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

Go back to Sodium Binding Sites List in 7wzv
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: Wed Oct 9 09:36:11 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy