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Calcium in PDB 1ktw: Iota-Carrageenase Complexed to Iota-Carrageenan Fragments

Enzymatic activity of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments

All present enzymatic activity of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments:
3.2.1.157;

Protein crystallography data

The structure of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments, PDB code: 1ktw was solved by G.Michel, R.Kahn, O.Dideberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.17 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.730, 122.310, 91.941, 90.00, 90.99, 90.00
R / Rfree (%) 20.3 / 23.8

Other elements in 1ktw:

The structure of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Sodium (Na) 4 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 10 in 1ktw

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Calcium binding site 1 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca496

b:14.9
occ:1.00
 OE2 A:GLU108 2.4 11.1 1.0
OE1 A:GLU108 2.4 10.6 1.0
CD A:GLU108 2.8 12.7 1.0
CG A:GLU108 4.3 10.1 1.0
ND2 A:ASN89 4.5 9.2 1.0
O A:HOH672 4.7 15.5 1.0
CB A:PRO88 4.7 12.7 1.0
O A:HOH579 4.7 19.3 1.0
O A:HOH548 4.8 9.5 1.0
N A:ASN89 4.9 12.4 1.0

Calcium binding site 2 out of 10 in 1ktw

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Calcium binding site 2 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:15.4
occ:1.00
 OD1 A:ASP447 2.2 13.6 1.0
O A:HOH654 2.4 15.1 1.0
OG1 A:THR438 2.5 14.5 1.0
O A:TYR446 2.6 17.6 1.0
OD2 A:ASP445 2.7 18.0 1.0
OD1 A:ASP445 2.7 17.9 1.0
CG A:ASP445 3.0 20.3 1.0
CG A:ASP447 3.4 17.7 1.0
CB A:THR438 3.4 16.5 1.0
C A:TYR446 3.5 17.9 1.0
CA A:ASP447 3.9 16.0 1.0
CA A:CA9 3.9 22.1 1.0
N A:ASP447 4.1 15.5 1.0
CB A:ASP447 4.1 17.0 1.0
N A:TYR446 4.3 19.8 1.0
CG2 A:THR438 4.3 14.5 1.0
OD2 A:ASP447 4.4 19.3 1.0
O A:HOH819 4.5 34.1 1.0
O A:THR438 4.5 20.3 1.0
CB A:ASP445 4.6 20.9 1.0
C A:THR438 4.6 20.2 1.0
CA A:TYR446 4.6 17.2 1.0
CA A:THR438 4.6 16.5 1.0
OD1 A:ASP436 4.6 13.9 1.0
O A:HOH707 4.6 34.8 1.0
CA A:GLU440 4.6 28.8 1.0
OD2 A:ASP436 4.7 18.8 1.0
N A:GLU440 4.8 26.1 1.0

Calcium binding site 3 out of 10 in 1ktw

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Calcium binding site 3 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca5

b:15.4
occ:1.00
 OD1 A:ASN145 2.3 14.5 1.0
O A:SER109 2.4 12.6 1.0
O A:GLY146 2.4 10.8 1.0
O A:HOH705 2.7 32.0 1.0
OG A:SER109 2.9 25.8 1.0
CG A:ASN145 3.4 16.7 1.0
C A:SER109 3.5 15.1 1.0
C A:GLY146 3.6 14.3 1.0
ND2 A:ASN145 3.9 18.2 1.0
CB A:SER109 4.1 16.6 1.0
CA A:SER109 4.1 15.1 1.0
C A:ASN145 4.2 14.8 1.0
O A:ASN145 4.3 14.7 1.0
N A:GLY146 4.3 14.4 1.0
CA A:GLY146 4.5 11.7 1.0
OD1 A:ASP110 4.5 22.8 0.8
N A:PHE147 4.6 13.0 1.0
CA A:PHE147 4.6 12.3 1.0
CB A:ASN145 4.6 15.6 1.0
N A:ASP110 4.6 15.3 1.0
O A:HOH777 4.7 32.0 1.0
O A:HOH710 4.7 25.4 1.0
CA A:ASN145 4.8 14.5 1.0
CA A:ASP110 4.8 17.2 1.0
O A:HOH682 4.9 30.1 1.0

Calcium binding site 4 out of 10 in 1ktw

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Calcium binding site 4 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca7

b:15.5
occ:1.00
 O A:HOH596 2.4 11.6 1.0
OD1 A:ASP61 2.4 16.9 1.0
O A:SER63 2.5 16.8 1.0
O A:HOH605 2.5 17.7 1.0
OD2 A:ASP65 2.5 12.3 1.0
O A:ASN58 2.5 16.5 1.0
OD1 A:ASP65 2.5 13.4 1.0
CG A:ASP65 2.8 14.9 1.0
CG A:ASP61 3.5 20.1 1.0
C A:SER63 3.5 17.8 1.0
C A:ASN58 3.6 14.6 1.0
OD2 A:ASP61 3.8 14.8 0.5
N A:SER63 3.9 18.3 1.0
CA A:SER63 4.1 18.6 1.0
CB A:ASN58 4.2 17.6 1.0
CA A:ASN58 4.3 16.4 1.0
N A:ASN58 4.3 15.7 1.0
CB A:ASP65 4.3 13.1 1.0
O A:ASP61 4.3 21.3 1.0
O A:THR91 4.4 14.9 1.0
CB A:SER63 4.5 21.2 1.0
C A:ASP64 4.5 16.0 1.0
C A:ASP61 4.6 20.7 1.0
N A:ASP64 4.6 16.5 1.0
O A:ASP64 4.6 13.1 1.0
N A:ASP65 4.6 13.9 1.0
N A:GLY59 4.7 16.5 1.0
CB A:ASP61 4.8 18.6 1.0
N A:HIS93 4.8 12.3 1.0
O A:HOH590 4.8 27.3 1.0
C A:THR62 4.8 18.7 1.0
N A:ASP61 4.9 20.4 1.0
CA A:TYR92 4.9 12.2 1.0
CA A:ASP65 4.9 13.2 1.0
ND1 A:HIS93 4.9 16.4 1.0
CA A:GLY59 5.0 17.6 1.0
CA A:ASP64 5.0 16.0 1.0
CA A:ASP61 5.0 19.9 1.0

Calcium binding site 5 out of 10 in 1ktw

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Calcium binding site 5 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca9

b:22.1
occ:1.00
 OD2 A:ASP447 2.4 19.3 1.0
OD2 A:ASP445 2.5 18.0 1.0
OD1 A:ASP447 2.5 13.6 1.0
O A:HOH780 2.6 26.8 1.0
CG A:ASP447 2.8 17.7 1.0
CG A:ASP445 3.7 20.3 1.0
CA A:CA3 3.9 15.4 1.0
CB A:ASP447 4.3 17.0 1.0
CB A:ASP445 4.4 20.9 1.0
OD1 A:ASP445 4.6 17.9 1.0
O A:GLU440 4.7 28.1 1.0
O A:TYR446 4.9 17.6 1.0
C A:TYR446 4.9 17.9 1.0
N A:ASP447 5.0 15.5 1.0

Calcium binding site 6 out of 10 in 1ktw

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Calcium binding site 6 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2

b:16.0
occ:1.00
 O B:HOH565 2.4 16.7 1.0
O B:HOH623 2.5 16.9 1.0
OE1 B:GLU108 2.5 10.8 1.0
OE2 B:GLU108 2.5 11.5 1.0
O B:HOH631 2.6 20.8 1.0
CD B:GLU108 2.9 13.0 1.0
CG B:GLU108 4.4 11.0 1.0
ND2 B:ASN89 4.6 14.2 1.0
CB B:PRO88 4.7 12.9 1.0
O B:HOH609 4.8 25.1 1.0
N B:ASN89 4.9 13.8 1.0
O B:HOH570 5.0 16.4 1.0

Calcium binding site 7 out of 10 in 1ktw

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Calcium binding site 7 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:17.5
occ:1.00
 OD1 B:ASP447 2.2 19.0 1.0
OG1 B:THR438 2.4 18.2 1.0
O B:HOH637 2.5 15.9 1.0
O B:TYR446 2.5 19.0 1.0
OD1 B:ASP445 2.6 22.3 1.0
OD2 B:ASP445 2.6 21.5 1.0
CG B:ASP445 2.9 24.0 1.0
CB B:THR438 3.4 19.4 1.0
CG B:ASP447 3.4 20.7 1.0
C B:TYR446 3.5 19.9 1.0
CA B:CA10 3.8 27.0 1.0
CA B:ASP447 3.9 19.2 1.0
N B:ASP447 4.1 18.9 1.0
CB B:ASP447 4.1 19.6 1.0
N B:TYR446 4.2 20.5 1.0
CG2 B:THR438 4.3 20.3 1.0
OD2 B:ASP447 4.4 21.5 1.0
CB B:ASP445 4.4 22.4 1.0
O B:THR438 4.5 20.7 1.0
C B:THR438 4.5 21.5 1.0
CA B:THR438 4.6 20.2 1.0
CA B:TYR446 4.6 18.9 1.0
CA B:GLU440 4.6 29.0 1.0
OD1 B:ASP436 4.7 19.7 1.0
OD2 B:ASP436 4.7 21.6 1.0
N B:GLU440 4.7 26.5 1.0
C B:ASP445 5.0 23.0 1.0

Calcium binding site 8 out of 10 in 1ktw

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Calcium binding site 8 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:18.4
occ:1.00
 OD1 B:ASN145 2.3 17.8 1.0
O B:GLY146 2.4 12.4 1.0
O B:SER109 2.4 18.4 1.0
O B:HOH589 2.5 21.6 1.0
O B:HOH698 2.7 41.5 1.0
OG B:SER109 2.9 26.6 1.0
CG B:ASN145 3.4 17.9 1.0
C B:SER109 3.5 18.5 1.0
C B:GLY146 3.6 15.1 1.0
ND2 B:ASN145 4.0 21.4 1.0
CB B:SER109 4.0 18.8 1.0
CA B:SER109 4.1 18.4 1.0
C B:ASN145 4.3 15.8 1.0
O B:ASN145 4.3 15.6 1.0
N B:GLY146 4.4 15.2 1.0
CA B:GLY146 4.5 13.3 1.0
N B:PHE147 4.6 14.8 1.0
CA B:PHE147 4.6 15.4 1.0
CB B:ASN145 4.6 17.7 1.0
N B:ASP110 4.6 18.9 1.0
O B:HOH569 4.7 16.7 1.0
OD1 B:ASP110 4.7 22.9 0.8
O B:HOH740 4.8 41.5 1.0
CA B:ASN145 4.9 15.4 1.0
CA B:ASP110 4.9 18.1 1.0
O B:HOH540 4.9 19.6 1.0

Calcium binding site 9 out of 10 in 1ktw

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Calcium binding site 9 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8

b:24.6
occ:1.00
 O B:SER63 2.4 25.9 1.0
O B:ASN58 2.5 22.2 1.0
OD2 B:ASP65 2.5 14.2 1.0
OD1 B:ASP61 2.5 29.3 1.0
O B:HOH731 2.5 22.1 1.0
OD1 B:ASP65 2.6 17.6 1.0
CG B:ASP65 2.8 18.6 1.0
C B:SER63 3.4 27.2 1.0
CG B:ASP61 3.6 31.9 1.0
C B:ASN58 3.6 21.3 1.0
N B:SER63 3.9 28.4 1.0
OD2 B:ASP61 3.9 30.0 0.5
CA B:SER63 4.0 28.6 1.0
CB B:ASN58 4.3 25.1 1.0
CB B:SER63 4.3 29.7 1.0
CA B:ASN58 4.3 22.3 1.0
CB B:ASP65 4.3 16.4 1.0
N B:ASN58 4.3 21.5 1.0
O B:ASP64 4.4 21.2 1.0
C B:ASP64 4.4 22.1 1.0
O B:ASP61 4.5 29.4 1.0
N B:ASP64 4.5 24.8 1.0
O B:THR91 4.6 18.8 1.0
C B:ASP61 4.6 31.9 1.0
N B:ASP65 4.6 19.1 1.0
N B:GLY59 4.7 21.9 1.0
ND1 B:HIS93 4.7 21.5 1.0
C B:THR62 4.8 29.9 1.0
CA B:ASP65 4.9 16.8 1.0
CB B:ASP61 4.9 30.8 1.0
O B:HOH597 4.9 19.5 1.0
CA B:GLY59 4.9 22.9 1.0
CA B:ASP64 4.9 23.4 1.0
N B:ASP61 4.9 32.7 1.0
N B:THR62 5.0 31.2 1.0
N B:HIS93 5.0 16.4 1.0

Calcium binding site 10 out of 10 in 1ktw

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Calcium binding site 10 out of 10 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca10

b:27.0
occ:1.00
 OD2 B:ASP447 2.4 21.5 1.0
OD2 B:ASP445 2.4 21.5 1.0
OD1 B:ASP447 2.5 19.0 1.0
CG B:ASP447 2.8 20.7 1.0
CG B:ASP445 3.6 24.0 1.0
CA B:CA4 3.8 17.5 1.0
CB B:ASP447 4.3 19.6 1.0
CB B:ASP445 4.4 22.4 1.0
OD1 B:ASP445 4.6 22.3 1.0
O B:GLU440 4.8 28.8 1.0
O B:TYR446 4.8 19.0 1.0
C B:TYR446 4.8 19.9 1.0
N B:ASP447 4.9 18.9 1.0

Reference:

G.Michel, W.Helbert, R.Kahn, O.Dideberg, B.Kloareg. The Structural Bases of the Processive Degradation of Iota-Carrageenan, A Main Cell Wall Polysaccharide of Red Algae. J.Mol.Biol. V. 334 421 2003.
ISSN: ISSN 0022-2836
PubMed: 14623184
DOI: 10.1016/J.JMB.2003.09.056
Page generated: Thu Jul 11 11:29:02 2024

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