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Sodium in PDB 4bax: Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor

Enzymatic activity of Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor

All present enzymatic activity of Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor:
6.3.1.2;

Protein crystallography data

The structure of Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor, PDB code: 4bax was solved by K.Zeth, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.996 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 97.120, 113.000, 194.440, 90.00, 98.55, 90.00
R / Rfree (%) 20.6 / 23.58

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor (pdb code 4bax). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor, PDB code: 4bax:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 4bax

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Sodium binding site 1 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1350

b:42.6
occ:1.00
 OD2 A:ASP158 3.3 34.3 1.0
O A:PHE216 3.9 28.9 1.0
OD1 A:ASP158 3.9 34.1 1.0
CB A:PHE216 4.0 28.1 1.0
CG A:ASP158 4.0 33.8 1.0
CG1 A:VAL218 4.2 38.7 1.0
CD2 A:PHE216 4.2 26.8 1.0
CG2 A:VAL159 4.5 15.4 1.0
CG A:PHE216 4.6 27.4 1.0
C A:PHE216 4.8 29.3 1.0
CA A:PHE216 4.8 29.4 1.0

Sodium binding site 2 out of 8 in 4bax

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Sodium binding site 2 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1351

b:45.6
occ:1.00
 O A:HOH2007 3.7 35.6 1.0
NZ A:LYS24 3.8 32.9 1.0
CZ A:TYR210 3.9 24.3 1.0
O B:HOH2049 4.1 39.7 1.0
CE1 A:TYR210 4.1 24.4 1.0
O B:VAL149 4.1 26.2 1.0
O A:HOH2008 4.2 41.2 1.0
CE2 A:TYR210 4.2 23.9 1.0
OE1 B:GLU153 4.3 35.3 1.0
OH A:TYR210 4.3 24.7 1.0
O A:HOH2081 4.4 36.5 1.0
CD1 A:TYR210 4.5 24.4 1.0
O B:HOH2048 4.5 34.0 1.0
CD2 A:TYR210 4.5 24.2 1.0
CG A:TYR210 4.7 24.5 1.0
O A:HOH2078 4.9 32.8 1.0
O A:HOH2080 4.9 16.0 1.0
CE A:LYS24 4.9 33.0 1.0
CG1 B:VAL149 5.0 9.6 1.0

Sodium binding site 3 out of 8 in 4bax

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Sodium binding site 3 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1350

b:37.3
occ:1.00
 OD2 B:ASP158 3.5 29.6 1.0
OD1 B:ASP158 3.6 30.0 1.0
CG B:ASP158 4.0 29.7 1.0
CG1 B:VAL218 4.2 30.1 1.0
CG2 B:VAL159 4.4 24.5 1.0
O B:PHE216 4.8 32.2 1.0
CB B:PHE216 4.8 30.8 1.0
CA B:GLY156 4.8 27.7 1.0
CD2 B:LEU131 4.9 24.3 1.0
CD2 B:PHE216 5.0 29.9 1.0

Sodium binding site 4 out of 8 in 4bax

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Sodium binding site 4 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1000

b:34.5
occ:1.00
 O C:HOH2012 3.6 22.4 1.0
O D:HOH2063 3.9 31.6 1.0
O D:VAL149 3.9 26.0 1.0
CZ C:TYR210 3.9 21.3 1.0
CE1 C:TYR210 4.0 21.5 1.0
NZ C:LYS24 4.0 31.1 1.0
CE2 C:TYR210 4.1 21.1 1.0
OE1 D:GLU153 4.2 33.8 1.0
O C:HOH2004 4.3 38.1 1.0
O C:HOH2097 4.3 28.4 1.0
CD1 C:TYR210 4.3 22.0 1.0
O D:HOH2062 4.3 29.6 1.0
CD2 C:TYR210 4.3 21.6 1.0
O C:HOH2013 4.3 42.5 1.0
OH C:TYR210 4.3 21.3 1.0
CG C:TYR210 4.4 22.3 1.0
CG1 D:VAL149 4.5 24.0 1.0
O D:HOH2064 4.6 28.4 1.0
O C:HOH2098 4.7 29.7 1.0
C D:VAL149 4.9 25.2 1.0
O C:HOH2094 4.9 12.5 1.0

Sodium binding site 5 out of 8 in 4bax

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Sodium binding site 5 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1350

b:35.0
occ:1.00
 OD2 D:ASP158 3.3 35.4 1.0
OD1 D:ASP158 3.5 35.6 1.0
CG D:ASP158 3.9 35.6 1.0
CG1 D:VAL218 4.1 33.2 1.0
O D:HOH2052 4.2 36.4 1.0
O D:PHE216 4.5 31.0 1.0
CG2 D:VAL159 4.5 24.1 1.0
CB D:PHE216 4.5 31.8 1.0
CD2 D:PHE216 4.7 32.1 1.0

Sodium binding site 6 out of 8 in 4bax

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Sodium binding site 6 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na1350

b:39.1
occ:1.00
 OG E:SER241 3.8 39.4 1.0
CB E:TYR316 4.0 44.2 1.0
CB E:PRO192 4.2 49.5 1.0
O E:ASN239 4.2 35.6 1.0
CB E:ASN239 4.3 37.2 1.0
CG E:TYR316 4.3 44.0 1.0
O E:VAL115 4.3 36.2 1.0
C E:ASN239 4.3 36.4 1.0
CB E:SER241 4.4 40.4 1.0
N E:SER241 4.4 40.5 1.0
N E:PHE240 4.4 37.2 1.0
CG1 E:VAL115 4.4 37.0 1.0
C E:PHE240 4.5 39.6 1.0
CA E:PHE240 4.6 38.2 1.0
C E:VAL115 4.6 36.4 1.0
CD1 E:TYR316 4.7 44.1 1.0
CB E:VAL115 4.8 37.6 1.0
N E:GLY117 4.8 34.1 1.0
CD2 E:TYR316 4.8 43.6 1.0
CG E:PRO192 4.9 49.5 1.0
C E:PHE116 4.9 34.3 1.0
CA E:ASN239 5.0 36.3 1.0

Sodium binding site 7 out of 8 in 4bax

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Sodium binding site 7 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1000

b:43.2
occ:1.00
 NZ J:LYS24 3.6 33.8 1.0
O J:HOH2012 3.7 32.7 1.0
CZ J:TYR210 4.0 26.1 1.0
O F:VAL149 4.1 29.1 1.0
CE1 J:TYR210 4.2 26.2 1.0
CE2 J:TYR210 4.2 25.9 1.0
CD1 J:TYR210 4.4 26.1 1.0
CD2 J:TYR210 4.4 25.8 1.0
OE1 F:GLU153 4.5 37.5 1.0
CG J:TYR210 4.5 25.8 1.0
OH J:TYR210 4.5 26.3 1.0
CG1 F:VAL149 4.6 26.8 1.0
CE J:LYS24 4.6 33.4 1.0
O J:HOH2075 4.8 26.9 1.0
O F:HOH2062 4.8 31.8 1.0

Sodium binding site 8 out of 8 in 4bax

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Sodium binding site 8 out of 8 in the Crystal Structure of Glutamine Synthetase From Streptomyces Coelicolor


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 Glutamine Synthetase From Streptomyces Coelicolor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1000

b:44.7
occ:1.00
 NZ G:LYS24 3.6 34.4 1.0
CZ G:TYR210 4.1 28.0 1.0
O G:HOH2012 4.1 36.1 1.0
OE1 H:GLU153 4.2 36.7 1.0
O H:VAL149 4.2 29.2 1.0
CE1 G:TYR210 4.3 27.6 1.0
CE2 G:TYR210 4.3 28.0 1.0
OH G:TYR210 4.4 28.1 1.0
O G:HOH2070 4.5 27.8 1.0
CE G:LYS24 4.7 34.5 1.0
CD1 G:TYR210 4.7 27.6 1.0
CD2 G:TYR210 4.7 27.9 1.0
O G:HOH2003 4.9 26.5 1.0
CG G:TYR210 4.9 27.7 1.0

Reference:

K.Zeth, K.Zeth. N/A N/A.
Page generated: Mon Oct 7 14:29:35 2024

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