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Sodium in PDB 1jed: Crystal Structure of Atp Sulfurylase in Complex with Adp

Enzymatic activity of Crystal Structure of Atp Sulfurylase in Complex with Adp

All present enzymatic activity of Crystal Structure of Atp Sulfurylase in Complex with Adp:
2.7.7.4;

Protein crystallography data

The structure of Crystal Structure of Atp Sulfurylase in Complex with Adp, PDB code: 1jed was solved by T.C.Ullrich, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.81 / 2.95
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 186.135, 186.135, 223.253, 90.00, 90.00, 120.00
R / Rfree (%) 19.2 / 22.7

Other elements in 1jed:

The structure of Crystal Structure of Atp Sulfurylase in Complex with Adp also contains other interesting chemical elements:

Cadmium (Cd) 11 atoms
Magnesium (Mg) 4 atoms
Calcium (Ca) 6 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Atp Sulfurylase in Complex with Adp (pdb code 1jed). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Crystal Structure of Atp Sulfurylase in Complex with Adp, PDB code: 1jed:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 1jed

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Sodium binding site 1 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na518

b:47.4
occ:1.00
 O A:HOH947 2.3 53.5 1.0
O A:HOH1083 3.0 46.1 1.0
CB A:ASP108 4.3 43.9 1.0
O A:ASP107 4.5 37.7 1.0
OE1 A:GLU109 4.9 45.7 1.0
O A:ASP108 4.9 42.0 1.0

Sodium binding site 2 out of 12 in 1jed

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Sodium binding site 2 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na522

b:30.6
occ:1.00
 O A:HOH1174 2.2 44.1 1.0
OD2 A:ASP309 2.5 34.3 1.0
OD1 A:ASP309 2.8 33.3 1.0
CG A:ASP309 3.0 32.2 1.0
N A:GLY306 4.3 26.1 1.0
CA A:GLY306 4.4 26.4 1.0
CB A:ASP309 4.5 29.9 1.0
NH2 A:ARG134 4.7 19.2 1.0
NH1 A:ARG134 4.7 17.3 1.0

Sodium binding site 3 out of 12 in 1jed

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Sodium binding site 3 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na523

b:43.8
occ:1.00
 O A:HOH1139 2.4 32.6 1.0
OD1 A:ASP322 2.7 35.9 1.0
OD2 A:ASP322 3.0 36.3 1.0
CG A:ASP322 3.3 33.3 1.0
CB A:PRO2 4.6 25.8 1.0
CB A:ASP322 4.8 29.1 1.0
O A:ASP322 4.9 28.0 1.0

Sodium binding site 4 out of 12 in 1jed

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Sodium binding site 4 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na525

b:2.1
occ:1.00
 OE1 A:GLU130 2.2 39.3 1.0
O A:HOH1022 2.3 26.6 1.0
OE2 A:GLU130 2.4 38.5 1.0
CD A:GLU130 2.6 38.8 1.0
O A:HOH654 2.8 2.6 1.0
CG A:GLU130 4.2 36.5 1.0
CG2 A:THR126 4.4 28.6 1.0
O A:HOH922 4.5 14.7 1.0
O A:HOH658 4.7 31.6 1.0

Sodium binding site 5 out of 12 in 1jed

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Sodium binding site 5 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na526

b:34.0
occ:1.00
 OE1 A:GLU324 2.8 44.4 1.0
CD A:GLU324 3.6 41.9 1.0
O A:HOH1178 3.9 40.4 1.0
NE2 A:HIS285 4.2 18.9 1.0
CG A:GLU324 4.3 37.9 1.0
OE2 A:GLU324 4.3 45.1 1.0
NH1 A:ARG190 4.4 28.1 1.0
O A:HOH1020 4.6 57.2 1.0

Sodium binding site 6 out of 12 in 1jed

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Sodium binding site 6 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na527

b:22.6
occ:1.00
 O A:HOH1036 2.2 33.5 1.0
OD1 A:ASP505 2.4 26.5 1.0
OD2 A:ASP505 2.4 24.6 1.0
O A:HOH1104 2.5 25.0 1.0
CG A:ASP505 2.7 24.9 1.0
CB A:ASP505 4.3 24.5 1.0
O A:ASP505 4.6 26.2 1.0

Sodium binding site 7 out of 12 in 1jed

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Sodium binding site 7 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na540

b:35.8
occ:1.00
 O B:HOH853 2.3 20.0 1.0
O B:ASP107 4.1 38.6 1.0
CB B:ASP108 4.4 42.4 1.0
OE1 B:GLU109 4.5 46.5 1.0
O B:ASP108 4.9 40.2 1.0

Sodium binding site 8 out of 12 in 1jed

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Sodium binding site 8 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na541

b:27.3
occ:1.00
 O B:HOH1031 2.4 20.5 1.0
OD2 B:ASP309 2.6 30.6 1.0
OD1 B:ASP309 3.0 30.0 1.0
CG B:ASP309 3.1 29.2 1.0
O B:HOH746 3.4 29.3 1.0
O B:HOH1163 3.5 37.0 1.0
N B:GLY306 4.5 28.1 1.0
CA B:GLY306 4.5 26.6 1.0
CB B:ASP309 4.6 27.6 1.0
NH2 B:ARG134 4.8 18.7 1.0
NH1 B:ARG134 4.9 17.3 1.0

Sodium binding site 9 out of 12 in 1jed

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Sodium binding site 9 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na542

b:24.0
occ:1.00
 O B:HOH823 2.0 41.2 1.0
OE1 B:GLU324 2.7 46.7 1.0
CD B:GLU324 3.4 44.7 1.0
O B:HOH1204 3.5 41.5 1.0
OE2 B:GLU324 4.0 47.4 1.0
CG B:GLU324 4.2 39.9 1.0
NE2 B:HIS285 4.5 21.6 1.0
NH1 B:ARG190 4.8 25.3 1.0

Sodium binding site 10 out of 12 in 1jed

Go back to Sodium Binding Sites List in 1jed
Sodium binding site 10 out of 12 in the Crystal Structure of Atp Sulfurylase in Complex with Adp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Atp Sulfurylase in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na543

b:45.9
occ:1.00
 O B:HOH1002 2.6 26.6 1.0
OD1 B:ASP322 3.4 35.6 1.0
O B:HOH868 3.6 29.7 1.0
CG B:ASP322 3.7 33.9 1.0
CB B:ASP322 4.1 30.2 1.0
O B:HOH951 4.2 41.4 1.0
OD2 B:ASP322 4.3 36.6 1.0
O B:HIS319 4.4 32.3 1.0
CA B:ASP322 4.8 27.3 1.0
O B:GLU320 5.0 30.4 1.0

Reference:

T.C.Ullrich, R.Huber. The Complex Structures of Atp Sulfurylase with Thiosulfate, Adp and Chlorate Reveal New Insights in Inhibitory Effects and the Catalytic Cycle. J.Mol.Biol. V. 313 1117 2001.
ISSN: ISSN 0022-2836
PubMed: 11700067
DOI: 10.1006/JMBI.2001.5098
Page generated: Sun Oct 6 18:55:48 2024

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