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Sodium in PDB 7wzv: The Structure of A Twitch Radical Sam Dehydrogenase Spey

Protein crystallography data

The structure of The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7wzv was solved by J.H.Zhou, X.L.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.76 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.28, 93.579, 108.146, 90, 90, 90
R / Rfree (%) 20 / 23.5

Other elements in 7wzv:

The structure of The Structure of A Twitch Radical Sam Dehydrogenase Spey also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Iron (Fe) 16 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the The Structure of A Twitch Radical Sam Dehydrogenase Spey (pdb code 7wzv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the The Structure of A Twitch Radical Sam Dehydrogenase Spey, PDB code: 7wzv:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 7wzv

Go back to Sodium Binding Sites List in 7wzv
Sodium binding site 1 out of 5 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:41.1
occ:1.00
 O A:HOH636 2.3 49.4 1.0
O A:HOH661 2.8 50.0 1.0
N A:THR106 3.1 35.8 1.0
OG1 A:THR106 3.5 38.4 1.0
CA A:ALA105 3.6 35.1 1.0
CB A:PHE109 3.7 29.2 1.0
C A:ALA105 3.8 36.3 1.0
CG2 A:THR106 4.0 34.3 1.0
CB A:ALA105 4.0 25.1 1.0
O A:HOH625 4.0 35.8 1.0
CB A:THR106 4.1 36.6 1.0
CA A:THR106 4.1 35.2 1.0
O A:HOH619 4.4 49.8 1.0
N A:PHE109 4.6 30.3 1.0
CG A:PHE109 4.6 29.7 1.0
O A:THR106 4.6 35.1 1.0
O A:ARG104 4.6 30.1 1.0
CA A:PHE109 4.7 30.4 1.0
C A:THR106 4.8 35.7 1.0
N A:ALA105 4.8 30.5 1.0
CG2 A:VAL78 4.9 32.3 1.0
CD1 A:PHE109 4.9 30.5 1.0
CG1 A:VAL77 4.9 33.8 1.0

Sodium binding site 2 out of 5 in 7wzv

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Sodium binding site 2 out of 5 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na410

b:31.6
occ:1.00
 O B:VAL171 2.6 28.9 1.0
OG1 B:THR174 2.8 31.8 1.0
N B:SER247 3.0 26.4 1.0
C B:THR174 3.2 26.5 1.0
N B:CYS175 3.2 27.9 1.0
CA B:CYS175 3.3 28.6 1.0
O B:THR174 3.3 26.3 1.0
C B:VAL171 3.6 28.2 1.0
CG1 B:VAL248 3.7 27.2 1.0
CA B:GLY246 3.7 26.9 1.0
CG2 B:VAL248 3.8 28.1 1.0
N B:VAL248 3.8 26.9 1.0
CB B:CYS175 3.8 28.9 1.0
CB B:THR174 3.8 30.7 1.0
CA B:SER247 3.8 26.1 1.0
C B:GLY246 3.8 26.6 1.0
CA B:VAL171 3.9 28.7 1.0
CB B:SER247 3.9 27.6 1.0
CA B:THR174 4.0 26.9 1.0
O B:LEU245 4.0 27.7 1.0
CG1 B:VAL171 4.0 28.5 1.0
C B:SER247 4.1 26.4 1.0
CB B:VAL248 4.2 28.2 1.0
N B:THR174 4.3 27.4 1.0
OG B:SER247 4.4 29.8 1.0
CB B:VAL171 4.5 32.3 1.0
C B:CYS175 4.6 27.6 1.0
CA B:VAL248 4.7 30.0 1.0
O B:ASP170 4.7 28.6 1.0
N B:GLY246 4.7 27.4 1.0
C B:LEU245 4.7 29.2 1.0
N B:PHE172 4.8 29.3 1.0
SG B:CYS175 4.9 28.0 1.0
N B:LYS176 4.9 26.9 1.0

Sodium binding site 3 out of 5 in 7wzv

Go back to Sodium Binding Sites List in 7wzv
Sodium binding site 3 out of 5 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na411

b:33.9
occ:1.00
 O B:GLN29 2.8 29.2 1.0
N B:GLN255 3.1 28.9 1.0
CD2 B:HIS254 3.2 29.7 1.0
CE1 B:HIS252 3.2 31.7 1.0
O B:GLN255 3.3 35.1 1.0
CD2 B:PHE153 3.4 26.6 1.0
CA B:HIS254 3.4 28.1 1.0
CG B:HIS254 3.5 29.3 1.0
N B:GLN29 3.6 28.8 1.0
NE2 B:HIS254 3.6 29.2 1.0
CB B:PHE153 3.7 26.9 1.0
C B:GLN29 3.7 28.4 1.0
CG B:PHE153 3.7 26.5 1.0
CB B:GLN29 3.7 29.4 1.0
C B:HIS254 3.8 28.7 1.0
CA B:GLN29 3.9 29.0 1.0
CB B:HIS254 4.0 27.5 1.0
ND1 B:HIS254 4.0 28.3 1.0
ND1 B:HIS252 4.0 32.7 1.0
CE1 B:HIS254 4.1 29.3 1.0
C B:GLN255 4.1 34.0 1.0
CE2 B:PHE153 4.2 26.3 1.0
NE2 B:HIS252 4.2 32.2 1.0
CA B:GLN255 4.2 30.6 1.0
CB B:CYS28 4.2 28.7 1.0
O B:PRO253 4.2 33.0 1.0
C B:CYS28 4.3 28.8 1.0
CA B:CYS28 4.5 28.6 1.0
N B:HIS254 4.5 35.7 1.0
CD1 B:PHE153 4.7 26.0 1.0
CG B:GLN29 4.7 40.5 1.0
C B:PRO253 4.8 34.2 1.0
N B:PHE153 4.8 31.2 1.0
CG B:GLN255 4.8 34.8 1.0
CA B:PHE153 4.9 26.7 1.0
OE1 B:GLN29 4.9 38.1 1.0
N B:SER30 4.9 30.0 1.0

Sodium binding site 4 out of 5 in 7wzv

Go back to Sodium Binding Sites List in 7wzv
Sodium binding site 4 out of 5 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na412

b:32.5
occ:1.00
 O B:ARG193 2.7 25.8 1.0
NE B:ARG193 2.8 29.3 1.0
CD2 B:HIS184 3.2 26.6 1.0
O B:ALA178 3.3 32.1 1.0
O B:LEU177 3.4 25.9 1.0
CB B:ARG193 3.4 26.6 1.0
CA B:ARG193 3.4 26.8 1.0
NE2 B:HIS184 3.5 27.7 1.0
C B:ARG193 3.5 27.0 1.0
CA B:ALA178 3.5 27.8 1.0
CD B:ARG193 3.6 29.3 1.0
CZ B:ARG193 3.7 31.0 1.0
NH2 B:ARG193 3.8 29.7 1.0
C B:ALA178 3.8 30.4 1.0
O B:HOH561 3.8 33.6 1.0
N B:SER183 4.1 25.1 1.0
CG B:ARG193 4.2 27.8 1.0
C B:LEU177 4.2 25.5 1.0
CA B:ASN182 4.2 26.2 1.0
C B:ASN182 4.3 27.2 1.0
N B:ALA178 4.4 26.8 1.0
CG B:HIS184 4.4 28.3 1.0
CB B:ALA178 4.5 26.4 1.0
N B:HIS184 4.5 25.5 1.0
C B:SER183 4.7 27.1 1.0
CE1 B:HIS184 4.8 27.4 1.0
N B:CYS194 4.8 25.9 1.0
N B:ARG193 4.8 26.4 1.0
CA B:HIS184 4.9 25.6 1.0
O B:HOH613 5.0 53.6 1.0
N B:HIS179 5.0 28.4 1.0
CA B:SER183 5.0 27.9 1.0
NH1 B:ARG193 5.0 31.6 1.0

Sodium binding site 5 out of 5 in 7wzv

Go back to Sodium Binding Sites List in 7wzv
Sodium binding site 5 out of 5 in the The Structure of A Twitch Radical Sam Dehydrogenase Spey


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of The Structure of A Twitch Radical Sam Dehydrogenase Spey within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na413

b:37.6
occ:1.00
 O B:GLU226 2.6 30.9 1.0
OE1 B:GLU226 2.7 39.0 1.0
CA B:GLU226 3.0 32.1 1.0
C B:GLU226 3.2 31.2 1.0
CB B:GLU226 3.3 33.7 1.0
CB B:HIS229 3.5 32.9 1.0
ND1 B:HIS229 3.6 32.0 1.0
CD B:GLU226 3.7 39.6 1.0
N B:ARG230 3.9 30.3 1.0
CG B:HIS229 4.0 32.7 1.0
CG B:GLU226 4.0 36.7 1.0
N B:GLU226 4.4 33.3 1.0
CA B:HIS229 4.4 31.4 1.0
C B:HIS229 4.4 31.2 1.0
CB B:ARG230 4.4 33.7 1.0
N B:ARG227 4.4 31.8 1.0
O B:LEU225 4.5 30.3 1.0
CA B:ARG230 4.6 31.6 1.0
N B:HIS229 4.7 31.5 1.0
CE1 B:HIS229 4.8 33.3 1.0
OE2 B:GLU226 4.8 37.9 1.0
C B:LEU225 4.9 34.1 1.0

Reference:

J.Zhang, X.Hou, Z.Chen, Y.Ko, M.W.Ruszczycky, Y.Chen, J.Zhou, H.W.Liu. Dioxane Bridge Formation During the Biosynthesis of Spectinomycin Involves A Twitch Radical S -Adenosyl Methionine Dehydrogenase That May Have Evolved From An Epimerase. J.Am.Chem.Soc. V. 144 9910 2022.
ISSN: ESSN 1520-5126
PubMed: 35622017
DOI: 10.1021/JACS.2C02676
Page generated: Fri Apr 7 17:09:06 2023

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