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Calcium in PDB 7rac: Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice

Enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice

All present enzymatic activity of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice:
1.10.3.2;

Protein crystallography data

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice, PDB code: 7rac was solved by M.M.Georgiadis, C.M.Ogata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 61.04 / 2.36
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 169.304, 176.193, 176.952, 90, 90, 90
R / Rfree (%) 13.9 / 17.7

Other elements in 7rac:

The structure of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice also contains other interesting chemical elements:

Copper (Cu) 24 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice (pdb code 7rac). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 17 binding sites of Calcium where determined in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice, PDB code: 7rac:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 17 in 7rac

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Calcium binding site 1 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:19.2
occ:0.87
 O A:PRO80 2.3 24.7 1.0
C A:PRO80 3.4 23.3 1.0
CA A:PRO80 4.1 20.9 1.0
N A:GLY82 4.3 24.0 1.0
N A:SER81 4.5 19.6 1.0
C A:SER81 4.5 23.9 1.0
CA A:SER81 4.7 21.0 1.0
O A:LEU79 4.8 23.4 1.0
CB A:PRO80 4.9 21.2 1.0
CA A:GLY82 4.9 22.9 1.0
O A:SER81 5.0 30.3 1.0

Calcium binding site 2 out of 17 in 7rac

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Calcium binding site 2 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:23.3
occ:1.00
 OD1 A:ASN243 2.3 23.7 1.0
O A:GLU247 2.3 23.7 1.0
OD1 A:ASP241 2.3 25.2 1.0
OE2 A:GLU249 2.4 34.3 1.0
OD1 A:ASP245 2.4 22.7 1.0
OE1 A:GLU249 2.5 24.2 1.0
CD A:GLU249 2.8 18.7 1.0
CG A:ASP245 3.3 21.9 1.0
CG A:ASN243 3.3 27.5 1.0
C A:GLU247 3.4 22.8 1.0
CG A:ASP241 3.5 24.8 1.0
OD2 A:ASP245 3.6 36.5 1.0
ND2 A:ASN243 3.8 26.6 1.0
N A:GLU247 3.9 24.2 1.0
CA A:GLU247 4.0 25.7 1.0
CB A:GLU247 4.1 21.2 1.0
O A:HOH505 4.2 28.6 1.0
CG A:GLU249 4.3 18.4 1.0
CB A:ASP241 4.3 17.2 1.0
N A:ASP245 4.3 23.6 1.0
CA A:ASP241 4.3 16.1 1.0
OD2 A:ASP241 4.3 29.8 1.0
N A:ASN243 4.3 23.1 1.0
CB A:ASP245 4.5 18.6 1.0
N A:ASN248 4.5 18.6 1.0
N A:PHE244 4.5 25.7 1.0
N A:THR242 4.5 19.7 1.0
C A:ASP241 4.6 17.2 1.0
CB A:ASN243 4.6 16.7 1.0
N A:GLU249 4.6 21.9 1.0
C A:ASN248 4.6 20.0 1.0
C A:ASN243 4.8 25.8 1.0
CA A:ASP245 4.8 25.0 1.0
CA A:ASN243 4.8 24.7 1.0
CA A:ASN248 4.8 18.6 1.0
C A:ASP245 4.9 21.2 1.0
N A:GLU246 4.9 24.2 1.0

Calcium binding site 3 out of 17 in 7rac

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Calcium binding site 3 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:19.9
occ:1.00
 OD1 B:ASN243 2.2 14.9 1.0
OD1 B:ASP241 2.3 20.5 1.0
O B:GLU247 2.3 19.1 1.0
OD1 B:ASP245 2.4 26.1 1.0
OE2 B:GLU249 2.5 31.1 1.0
OE1 B:GLU249 2.6 25.3 1.0
OE2 B:GLU247 2.6 64.2 1.0
CD B:GLU249 2.9 24.8 1.0
CD B:GLU247 3.2 68.6 1.0
CG B:ASP245 3.2 29.4 1.0
CG B:ASN243 3.3 27.7 1.0
CG B:ASP241 3.4 20.2 1.0
C B:GLU247 3.5 21.3 1.0
OD2 B:ASP245 3.6 39.1 1.0
CG B:GLU247 3.7 53.5 1.0
ND2 B:ASN243 3.9 31.2 1.0
N B:GLU247 4.0 22.9 1.0
O B:HOH501 4.0 37.1 1.0
OE1 B:GLU247 4.1 69.1 1.0
CA B:GLU247 4.1 27.9 1.0
CB B:ASP241 4.2 17.3 1.0
CA B:ASP241 4.2 16.8 1.0
OD2 B:ASP241 4.3 21.4 1.0
N B:ASN243 4.3 20.5 1.0
N B:ASP245 4.3 24.2 1.0
CG B:GLU249 4.4 16.5 1.0
CB B:GLU247 4.4 25.1 1.0
O B:HOH534 4.4 58.8 1.0
C B:ASP241 4.5 18.1 1.0
CB B:ASP245 4.5 20.6 1.0
N B:THR242 4.5 17.2 1.0
N B:PHE244 4.5 20.2 1.0
N B:ASN248 4.5 20.1 1.0
CB B:ASN243 4.6 15.8 1.0
C B:ASN248 4.6 17.7 1.0
N B:GLU249 4.7 18.9 1.0
C B:ASN243 4.7 24.4 1.0
CA B:ASN243 4.7 21.1 1.0
CA B:ASP245 4.8 24.6 1.0
CA B:ASN248 4.8 17.3 1.0
N B:GLU246 4.8 20.1 1.0
C B:ASP245 4.8 19.8 1.0
O B:ASN248 4.9 21.6 1.0

Calcium binding site 4 out of 17 in 7rac

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Calcium binding site 4 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca405

b:29.5
occ:0.85
 O C:HOH602 2.3 34.7 1.0
O C:HOH601 2.4 23.5 1.0
O C:PRO80 2.4 24.6 1.0
C C:PRO80 3.6 23.1 1.0
CA C:PRO80 4.2 18.0 1.0
N C:GLY82 4.5 17.9 1.0
N C:SER81 4.7 18.0 1.0
C C:SER81 4.7 25.9 1.0
O C:LEU79 4.8 20.9 1.0
CA C:SER81 5.0 29.9 1.0
CB C:PRO80 5.0 16.7 1.0

Calcium binding site 5 out of 17 in 7rac

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Calcium binding site 5 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca406

b:20.3
occ:1.00
 OD1 C:ASP245 2.3 27.9 1.0
OD1 C:ASN243 2.3 20.4 1.0
O C:GLU247 2.3 27.0 1.0
OE2 C:GLU249 2.4 37.0 1.0
OD1 C:ASP241 2.4 19.3 1.0
OE1 C:GLU249 2.5 23.4 1.0
O C:HOH501 2.8 42.3 1.0
CD C:GLU249 2.8 25.2 1.0
CG C:ASP245 3.2 26.2 1.0
CG C:ASN243 3.4 28.0 1.0
C C:GLU247 3.5 25.5 1.0
OD2 C:ASP245 3.5 33.8 1.0
CG C:ASP241 3.5 19.1 1.0
ND2 C:ASN243 3.9 34.6 1.0
N C:GLU247 3.9 23.7 1.0
CA C:GLU247 4.1 25.3 1.0
CB C:GLU247 4.2 22.6 1.0
N C:ASP245 4.2 22.0 1.0
CA C:ASP241 4.3 14.6 1.0
CB C:ASP241 4.3 18.7 1.0
O C:HOH506 4.3 26.9 1.0
N C:ASN243 4.3 19.1 1.0
CG C:GLU249 4.3 21.0 1.0
OD2 C:ASP241 4.4 25.7 1.0
CB C:ASP245 4.5 19.9 1.0
C C:ASP241 4.5 18.2 1.0
N C:THR242 4.5 22.8 1.0
N C:PHE244 4.6 19.4 1.0
N C:ASN248 4.6 17.6 1.0
C C:ASN248 4.6 18.5 1.0
CB C:ASN243 4.6 18.8 1.0
N C:GLU249 4.7 20.6 1.0
CA C:ASP245 4.7 25.4 1.0
C C:ASN243 4.8 22.1 1.0
CA C:ASN243 4.8 22.7 1.0
N C:GLU246 4.8 22.1 1.0
CA C:ASN248 4.8 17.5 1.0
C C:ASP245 4.9 23.2 1.0
O C:ASN248 5.0 18.4 1.0

