Atomistry » Sodium » PDB 1k7e-1l0i » 1ktw
Atomistry »
  Sodium »
    PDB 1k7e-1l0i »
      1ktw »

Sodium 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
Calcium (Ca) 10 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 4 in 1ktw

Go back to Sodium Binding Sites List in 1ktw
Sodium binding site 1 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na11

b:13.5
occ:1.00
O A:LEU159 2.3 12.6 1.0
O A:PHE184 2.4 10.1 1.0
O A:HOH531 2.4 9.8 1.0
OG1 A:THR182 2.4 11.4 1.0
O A:ILE183 2.5 12.8 1.0
C A:ILE183 3.4 13.7 1.0
C A:PHE184 3.4 10.8 1.0
CB A:THR182 3.5 13.4 1.0
C A:LEU159 3.5 14.4 1.0
C A:THR182 3.9 14.4 1.0
CA A:PHE184 3.9 11.8 1.0
CB A:PHE184 3.9 13.2 1.0
O A:THR182 3.9 14.5 1.0
N A:PHE184 4.0 10.8 1.0
O A:HOH533 4.0 9.1 1.0
N A:ILE183 4.1 13.8 1.0
CA A:THR182 4.3 13.4 1.0
N A:ALA160 4.4 13.7 1.0
CA A:LEU159 4.4 15.8 1.0
CA A:ILE183 4.4 13.5 1.0
O A:ALA185 4.5 8.9 1.0
O A:HOH551 4.5 13.5 1.0
N A:ALA185 4.5 9.4 1.0
C A:ALA185 4.5 9.0 1.0
N A:LEU159 4.5 17.0 1.0
CA A:ALA160 4.5 13.0 1.0
OD2 A:ASP179 4.6 12.7 1.0
CG2 A:THR182 4.7 11.4 1.0
CE2 A:PHE151 4.7 15.1 1.0
CB A:LEU159 4.7 14.4 1.0
N A:SER186 4.8 8.6 1.0
OD1 A:ASP179 4.9 14.9 1.0
CA A:ALA185 4.9 10.0 1.0

Sodium binding site 2 out of 4 in 1ktw

Go back to Sodium Binding Sites List in 1ktw
Sodium binding site 2 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na13

b:14.4
occ:1.00
OD2 A:ASP178 2.0 18.5 1.0
O A:HOH724 2.6 38.1 1.0
CG A:ASP178 2.8 16.2 1.0
OD1 A:ASP178 2.9 15.8 1.0
NZ A:LYS152 4.1 17.9 1.0
CB A:ASP178 4.3 15.3 1.0
CE A:LYS152 4.7 18.9 1.0
ND2 A:ASN212 4.7 12.2 1.0
CD1 A:LEU148 5.0 10.8 1.0

Sodium binding site 3 out of 4 in 1ktw

Go back to Sodium Binding Sites List in 1ktw
Sodium binding site 3 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na12

b:19.7
occ:1.00
O B:LEU159 2.3 16.2 1.0
O B:PHE184 2.4 16.6 1.0
OG1 B:THR182 2.4 17.4 1.0
O B:HOH537 2.5 12.5 1.0
O B:ILE183 2.6 20.5 1.0
C B:PHE184 3.4 17.7 1.0
C B:ILE183 3.5 20.2 1.0
C B:LEU159 3.5 19.3 1.0
CB B:THR182 3.5 18.6 1.0
CB B:PHE184 3.8 18.9 1.0
CA B:PHE184 3.9 18.9 1.0
C B:THR182 3.9 20.2 1.0
N B:PHE184 4.0 19.2 1.0
O B:THR182 4.0 21.6 1.0
O B:HOH542 4.0 15.1 1.0
N B:ILE183 4.2 19.3 1.0
CA B:THR182 4.4 19.3 1.0
O B:ALA185 4.4 13.1 1.0
CA B:LEU159 4.4 19.9 1.0
N B:ALA160 4.4 18.3 1.0
C B:ALA185 4.5 13.5 1.0
N B:LEU159 4.5 21.0 1.0
N B:ALA185 4.5 16.6 1.0
CA B:ILE183 4.5 20.7 1.0
O B:HOH582 4.5 22.4 1.0
CA B:ALA160 4.6 16.8 1.0
OD2 B:ASP179 4.6 19.6 1.0
CG2 B:THR182 4.7 18.8 1.0
CB B:LEU159 4.8 19.2 1.0
OD1 B:ASP179 4.8 20.8 1.0
N B:SER186 4.8 12.9 1.0
CE2 B:PHE151 4.8 20.6 1.0
CA B:ALA185 4.8 14.3 1.0

Sodium binding site 4 out of 4 in 1ktw

Go back to Sodium Binding Sites List in 1ktw
Sodium binding site 4 out of 4 in the Iota-Carrageenase Complexed to Iota-Carrageenan Fragments


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Iota-Carrageenase Complexed to Iota-Carrageenan Fragments within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na14

b:19.7
occ:1.00
OD2 B:ASP178 2.1 19.8 1.0
O B:HOH748 2.4 46.3 1.0
CG B:ASP178 2.9 20.0 1.0
OD1 B:ASP178 2.9 18.6 1.0
NZ B:LYS152 4.2 27.4 1.0
CB B:ASP178 4.3 19.6 1.0
ND2 B:ASN212 4.6 18.7 1.0
CE B:LYS152 4.7 27.2 1.0
CD1 B:LEU148 5.0 15.1 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: Tue Dec 15 05:28:43 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy