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Sodium in PDB 7cdm: Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set)

Enzymatic activity of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set)

All present enzymatic activity of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set):
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set), PDB code: 7cdm 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 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.382, 78.382, 38.763, 90, 90, 90
R / Rfree (%) 18.7 / 21.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set) (pdb code 7cdm). 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, 42 Kgy (4500 Images From 2ND Half of Data Set), PDB code: 7cdm:

Sodium binding site 1 out of 1 in 7cdm

Go back to Sodium Binding Sites List in 7cdm
Sodium binding site 1 out of 1 in the Lysozyme Room-Temperature Structure Determined By Ss-Rox Combined with Hag Method, 42 Kgy (4500 Images From 2ND Half of Data Set)


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, 42 Kgy (4500 Images From 2ND Half of Data Set) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:13.2
occ:1.00
 O A:SER60 2.3 13.0 1.0
O A:CYS64 2.4 10.2 1.0
O A:ARG73 2.4 16.3 1.0
O6 A:MLI201 2.4 16.4 1.0
OG A:SER72 2.5 17.0 1.0
O7 A:MLI201 2.6 16.4 1.0
C2 A:MLI201 2.8 21.6 1.0
CB A:SER72 3.3 14.8 1.0
C A:CYS64 3.5 11.4 1.0
C A:ARG73 3.5 16.8 1.0
C A:SER60 3.5 11.2 1.0
N A:ARG73 3.9 14.7 1.0
CA A:ASN65 4.1 13.6 1.0
C A:SER72 4.1 20.3 1.0
CA A:SER60 4.1 8.2 1.0
N A:ASN65 4.2 10.9 1.0
C1 A:MLI201 4.2 17.5 1.0
N A:CYS64 4.3 11.0 1.0
CA A:ARG73 4.3 16.6 1.0
CB A:SER60 4.3 8.9 1.0
CA A:SER72 4.3 18.1 1.0
N A:ASN74 4.4 13.8 1.0
C A:ARG61 4.5 16.6 1.0
O A:ARG61 4.5 15.9 1.0
CA A:ASN74 4.5 16.0 1.0
CA A:CYS64 4.5 11.7 1.0
N A:ARG61 4.5 10.1 1.0
O A:SER72 4.6 20.5 1.0
CB A:ASN74 4.6 14.3 1.0
CB A:THR69 4.7 12.5 1.0
CA A:ARG61 4.8 12.1 1.0
N A:TRP62 4.8 14.0 1.0
O A:THR69 4.8 16.1 1.0
N A:TRP63 4.9 11.3 1.0
CB A:ASN65 4.9 15.7 1.0
C A:TRP62 5.0 12.9 1.0
O9 A:MLI201 5.0 17.3 1.0
N A:ASP66 5.0 9.4 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 16:20:37 2024

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