Calcium binding site 6 out of 17 in 7rac

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Calcium binding site 6 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca405

b:35.3
occ:1.00
 O B:HOH592 2.5 23.2 1.0
O D:HOH571 2.5 22.6 1.0
O D:HOH618 2.5 37.3 1.0
O D:GLY156 2.5 29.2 1.0
OE2 B:GLU166 2.7 27.0 1.0
C D:GLY156 3.4 29.3 1.0
CD B:GLU166 3.6 30.9 1.0
OE1 B:GLU166 3.9 25.8 1.0
CA D:GLY156 4.1 31.1 1.0
N D:THR157 4.3 18.6 1.0
O B:HOH538 4.3 30.8 1.0
CA D:THR157 4.4 18.3 1.0
O D:GLY158 4.6 20.1 1.0
O D:HOH625 4.7 26.3 1.0
O B:HOH510 4.8 26.1 1.0
C D:THR157 4.9 23.4 1.0
CG B:GLU166 4.9 19.4 1.0
O D:HOH604 4.9 21.6 1.0

Calcium binding site 7 out of 17 in 7rac

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Calcium binding site 7 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca406

b:23.7
occ:1.00
 OD1 D:ASN243 2.2 24.2 1.0
OE2 D:GLU249 2.2 30.5 1.0
O D:GLU247 2.3 22.6 1.0
OD1 D:ASP241 2.3 22.6 1.0
OD1 D:ASP245 2.4 25.3 1.0
OE1 D:GLU249 2.6 26.9 1.0
CD D:GLU249 2.7 24.6 1.0
CG D:ASP245 3.2 27.7 1.0
CG D:ASN243 3.3 23.6 1.0
C D:GLU247 3.4 23.8 1.0
CG D:ASP241 3.4 22.6 1.0
OD2 D:ASP245 3.6 34.8 1.0
ND2 D:ASN243 3.7 25.9 1.0
N D:GLU247 3.9 24.8 1.0
CA D:GLU247 4.0 23.4 1.0
CB D:GLU247 4.1 27.1 1.0
CB D:ASP241 4.2 17.9 1.0
CA D:ASP241 4.2 15.7 1.0
CG D:GLU249 4.3 19.4 1.0
O D:HOH516 4.3 32.4 1.0
OD2 D:ASP241 4.3 24.1 1.0
N D:ASN243 4.3 21.3 1.0
N D:ASP245 4.3 21.8 1.0
C D:ASP241 4.5 19.0 1.0
N D:ASN248 4.5 20.3 1.0
CB D:ASP245 4.5 16.7 1.0
N D:THR242 4.5 19.6 1.0
CB D:ASN243 4.6 17.5 1.0
N D:PHE244 4.6 22.6 1.0
C D:ASN248 4.6 18.7 1.0
N D:GLU249 4.7 18.6 1.0
C D:ASN243 4.7 25.9 1.0
CA D:ASN243 4.7 21.6 1.0
CA D:ASP245 4.8 26.6 1.0
CA D:ASN248 4.8 19.2 1.0
N D:GLU246 4.9 23.8 1.0
C D:ASP245 4.9 22.7 1.0
O D:ASN248 4.9 22.1 1.0

Calcium binding site 8 out of 17 in 7rac

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Calcium binding site 8 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca406

b:21.2
occ:1.00
 O E:GLU247 2.3 21.7 1.0
OD1 E:ASN243 2.3 23.1 1.0
OE2 E:GLU249 2.3 34.2 1.0
OD1 E:ASP245 2.3 26.1 1.0
OD1 E:ASP241 2.3 19.8 1.0
OE1 E:GLU249 2.4 21.0 1.0
CD E:GLU249 2.7 23.5 1.0
CG E:ASP245 3.2 26.0 1.0
CG E:ASP241 3.4 25.2 1.0
CG E:ASN243 3.4 28.3 1.0
C E:GLU247 3.4 24.6 1.0
OD2 E:ASP245 3.5 34.0 1.0
ND2 E:ASN243 3.9 29.9 1.0
N E:GLU247 4.0 21.6 1.0
CA E:GLU247 4.1 23.2 1.0
O E:HOH503 4.1 35.4 1.0
CB E:ASP241 4.2 18.8 1.0
CB E:GLU247 4.2 22.3 1.0
CG E:GLU249 4.2 15.5 1.0
OD2 E:ASP241 4.2 27.4 1.0
CA E:ASP241 4.2 18.3 1.0
N E:ASP245 4.3 22.2 1.0
N E:ASN243 4.4 18.9 1.0
N E:THR242 4.5 18.6 1.0
CB E:ASP245 4.5 19.7 1.0
N E:ASN248 4.5 18.0 1.0
C E:ASP241 4.5 16.6 1.0
N E:PHE244 4.6 21.7 1.0
N E:GLU249 4.6 16.9 1.0
C E:ASN248 4.6 18.7 1.0
CB E:ASN243 4.7 20.2 1.0
CA E:ASP245 4.8 29.5 1.0
C E:ASN243 4.8 21.0 1.0
CA E:ASN248 4.8 20.8 1.0
CA E:ASN243 4.8 25.0 1.0
C E:ASP245 4.9 24.5 1.0
N E:GLU246 4.9 24.0 1.0

Calcium binding site 9 out of 17 in 7rac

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Calcium binding site 9 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca405

b:22.4
occ:1.00
 OD1 F:ASN243 2.2 24.5 1.0
O F:GLU247 2.3 21.4 1.0
OD1 F:ASP245 2.4 25.9 1.0
OE2 F:GLU249 2.4 32.9 1.0
OD1 F:ASP241 2.4 19.5 1.0
OE1 F:GLU249 2.6 22.4 1.0
CD F:GLU249 2.8 26.9 1.0
O F:HOH504 2.8 32.9 1.0
CG F:ASP245 3.2 31.7 1.0
CG F:ASN243 3.3 27.1 1.0
CG F:ASP241 3.5 19.6 1.0
OD2 F:ASP245 3.5 33.1 1.0
C F:GLU247 3.5 20.3 1.0
ND2 F:ASN243 3.8 29.2 1.0
N F:GLU247 4.0 22.8 1.0
CA F:GLU247 4.2 24.5 1.0
N F:ASP245 4.2 25.4 1.0
CA F:ASP241 4.3 18.1 1.0
OD2 F:ASP241 4.3 22.5 1.0
CB F:ASP241 4.3 17.6 1.0
CG F:GLU249 4.3 19.6 1.0
O F:HOH505 4.3 30.6 1.0
N F:ASN243 4.3 16.4 1.0
CB F:GLU247 4.4 21.3 1.0
CB F:ASP245 4.4 23.8 1.0
C F:ASP241 4.5 21.1 1.0
N F:ASN248 4.5 19.0 1.0
N F:THR242 4.5 17.4 1.0
N F:PHE244 4.6 24.0 1.0
CB F:ASN243 4.6 20.4 1.0
C F:ASN248 4.6 22.1 1.0
N F:GLU249 4.7 18.1 1.0
CA F:ASP245 4.7 26.0 1.0
C F:ASN243 4.8 23.3 1.0
CA F:ASN243 4.8 23.0 1.0
CA F:ASN248 4.8 20.0 1.0
C F:ASP245 4.9 23.7 1.0
N F:GLU246 4.9 21.5 1.0
O F:ASN248 5.0 21.0 1.0

Calcium binding site 10 out of 17 in 7rac

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Calcium binding site 10 out of 17 in the Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Dodecameric Multicopper Oxidase From M. Hydrothermalis in An Orthorhombic Lattice within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca405

b:24.7
occ:0.78
 O G:HOH610 2.3 28.9 1.0
O A:HOH575 2.3 19.6 1.0
O G:GLY156 2.5 29.8 1.0
O A:HOH587 2.5 33.6 1.0
OE2 A:GLU166 2.5 23.9 1.0
O G:HOH550 2.5 27.9 1.0
C G:GLY156 3.3 28.8 1.0
CD A:GLU166 3.5 21.8 1.0
OE1 A:GLU166 3.9 20.3 1.0
CA G:GLY156 4.0 27.9 1.0
O A:HOH516 4.2 34.2 1.0
N G:THR157 4.2 22.6 1.0
O G:HOH634 4.3 26.6 1.0
CA G:THR157 4.4 21.7 1.0
O G:GLY158 4.5 24.4 1.0
O G:HOH629 4.6 24.2 1.0
CG A:GLU166 4.8 16.6 1.0
C G:THR157 4.9 24.8 1.0
O A:HOH515 4.9 25.8 1.0
CD1 A:TYR163 5.0 16.6 1.0

Reference:

J.L.Paavola, U.Battistin, C.M.Ogata, M.M.Georgiadis. Crystal Structures of A Dodecameric Multicopper Oxidase From Marinithermus Hydrothermalis. Acta Crystallogr D Struct V. 77 1336 2021BIOL.
ISSN: ISSN 2059-7983
PubMed: 34605435
DOI: 10.1107/S205979832100944X
Page generated: Fri Jul 19 03:38:13 2024

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