0
O D:HOH1176 3.3 40.8 1.0
O D:HOH1093 3.5 29.8 1.0
CB D:SER255 3.7 26.8 1.0
CA D:GLY213 3.7 23.8 1.0
CD2 D:PHE476 3.8 28.6 1.0
N D:GLY213 4.1 23.6 1.0
CE2 D:PHE476 4.3 30.0 1.0
O D:HOH1076 4.4 29.7 1.0
CG2 D:VAL539 4.5 51.0 1.0
CG D:GLU473 4.6 38.3 1.0
NH1 D:ARG689 4.6 29.1 1.0
OE2 D:GLU473 4.7 44.7 1.0
O D:LEU256 4.7 23.4 1.0
CG2 D:ILE538 4.8 34.8 1.0
CB D:ILE538 4.8 34.0 1.0
CD1 D:ILE538 4.8 34.2 1.0
CG D:PHE476 4.9 28.5 1.0
C D:GLY213 5.0 23.7 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: Wed Jul 9 11:49:31 2025

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