Atomistry » Sodium » PDB 7bqj-7cdu » 7cdo
Atomistry »
  Sodium »
    PDB 7bqj-7cdu »
      7cdo »

Sodium in PDB 7cdo: Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images)

Enzymatic activity of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images)

All present enzymatic activity of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images), PDB code: 7cdo was solved by K.Hasegawa, S.Baba, T.Kawamura, M.Yamamoto, T.Kumasaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.42 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.377, 78.377, 38.785, 90, 90, 90
R / Rfree (%) 19.4 / 22.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images) (pdb code 7cdo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images), PDB code: 7cdo:

Sodium binding site 1 out of 1 in 7cdo

Go back to Sodium Binding Sites List in 7cdo
Sodium binding site 1 out of 1 in the Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 21 Kgy (3000 Images) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:16.4
occ:1.00
 O A:SER60 2.4 16.7 1.0
O A:CYS64 2.4 12.2 1.0
O A:ARG73 2.5 18.9 1.0
O6 A:MLI201 2.5 17.5 1.0
O7 A:MLI201 2.6 18.2 1.0
OG A:SER72 2.7 19.5 1.0
C2 A:MLI201 2.8 22.8 1.0
CB A:SER72 3.4 17.6 1.0
C A:CYS64 3.5 13.3 1.0
C A:ARG73 3.5 21.6 1.0
C A:SER60 3.5 13.2 1.0
N A:ARG73 3.9 18.1 1.0
CA A:ASN65 4.1 15.7 1.0
C A:SER72 4.1 23.4 1.0
CA A:SER60 4.1 12.0 1.0
N A:ASN65 4.2 12.9 1.0
C1 A:MLI201 4.2 18.2 1.0
CA A:ARG73 4.3 20.3 1.0
N A:CYS64 4.3 13.3 1.0
N A:ASN74 4.3 19.1 1.0
CB A:SER60 4.4 12.0 1.0
CA A:SER72 4.4 22.2 1.0
C A:ARG61 4.5 20.3 1.0
O A:ARG61 4.5 19.4 1.0
CA A:ASN74 4.5 18.7 1.0
CA A:CYS64 4.5 13.7 1.0
N A:ARG61 4.6 12.5 1.0
O A:SER72 4.6 22.8 1.0
CB A:THR69 4.6 15.7 1.0
CB A:ASN74 4.7 19.4 1.0
O A:THR69 4.8 17.2 1.0
N A:TRP62 4.8 18.6 1.0
CA A:ARG61 4.8 16.2 1.0
CB A:ASN65 4.9 17.4 1.0
N A:TRP63 4.9 13.6 1.0
O9 A:MLI201 5.0 19.2 1.0
CG2 A:THR69 5.0 13.6 1.0
N A:ASP66 5.0 12.3 1.0
C A:TRP62 5.0 17.2 1.0

Reference:

K.Hasegawa, S.Baba, T.Kawamura, M.Yamamoto, T.Kumasaka. Evaluation of the Data-Collection Strategy For Room-Temperature Micro-Crystallography Studied By Serial Synchrotron Rotation Crystallography Combined with the Humid Air and Glue-Coating Method. Acta Crystallogr.,Sect.D V. 77 300 2021.
ISSN: ESSN 1399-0047
DOI: 10.1107/S2059798321001686
Page generated: Tue Oct 8 16:20:59 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy