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Sodium in PDB 4nte: Crystal Structure of Deph

Protein crystallography data

The structure of Crystal Structure of Deph, PDB code: 4nte was solved by D.H.Scharf, M.Groll, A.Habel, T.Heinekamp, C.Hertweck, A.A.Brakhage, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.90
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 78.220, 78.220, 188.080, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 19.9

Other elements in 4nte:

The structure of Crystal Structure of Deph also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 7 in 4nte

Go back to Sodium Binding Sites List in 4nte
Sodium binding site 1 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:30.6
occ:1.00
 OD1 A:ASP268 2.8 24.0 1.0
O A:THR275 2.8 23.5 1.0
N A:GLY274 3.4 32.8 1.0
N A:ASP268 3.4 21.1 1.0
C A:GLY267 3.5 20.9 1.0
N A:ALA279 3.5 21.5 1.0
CA A:GLY273 3.5 39.2 1.0
CB A:ALA279 3.5 21.7 1.0
N A:THR275 3.7 25.6 1.0
CA A:ALA279 3.7 21.7 1.0
CA A:GLY267 3.7 20.7 1.0
C A:THR275 3.8 23.4 1.0
O3' A:FAD301 3.8 20.1 1.0
CG A:ASP268 3.9 22.5 1.0
C A:GLY273 3.9 37.2 1.0
O A:GLY267 3.9 21.2 1.0
CA A:ASP268 3.9 21.5 1.0
C5' A:FAD301 4.1 20.1 1.0
C A:LEU278 4.2 22.5 1.0
CA A:THR275 4.3 24.7 1.0
CB A:LEU278 4.4 24.3 1.0
CA A:GLY274 4.4 30.2 1.0
C A:GLY274 4.4 27.9 1.0
CB A:ASP268 4.5 22.2 1.0
O1P A:FAD301 4.6 19.6 1.0
CA A:LEU278 4.8 22.7 1.0
O5' A:FAD301 4.8 19.9 1.0
OD2 A:ASP268 4.9 22.9 1.0
N A:GLY267 4.9 20.7 1.0
N A:GLY273 4.9 41.1 1.0
C4' A:FAD301 4.9 20.0 1.0
N A:VAL276 4.9 21.9 1.0
C3' A:FAD301 4.9 19.6 1.0
O A:ARG272 4.9 46.0 1.0
O A:LEU278 4.9 23.0 1.0

Sodium binding site 2 out of 7 in 4nte

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Sodium binding site 2 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:28.7
occ:1.00
 OG A:SER47 2.8 22.8 1.0
O A:GLN53 3.2 22.4 1.0
N A:HIS48 3.2 20.4 1.0
N A:VAL50 3.3 20.5 1.0
C A:SER47 3.3 21.2 1.0
C A:HIS48 3.3 20.8 1.0
CA A:HIS48 3.4 20.7 1.0
O A:SER47 3.4 20.2 1.0
CB A:VAL50 3.4 21.7 1.0
CB A:SER47 3.5 22.1 1.0
CG2 A:VAL50 3.6 22.2 1.0
C A:GLN53 3.6 22.8 1.0
O A:HIS48 3.7 20.7 1.0
N A:GLY49 3.7 20.8 1.0
CA A:VAL50 3.8 20.9 1.0
CA A:ASP54 3.9 22.1 1.0
O A:VAL50 3.9 20.5 1.0
N A:ASP54 4.0 21.9 1.0
CA A:SER47 4.0 21.7 1.0
CB A:GLN53 4.1 24.9 1.0
C A:GLY49 4.3 20.9 1.0
C A:VAL50 4.3 20.9 1.0
CD1 A:ILE61 4.4 22.9 1.0
CA A:GLN53 4.5 23.9 1.0
CA A:GLY49 4.5 21.1 1.0
N A:GLY55 4.6 22.9 1.0
OD1 A:ASP54 4.6 22.1 1.0
C A:ASP54 4.8 22.4 1.0
CG1 A:VAL50 4.8 21.8 1.0
CB A:ASP54 4.8 22.0 1.0
CB A:HIS48 4.9 21.2 1.0
N3 A:FAD301 4.9 19.4 1.0

Sodium binding site 3 out of 7 in 4nte

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Sodium binding site 3 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:26.6
occ:1.00
 O2A A:FAD301 2.7 19.3 1.0
OD2 A:ASP268 2.8 22.9 1.0
N A:VAL113 3.0 20.0 1.0
O3P A:FAD301 3.3 19.6 1.0
CB A:ASP268 3.4 22.2 1.0
CA A:GLY112 3.4 19.4 1.0
O A:HOH408 3.4 23.2 1.0
CG A:ASP268 3.4 22.5 1.0
CB A:ARG40 3.5 25.8 1.0
O A:VAL113 3.6 19.9 1.0
PA A:FAD301 3.6 19.4 1.0
NE A:ARG40 3.7 32.6 1.0
C A:GLY112 3.7 19.7 1.0
CG2 A:VAL113 3.8 20.4 1.0
CD A:ARG40 3.9 30.6 1.0
C5' A:FAD301 4.0 20.1 1.0
CA A:VAL113 4.0 20.3 1.0
C A:VAL113 4.2 20.2 1.0
O1P A:FAD301 4.2 19.6 1.0
CG A:ARG40 4.2 27.8 1.0
P A:FAD301 4.3 19.6 1.0
CB A:VAL113 4.4 20.4 1.0
O1A A:FAD301 4.5 19.2 1.0
OD1 A:ASP268 4.5 24.0 1.0
O5' A:FAD301 4.6 19.9 1.0
O4' A:FAD301 4.7 20.2 1.0
C4' A:FAD301 4.7 20.0 1.0
N A:GLY112 4.7 19.2 1.0
C3' A:FAD301 4.7 19.6 1.0
CA A:ARG40 4.8 24.4 1.0
CA A:ASP268 4.8 21.5 1.0
CZ A:ARG40 4.8 33.3 1.0
O5B A:FAD301 4.8 19.2 1.0
N A:ARG40 4.8 22.8 1.0
CG1 A:VAL113 4.9 21.1 1.0
O A:GLY112 4.9 20.0 1.0

Sodium binding site 4 out of 7 in 4nte

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Sodium binding site 4 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na302

b:31.2
occ:1.00
 O B:HOH584 2.6 38.5 1.0
OD1 B:ASP268 2.7 21.6 1.0
O B:THR275 2.8 23.3 1.0
N B:GLY274 3.4 34.3 1.0
N B:ALA279 3.5 20.6 1.0
N B:ASP268 3.6 18.4 1.0
CA B:GLY273 3.6 39.8 1.0
N B:THR275 3.6 27.6 1.0
CB B:ALA279 3.6 20.5 1.0
C B:GLY267 3.7 18.0 1.0
O3' B:FAD301 3.7 20.0 1.0
C B:THR275 3.8 23.9 1.0
CA B:ALA279 3.8 20.3 1.0
CG B:ASP268 3.8 20.0 1.0
C B:GLY273 3.9 37.7 1.0
CA B:GLY267 4.0 17.7 1.0
CA B:ASP268 4.0 19.1 1.0
CB B:LEU278 4.2 24.7 1.0
C5' B:FAD301 4.2 18.6 1.0
O B:GLY267 4.3 18.1 1.0
CA B:THR275 4.3 25.6 1.0
C B:LEU278 4.3 21.5 1.0
C B:GLY274 4.4 30.6 1.0
CA B:GLY274 4.4 32.1 1.0
CB B:ASP268 4.5 19.5 1.0
O1P B:FAD301 4.7 16.9 1.0
OD2 B:ASP268 4.8 21.1 1.0
CA B:LEU278 4.8 23.1 1.0
O B:ARG272 4.8 44.2 1.0
O5' B:FAD301 4.8 18.1 1.0
C3' B:FAD301 4.8 19.9 1.0
C4' B:FAD301 4.9 19.1 1.0
N B:VAL276 4.9 22.1 1.0
N B:GLY273 4.9 42.2 1.0
O B:GLY273 4.9 39.9 1.0

Sodium binding site 5 out of 7 in 4nte

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Sodium binding site 5 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na303

b:47.1
occ:1.00
 O B:ASP197 2.5 48.4 1.0
O B:VAL195 3.1 38.8 1.0
N B:ASP174 3.4 45.6 1.0
C B:ASP197 3.6 48.4 1.0
CA B:ASP174 3.7 48.4 1.0
C B:LEU172 3.7 34.6 1.0
CA B:LEU172 3.8 32.9 1.0
CB B:LEU172 3.8 33.4 1.0
N B:THR173 3.8 37.1 1.0
CG1 B:ILE199 3.8 39.1 1.0
C B:VAL195 3.9 39.9 1.0
C B:ARG196 3.9 45.7 1.0
N B:ASP197 4.0 46.5 1.0
CB B:ASP174 4.0 47.8 1.0
CD2 B:LEU172 4.1 33.9 1.0
O B:ARG196 4.1 45.3 1.0
O B:LEU172 4.2 32.8 1.0
CG1 B:VAL195 4.3 37.8 1.0
CD2 B:LEU210 4.3 36.5 1.0
CD1 B:ILE199 4.3 38.7 1.0
CA B:ARG196 4.4 44.9 1.0
N B:ARG196 4.4 43.0 1.0
CA B:ASP197 4.4 48.6 1.0
C B:THR173 4.4 42.5 1.0
CG B:LEU172 4.6 33.3 1.0
CB B:VAL195 4.7 37.4 1.0
N B:ARG198 4.7 47.2 1.0
OD1 B:ASP174 4.7 49.0 1.0
CG B:ASP174 4.7 48.1 1.0
CA B:THR173 4.7 39.6 1.0
N B:ILE199 4.7 41.0 1.0
C B:ARG198 4.8 44.1 1.0
CA B:ARG198 4.8 47.2 1.0
CA B:VAL195 4.9 38.2 1.0

Sodium binding site 6 out of 7 in 4nte

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Sodium binding site 6 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na304

b:33.3
occ:1.00
 O B:HOH461 2.5 28.9 1.0
O B:HOH481 2.7 29.0 1.0
O B:ALA63 2.9 24.8 1.0
C B:ALA63 3.6 24.4 1.0
CA B:ALA63 3.7 23.9 1.0
N B:ALA67 3.8 21.0 1.0
CB B:ALA63 3.8 24.3 1.0
CB B:ALA67 3.9 21.5 1.0
CB B:LYS66 4.0 21.6 1.0
CG B:LYS66 4.2 22.0 1.0
CD B:LYS66 4.2 22.7 1.0
CA B:ALA67 4.2 21.2 1.0
O B:HOH458 4.3 30.0 1.0
C B:LYS66 4.5 21.2 1.0
O B:HOH493 4.5 44.9 1.0
O B:HOH475 4.6 35.6 1.0
O B:HOH542 4.6 44.6 1.0
CA B:LYS66 4.7 21.5 1.0
O B:HOH465 4.8 39.6 1.0
N B:ASP64 4.8 25.3 1.0

Sodium binding site 7 out of 7 in 4nte

Go back to Sodium Binding Sites List in 4nte
Sodium binding site 7 out of 7 in the Crystal Structure of Deph


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 Deph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na305

b:30.0
occ:1.00
 OD1 B:ASN41 2.7 33.7 1.0
O B:HOH578 2.9 47.9 1.0
OG B:SER47 3.0 27.6 1.0
C4X B:FAD301 3.4 21.3 1.0
CG B:ASN41 3.5 34.4 1.0
C4 B:FAD301 3.5 21.3 1.0
CB B:SER47 3.5 26.9 1.0
CB B:ASN41 3.5 32.8 1.0
C10 B:FAD301 3.7 21.0 1.0
CG2 B:VAL276 3.8 20.7 1.0
N5 B:FAD301 3.8 22.0 1.0
N3 B:FAD301 3.9 21.1 1.0
O4 B:FAD301 3.9 21.3 1.0
N1 B:FAD301 4.0 21.1 1.0
CA B:SER47 4.1 26.4 1.0
C2 B:FAD301 4.1 22.2 1.0
N10 B:FAD301 4.4 21.5 1.0
O2' B:FAD301 4.4 21.3 1.0
CG B:PRO58 4.4 24.9 1.0
C5X B:FAD301 4.4 22.5 1.0
NE2 B:HIS15 4.6 22.5 1.0
C2' B:FAD301 4.7 20.6 1.0
CB B:PRO58 4.7 25.2 1.0
C9A B:FAD301 4.7 22.4 1.0
ND2 B:ASN41 4.8 35.4 1.0
O2 B:FAD301 4.9 22.5 1.0
N B:SER47 5.0 27.0 1.0

Reference:

D.H.Scharf, M.Groll, A.Habel, T.Heinekamp, C.Hertweck, A.A.Brakhage, E.M.Huber. Flavoenzyme-Catalyzed Formation of Disulfide Bonds in Natural Products Angew.Chem.Int.Ed.Engl. V. 53 2221 2014.
ISSN: ISSN 1433-7851
PubMed: 24446392
DOI: 10.1002/ANIE.201309302
Page generated: Mon Oct 7 17:17:08 2024

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