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Sodium in PDB 1g8g: Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps

Enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps

All present enzymatic activity of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps:
2.7.7.4;

Protein crystallography data

The structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps, PDB code: 1g8g was solved by T.C.Ullrich, M.Blaesse, R.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.85 / 2.60
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 185.922, 185.922, 223.674, 90.00, 90.00, 120.00
R / Rfree (%) 17.6 / 22.7

Other elements in 1g8g:

The structure of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps also contains other interesting chemical elements:

Cadmium (Cd) 11 atoms
Magnesium (Mg) 2 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 Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps (pdb code 1g8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 12 binding sites of Sodium where determined in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps, PDB code: 1g8g:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 12 in 1g8g

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Sodium binding site 1 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na518

b:48.2
occ:1.00
 O A:HOH1135 2.3 54.2 1.0
O A:ASP107 4.5 40.2 1.0
O A:HOH971 4.6 54.8 1.0
CB A:ASP108 4.7 44.3 1.0

Sodium binding site 2 out of 12 in 1g8g

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Sodium binding site 2 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na522

b:36.0
occ:1.00
 O A:HOH1190 2.2 56.4 1.0
O A:HOH1173 2.5 50.4 1.0
OD2 A:ASP309 2.7 37.1 1.0
OD1 A:ASP309 2.9 36.6 1.0
CG A:ASP309 3.1 35.8 1.0
CA A:GLY306 4.3 30.2 1.0
O A:HOH1174 4.3 40.3 1.0
N A:GLY306 4.3 30.3 1.0
CB A:ASP309 4.6 33.1 1.0
NH1 A:ARG134 4.9 31.0 1.0
O A:HOH762 4.9 40.4 1.0
NH2 A:ARG134 4.9 31.3 1.0

Sodium binding site 3 out of 12 in 1g8g

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Sodium binding site 3 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na523

b:56.0
occ:1.00
 O A:HOH740 2.3 39.5 1.0
OD1 A:ASP322 2.3 42.8 1.0
OD2 A:ASP322 2.7 40.9 1.0
CG A:ASP322 2.9 40.5 1.0
CB A:ASP322 4.4 35.2 1.0
O A:HOH1161 4.5 41.0 1.0
O A:ASP322 4.9 33.3 1.0

Sodium binding site 4 out of 12 in 1g8g

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Sodium binding site 4 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na525

b:16.6
occ:1.00
 OE1 A:GLU130 2.1 47.0 1.0
O A:HOH1101 2.6 39.9 1.0
OE2 A:GLU130 2.6 49.2 1.0
CD A:GLU130 2.7 48.2 1.0
O A:HOH1002 2.8 35.7 1.0
CG A:GLU130 4.2 45.1 1.0
CG2 A:THR126 4.3 39.0 1.0
O A:HOH693 4.7 43.1 1.0
O A:HOH1131 4.7 50.1 1.0

Sodium binding site 5 out of 12 in 1g8g

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Sodium binding site 5 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na526

b:36.4
occ:1.00
 OE2 A:GLU324 2.3 46.8 1.0
O A:HOH985 2.6 51.6 1.0
CD A:GLU324 3.4 46.5 1.0
NE2 A:HIS285 4.0 26.3 1.0
NH1 A:ARG190 4.1 21.1 1.0
OE1 A:GLU324 4.2 48.7 1.0
CG A:GLU324 4.3 42.4 1.0
CD2 A:HIS285 4.8 26.4 1.0
O A:HOH1116 4.9 56.4 1.0
CE1 A:HIS285 4.9 24.8 1.0

Sodium binding site 6 out of 12 in 1g8g

Go back to Sodium Binding Sites List in 1g8g
Sodium binding site 6 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na527

b:41.7
occ:1.00
 O A:HOH930 1.9 41.5 1.0
O A:HOH987 2.5 45.0 1.0
OD1 A:ASP505 2.5 34.7 1.0
OD2 A:ASP505 2.5 37.9 1.0
CG A:ASP505 2.8 34.6 1.0
CB A:ASP505 4.3 33.4 1.0
O A:ASP505 4.7 31.4 1.0

Sodium binding site 7 out of 12 in 1g8g

Go back to Sodium Binding Sites List in 1g8g
Sodium binding site 7 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na536

b:37.0
occ:1.00
 O B:HOH851 2.3 59.3 1.0
O B:HOH821 2.7 43.8 1.0
O B:ASP107 4.5 47.6 1.0
OE1 B:GLU109 4.6 53.5 1.0
CB B:ASP108 5.0 50.4 1.0

Sodium binding site 8 out of 12 in 1g8g

Go back to Sodium Binding Sites List in 1g8g
Sodium binding site 8 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na540

b:43.1
occ:1.00
 O B:HOH809 2.0 29.3 1.0
O B:HOH1141 2.0 49.5 1.0
OD2 B:ASP309 2.7 35.0 1.0
OD1 B:ASP309 2.9 35.6 1.0
CG B:ASP309 3.0 33.7 1.0
O B:HOH897 3.3 64.2 1.0
CB B:ASP309 4.3 33.0 1.0
O B:HOH1010 4.4 55.6 1.0
OE2 B:GLU312 4.5 45.8 1.0
NH1 B:ARG134 4.6 29.2 1.0
NH2 B:ARG134 4.8 30.1 1.0
N B:GLY306 4.8 30.7 1.0
O B:HOH1111 4.8 49.3 1.0
CA B:ASP309 4.9 31.1 1.0
CA B:GLY306 4.9 31.2 1.0
O B:HOH902 4.9 36.2 1.0

Sodium binding site 9 out of 12 in 1g8g

Go back to Sodium Binding Sites List in 1g8g
Sodium binding site 9 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na541

b:39.6
occ:1.00
 O B:HOH868 2.2 43.4 1.0
OE1 B:GLU324 2.4 54.5 1.0
O B:HOH1385 2.6 60.8 1.0
CD B:GLU324 3.5 52.7 1.0
CG B:GLU324 3.9 46.6 1.0
NE2 B:HIS285 4.4 27.4 1.0
NH1 B:ARG190 4.4 26.1 1.0
OE2 B:GLU324 4.6 54.4 1.0
O B:HOH1041 5.0 46.9 1.0

Sodium binding site 10 out of 12 in 1g8g

Go back to Sodium Binding Sites List in 1g8g
Sodium binding site 10 out of 12 in the Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Atp Sulfurylase From S. Cerevisiae: the Binary Product Complex with Aps within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na542

b:55.0
occ:1.00
 O B:HOH892 2.1 60.1 1.0
O B:HOH899 2.3 53.7 1.0
O B:HOH965 3.2 47.4 1.0
OD1 B:ASP322 3.3 48.1 1.0
O B:HOH1106 3.7 39.0 1.0
O B:HIS319 3.9 34.9 1.0
CG B:ASP322 4.1 43.8 1.0
CB B:ASP322 4.5 39.5 1.0

Reference:

T.C.Ullrich, M.Blaesse, R.Huber. Crystal Structure of Atp Sulfurylase From Saccharomyces Cerevisiae, A Key Enzyme in Sulfate Activation. Embo J. V. 20 316 2001.
ISSN: ISSN 0261-4189
PubMed: 11157739
DOI: 10.1093/EMBOJ/20.3.316
Page generated: Sun Oct 6 18:30:55 2024

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