Atomistry » Sodium » PDB 3nte-3off » 3nvd
Atomistry »
  Sodium »
    PDB 3nte-3off »
      3nvd »

Sodium in PDB 3nvd: Structure of Ybbd in Complex with Pugnac

Enzymatic activity of Structure of Ybbd in Complex with Pugnac

All present enzymatic activity of Structure of Ybbd in Complex with Pugnac:
3.2.1.52;

Protein crystallography data

The structure of Structure of Ybbd in Complex with Pugnac, PDB code: 3nvd was solved by K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.55 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.473, 73.206, 83.788, 79.83, 69.45, 88.22
R / Rfree (%) 18.7 / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Ybbd in Complex with Pugnac (pdb code 3nvd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Ybbd in Complex with Pugnac, PDB code: 3nvd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3nvd

Go back to Sodium Binding Sites List in 3nvd
Sodium binding site 1 out of 2 in the Structure of Ybbd in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Ybbd in Complex with Pugnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na643

b:20.6
occ:1.00
HG A:SER233 2.0 15.8 1.0
H A:HIS270 2.4 16.9 1.0
OG A:SER233 2.8 13.2 1.0
OD2 A:ASP318 2.8 11.9 1.0
HD2 A:HIS226 2.9 4.8 1.0
HE1 A:MET322 2.9 10.7 1.0
HA A:ALA269 2.9 13.5 1.0
N A:HIS270 3.2 14.1 1.0
HB2 A:HIS270 3.2 12.0 1.0
HB2 A:SER233 3.4 26.3 1.0
CD2 A:HIS226 3.5 4.1 1.0
CB A:SER233 3.6 22.0 1.0
NE2 A:HIS226 3.6 15.1 1.0
CAH A:OAN646 3.7 11.6 1.0
CE A:MET322 3.7 9.0 1.0
HE2 A:MET322 3.7 10.7 1.0
CA A:ALA269 3.8 11.3 1.0
CG A:ASP318 3.8 3.7 1.0
CB A:HIS270 3.8 10.0 1.0
HB3 A:SER233 3.8 26.3 1.0
HB3 A:ASP318 3.9 9.5 1.0
HD2 A:HIS270 3.9 16.2 1.0
HB1 A:ALA269 3.9 7.6 1.0
CG A:HIS270 3.9 7.0 1.0
HG23 A:VAL271 3.9 12.3 1.0
C A:ALA269 3.9 13.3 1.0
HB2 A:ASP318 3.9 9.5 1.0
CD2 A:HIS270 4.0 13.6 1.0
CA A:HIS270 4.0 8.9 1.0
CB A:ASP318 4.1 8.0 1.0
CB A:ALA269 4.3 6.4 1.0
SD A:MET322 4.5 16.4 1.0
HE3 A:MET322 4.5 10.7 1.0
HB3 A:HIS222 4.5 22.0 1.0
C A:HIS270 4.5 9.0 1.0
HD2 A:HIS222 4.5 20.1 1.0
HB2 A:ALA269 4.6 7.6 1.0
NAI A:OAN646 4.6 7.7 1.0
O A:HIS270 4.6 11.7 1.0
O A:THR268 4.6 11.3 1.0
CAG A:OAN646 4.7 15.5 1.0
HB3 A:HIS270 4.7 12.0 1.0
CG2 A:VAL271 4.8 10.3 1.0
ND1 A:HIS270 4.8 7.1 1.0
CD2 A:HIS222 4.8 16.8 1.0
CG A:HIS226 4.8 15.5 1.0
OD1 A:ASP318 4.8 7.4 1.0
NE2 A:HIS270 4.9 10.8 1.0
HA A:HIS270 4.9 10.6 1.0
HB2 A:HIS222 4.9 22.0 1.0
N A:ALA269 4.9 10.9 1.0
CE1 A:HIS226 4.9 15.9 1.0
HG22 A:VAL271 4.9 12.3 1.0
CA A:SER233 5.0 21.4 1.0
HG21 A:VAL271 5.0 12.3 1.0
CG A:HIS222 5.0 16.1 1.0

Sodium binding site 2 out of 2 in 3nvd

Go back to Sodium Binding Sites List in 3nvd
Sodium binding site 2 out of 2 in the Structure of Ybbd in Complex with Pugnac


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Ybbd in Complex with Pugnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na643

b:19.5
occ:1.00
H B:HIS270 2.3 7.9 1.0
HG B:SER233 2.4 25.6 1.0
HA B:ALA269 2.6 18.8 1.0
HD2 B:HIS226 2.8 14.6 1.0
OD2 B:ASP318 2.8 11.1 1.0
N B:HIS270 3.0 6.6 1.0
OG B:SER233 3.2 21.4 1.0
HB2 B:SER233 3.4 14.8 1.0
CD2 B:HIS226 3.4 12.2 1.0
CA B:ALA269 3.4 15.7 1.0
HB1 B:ALA269 3.5 10.0 1.0
HB3 B:SER233 3.6 14.8 1.0
NE2 B:HIS226 3.6 18.7 1.0
HB2 B:HIS270 3.6 17.0 1.0
CB B:SER233 3.6 12.4 1.0
HD2 B:HIS270 3.6 14.3 1.0
HE1 B:MET322 3.7 15.2 1.0
C B:ALA269 3.7 10.5 1.0
CG B:ASP318 3.8 10.0 1.0
CD2 B:HIS270 3.8 12.0 1.0
HG23 B:VAL271 3.8 12.6 1.0
HB3 B:ASP318 3.9 14.3 1.0
HB2 B:ASP318 3.9 14.3 1.0
CAH B:OAN646 3.9 11.9 1.0
CG B:HIS270 3.9 14.7 1.0
CA B:HIS270 3.9 14.0 1.0
CB B:HIS270 4.0 14.2 1.0
CB B:ALA269 4.0 8.4 1.0
CB B:ASP318 4.1 12.0 1.0
HB2 B:ALA269 4.3 10.0 1.0
HB3 B:HIS222 4.3 13.0 1.0
C B:HIS270 4.3 16.0 1.0
CE B:MET322 4.4 12.8 1.0
HE2 B:MET322 4.4 15.2 1.0
O B:THR268 4.5 17.6 1.0
O B:HIS270 4.5 15.6 1.0
HD2 B:HIS222 4.6 10.1 1.0
NE2 B:HIS270 4.6 16.5 1.0
N B:ALA269 4.6 22.7 1.0
CG2 B:VAL271 4.6 10.6 1.0
CG B:HIS226 4.7 7.2 1.0
SD B:MET322 4.7 20.8 1.0
ND1 B:HIS270 4.8 18.2 1.0
HA B:HIS270 4.8 16.7 1.0
CD2 B:HIS222 4.8 8.4 1.0
NAI B:OAN646 4.8 12.9 1.0
HG21 B:VAL271 4.8 12.6 1.0
HB3 B:ALA269 4.8 10.0 1.0
HG22 B:VAL271 4.9 12.6 1.0
OD1 B:ASP318 4.9 12.6 1.0
O B:ALA269 4.9 8.7 1.0
CAG B:OAN646 4.9 11.9 1.0
CE1 B:HIS226 4.9 15.0 1.0
HB3 B:HIS270 4.9 17.0 1.0
CB B:HIS222 5.0 10.9 1.0
C B:THR268 5.0 18.1 1.0
CG B:HIS222 5.0 10.3 1.0

Reference:

S.Litzinger, S.Fischer, P.Polzer, K.Diederichs, W.Welte, C.Mayer. Structural and Kinetic Analysis of Bacillus Subtilis N-Acetylglucosaminidase Reveals A Unique Asp-His Dyad Mechanism J.Biol.Chem. V. 285 35675 2010.
ISSN: ISSN 0021-9258
PubMed: 20826810
DOI: 10.1074/JBC.M110.131037
Page generated: Tue Dec 15 06:19:27 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy