Calcium in PDB 5yem: Catpo Mutant - T188F

Enzymatic activity of Catpo Mutant - T188F

All present enzymatic activity of Catpo Mutant - T188F:
1.11.1.6;

Protein crystallography data

The structure of Catpo Mutant - T188F, PDB code: 5yem was solved by Y.Yuzugullu Karakus, S.Balci, G.Goc, A.R.Pearson, B.Yorke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 112.89 / 1.49
Space group I 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.109, 121.539, 186.025, 90.00, 101.82, 90.00
R / Rfree (%) 15.8 / 18.7

Other elements in 5yem:

The structure of Catpo Mutant - T188F also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Catpo Mutant - T188F (pdb code 5yem). 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 - T188F, PDB code: 5yem:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5yem

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Calcium binding site 1 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:14.9
occ:1.00
 O A:HOH1345 3.1 16.7 1.0
ND1 A:HIS190 3.2 9.3 1.0
N A:SER192 3.2 8.6 1.0
O B:HOH1130 3.2 15.1 1.0
OG A:SER192 3.4 8.5 1.0
CB A:SER192 3.6 8.3 1.0
CD A:ARG178 3.7 9.4 1.0
N A:ASP191 3.7 8.7 1.0
CB A:HIS190 3.7 9.4 1.0
CG A:HIS190 3.9 9.4 1.0
CG A:ARG178 4.0 9.1 1.0
CA A:SER192 4.0 8.2 1.0
CB A:ARG178 4.0 8.0 1.0
CB A:ASP191 4.1 10.8 1.0
C A:ASP191 4.1 8.6 1.0
CA A:ASP191 4.2 8.8 1.0
CE1 A:HIS190 4.3 10.8 1.0
C A:HIS190 4.3 8.8 1.0
CE1 B:TYR412 4.4 9.7 1.0
O A:HOH1161 4.5 11.8 1.0
CA A:HIS190 4.6 9.1 1.0
CA A:ARG178 4.8 7.6 1.0
O A:HOH1270 4.8 24.9 1.0
NE A:ARG178 4.9 10.0 1.0
CG A:ASP191 5.0 11.9 1.0

Calcium binding site 2 out of 10 in 5yem

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Calcium binding site 2 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:17.7
occ:0.70
 O A:HOH1358 3.0 13.9 1.0
NH1 B:ARG449 3.1 10.2 1.0
N A:THR437 3.2 10.1 1.0
O A:HOH866 3.3 17.2 1.0
CD B:ARG449 3.7 10.7 1.0
CA A:PHE436 3.8 9.5 1.0
CB A:THR437 3.8 10.7 1.0
O B:HOH1067 3.9 19.4 1.0
OG1 A:THR437 3.9 10.4 1.0
C A:PHE436 4.0 9.4 1.0
CB A:PHE436 4.1 10.0 1.0
CA A:THR437 4.1 10.2 1.0
CG B:ARG449 4.1 10.4 1.0
CZ B:ARG449 4.1 11.2 1.0
O A:HOH1257 4.2 11.8 1.0
NE B:ARG449 4.3 10.6 1.0
CB B:ARG449 4.5 10.7 1.0
O A:THR437 4.5 10.9 1.0
O A:HOH987 4.5 12.2 1.0
C A:THR437 4.8 10.7 1.0
CD1 D:LEU49 4.8 8.8 1.0
O A:PHE435 4.9 10.6 1.0
O A:HOH1051 4.9 12.1 1.0
N B:ARG449 5.0 10.7 1.0

Calcium binding site 3 out of 10 in 5yem

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Calcium binding site 3 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:26.6
occ:1.00
 O B:HOH1297 3.0 17.8 1.0
O A:HOH1181 3.0 29.3 1.0
NH1 A:ARG449 3.0 11.6 1.0
N B:THR437 3.1 10.0 1.0
O B:HOH832 3.6 18.8 1.0
CD A:ARG449 3.7 9.6 1.0
CB B:THR437 3.8 9.6 1.0
CA B:PHE436 3.8 10.0 1.0
OG1 B:THR437 3.8 10.0 1.0
C B:PHE436 4.0 9.8 1.0
CA B:THR437 4.0 9.5 1.0
CZ A:ARG449 4.1 11.1 1.0
CB B:PHE436 4.1 10.5 1.0
CG A:ARG449 4.1 9.9 1.0
O A:HOH1029 4.3 20.8 1.0
NE A:ARG449 4.3 10.0 1.0
O B:HOH1227 4.3 9.0 1.0
CB A:ARG449 4.5 10.4 1.0
O B:THR437 4.6 10.9 1.0
O B:HOH996 4.7 14.4 1.0
O B:HOH911 4.8 11.3 1.0
O B:PHE435 4.8 9.1 1.0
C B:THR437 4.8 10.4 1.0
O A:HOH1364 4.9 17.6 1.0
CD1 C:LEU49 5.0 10.7 1.0

Calcium binding site 4 out of 10 in 5yem

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Calcium binding site 4 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:16.5
occ:0.50
 O A:HOH814 2.6 24.5 1.0
O B:HOH810 2.6 25.5 1.0
O A:HOH1329 2.7 24.2 1.0
O D:HOH1313 2.8 29.1 1.0
O A:HOH1388 2.8 37.3 1.0
O B:HOH1339 2.9 38.1 1.0
O C:GLY378 4.1 13.6 1.0
O B:GLY378 4.1 15.0 1.0
O D:GLY378 4.1 14.3 1.0
O A:GLY378 4.2 14.2 1.0
O D:HOH1095 4.3 18.0 1.0
O C:HOH1234 4.3 32.8 1.0
O C:HOH1125 4.3 19.0 1.0
O A:HOH1200 4.4 18.8 1.0
O B:HOH1150 4.4 16.5 1.0
O D:HOH1286 4.4 36.1 1.0
CA C:GLY378 4.7 10.8 1.0
CA D:GLY378 4.7 12.8 1.0
CA B:GLY378 4.7 12.4 1.0
CA A:GLY378 4.8 12.1 1.0
C C:GLY378 4.8 11.5 1.0
C D:GLY378 4.9 13.7 1.0
C B:GLY378 4.9 14.3 1.0
C A:GLY378 5.0 13.3 1.0

Calcium binding site 5 out of 10 in 5yem

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Calcium binding site 5 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:14.8
occ:1.00
 O B:HOH1290 3.1 15.9 1.0
O A:HOH1143 3.1 14.1 1.0
ND1 B:HIS190 3.3 10.4 1.0
N B:SER192 3.3 9.9 1.0
OG B:SER192 3.4 8.7 1.0
CB B:SER192 3.6 9.1 1.0
N B:ASP191 3.7 8.8 1.0
CD B:ARG178 3.7 9.1 1.0
CB B:HIS190 3.7 10.4 1.0
CG B:HIS190 3.9 9.1 1.0
CG B:ARG178 4.0 8.1 1.0
CA B:SER192 4.0 8.9 1.0
CB B:ARG178 4.1 8.3 1.0
CB B:ASP191 4.1 10.7 1.0
CA B:ASP191 4.2 10.0 1.0
C B:ASP191 4.2 9.7 1.0
C B:HIS190 4.3 9.0 1.0
CE1 B:HIS190 4.4 9.7 1.0
CE1 A:TYR412 4.4 11.1 1.0
O B:HOH1158 4.5 11.5 1.0
CA B:HIS190 4.6 9.7 1.0
O B:HOH1100 4.8 22.5 1.0
CA B:ARG178 4.9 8.1 1.0
NE B:ARG178 4.9 9.2 1.0
NH1 B:ARG178 5.0 12.4 1.0

Calcium binding site 6 out of 10 in 5yem

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Calcium binding site 6 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:18.8
occ:1.00
 O B:HOH1185 3.0 12.2 1.0
OG B:SER255 3.0 14.1 1.0
O B:HOH1109 3.1 26.6 1.0
O B:HOH951 3.3 13.8 1.0
CD2 B:PHE476 3.8 13.3 1.0
CA B:GLY213 3.8 9.8 1.0
CB B:SER255 3.9 12.2 1.0
CG2 B:VAL539 4.1 22.6 1.0
CE2 B:PHE476 4.2 15.3 1.0
N B:GLY213 4.2 10.2 1.0
O B:HOH1168 4.4 11.8 1.0
NH1 B:ARG689 4.6 16.4 1.0
OE2 B:GLU473 4.7 17.2 1.0
CB B:ILE538 4.7 15.3 1.0
CG B:GLU473 4.7 17.1 1.0
O B:LEU256 4.8 11.3 1.0
CG2 B:ILE538 4.8 17.0 1.0
CG B:PHE476 4.9 13.2 1.0
CD1 B:ILE538 5.0 16.7 1.0

Calcium binding site 7 out of 10 in 5yem

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Calcium binding site 7 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca701

b:15.8
occ:1.00
 O C:HOH1325 3.1 12.2 1.0
O D:HOH1098 3.1 12.3 1.0
ND1 C:HIS190 3.2 10.2 1.0
N C:SER192 3.3 10.6 1.0
OG C:SER192 3.4 10.1 1.0
CB C:SER192 3.6 10.0 1.0
N C:ASP191 3.7 9.2 1.0
CB C:HIS190 3.7 10.3 1.0
CD C:ARG178 3.8 10.2 1.0
CG C:HIS190 3.9 9.3 1.0
CA C:SER192 4.0 9.5 1.0
CG C:ARG178 4.1 9.8 1.0
CB C:ARG178 4.1 10.0 1.0
CB C:ASP191 4.2 10.7 1.0
C C:ASP191 4.2 10.4 1.0
CA C:ASP191 4.2 9.8 1.0
C C:HIS190 4.3 9.8 1.0
CE1 C:HIS190 4.3 10.4 1.0
CE1 D:TYR412 4.4 11.7 1.0
O C:HOH1056 4.4 10.4 1.0
CA C:HIS190 4.6 10.9 1.0
O C:HOH1099 4.9 27.1 1.0
CA C:ARG178 4.9 9.6 1.0
NE C:ARG178 5.0 11.0 1.0
CG C:ASP191 5.0 11.9 1.0
O C:HIS190 5.0 10.5 1.0

Calcium binding site 8 out of 10 in 5yem

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Calcium binding site 8 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca702

b:9.4
occ:0.60
 OG C:SER255 3.0 11.5 1.0
O C:HOH1110 3.0 12.2 1.0
O C:HOH981 3.1 17.3 1.0
O C:HOH991 3.2 12.5 1.0
CD2 C:PHE476 3.8 15.3 1.0
CB C:SER255 3.9 11.0 1.0
CA C:GLY213 3.9 8.5 1.0
CG2 C:VAL539 3.9 18.6 1.0
CE2 C:PHE476 4.2 17.8 1.0
N C:GLY213 4.2 8.8 1.0
O C:HOH1132 4.4 12.2 1.0
OE2 C:GLU473 4.6 15.5 1.0
NH1 C:ARG689 4.6 11.7 1.0
CB C:ILE538 4.7 14.1 1.0
CG2 C:ILE538 4.7 13.8 1.0
CG C:GLU473 4.7 15.2 1.0
O C:LEU256 4.8 10.1 1.0
CG C:PHE476 4.9 12.5 1.0

Calcium binding site 9 out of 10 in 5yem

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Calcium binding site 9 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca701

b:9.7
occ:0.70
 O C:HOH1094 3.1 14.4 1.0
O D:HOH1318 3.1 14.7 1.0
ND1 D:HIS190 3.3 10.3 1.0
N D:SER192 3.3 10.4 1.0
OG D:SER192 3.5 9.6 1.0
CB D:SER192 3.6 9.8 1.0
N D:ASP191 3.7 9.9 1.0
CB D:HIS190 3.8 11.3 1.0
CD D:ARG178 3.8 10.4 1.0
CG D:ARG178 4.0 10.1 1.0
CG D:HIS190 4.0 9.5 1.0
CA D:SER192 4.0 8.8 1.0
CB D:ARG178 4.1 10.0 1.0
CB D:ASP191 4.1 11.6 1.0
CA D:ASP191 4.2 10.3 1.0
C D:ASP191 4.2 10.8 1.0
C D:HIS190 4.3 9.7 1.0
CE1 D:HIS190 4.4 10.6 1.0
CE1 C:TYR412 4.4 11.3 1.0
O D:HOH1126 4.5 10.1 1.0
CA D:HIS190 4.6 10.4 1.0
O D:HOH1220 4.8 22.7 1.0
CA D:ARG178 4.9 9.3 1.0
O D:HIS190 5.0 11.2 1.0
NE D:ARG178 5.0 11.2 1.0

Calcium binding site 10 out of 10 in 5yem

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Calcium binding site 10 out of 10 in the Catpo Mutant - T188F


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Catpo Mutant - T188F within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca702

b:12.9
occ:0.70
 OG D:SER255 3.0 13.2 1.0
O D:HOH1037 3.0 13.6 1.0
O D:HOH1137 3.2 21.1 1.0
O D:HOH1097 3.3 12.1 1.0
CB D:SER255 3.8 11.3 1.0
CA D:GLY213 3.9 9.0 1.0
CD2 D:PHE476 3.9 14.7 1.0
CG2 D:VAL539 4.0 22.1 1.0
N D:GLY213 4.2 8.7 1.0
CE2 D:PHE476 4.2 15.1 1.0
O D:HOH1121 4.4 12.3 1.0
OE2 D:GLU473 4.5 17.7 1.0
NH1 D:ARG689 4.6 14.1 1.0
CB D:ILE538 4.6 15.1 1.0
CG D:GLU473 4.7 17.9 1.0
CG2 D:ILE538 4.7 15.6 1.0
CD1 D:ILE538 4.8 16.2 1.0
O D:LEU256 4.9 12.2 1.0
CG D:PHE476 5.0 12.8 1.0

Reference:

Y.Yuzugullu Karakus, S.Balci, G.Goc, A.R.Pearson, B.Yorke. Catpo Mutant - T188F To Be Published.
Page generated: Sat Dec 12 05:54:21 2020

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