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Sodium in PDB 6apm: Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation

Enzymatic activity of Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation

All present enzymatic activity of Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation:
3.2.1.17;

Protein crystallography data

The structure of Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation, PDB code: 6apm was solved by A.Y.Lyubimov, I.I.Mathews, M.Uervivojnangkoorn, S.M.Soltis, A.E.Cohen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.50 / 2.05
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.035, 79.035, 38.245, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 23.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation (pdb code 6apm). 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 Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation, PDB code: 6apm:

Sodium binding site 1 out of 1 in 6apm

Go back to Sodium Binding Sites List in 6apm
Sodium binding site 1 out of 1 in the Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Hen Egg-White Lysozyme (Wt), Solved with Serial Millisecond Crystallography Using Synchrotron Radiation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:12.8
occ:1.00
 O A:SER60 2.4 9.1 1.0
O A:HOH360 2.5 6.7 1.0
OG A:SER72 2.5 18.4 1.0
O A:CYS64 2.6 9.2 1.0
HB2 A:SER72 2.6 18.9 1.0
O A:HOH350 2.6 7.7 1.0
O A:ARG73 2.7 18.9 1.0
HA A:ASN65 3.0 13.4 1.0
CB A:SER72 3.0 18.4 1.0
C A:CYS64 3.5 8.8 1.0
C A:SER60 3.6 8.6 1.0
C A:ARG73 3.6 19.1 1.0
HB3 A:SER72 3.7 18.9 1.0
HB2 A:SER60 3.8 7.9 1.0
H A:ARG73 3.8 22.1 1.0
HB A:THR69 3.8 21.7 1.0
N A:ARG73 3.8 18.4 1.0
CA A:ASN65 3.8 10.5 1.0
C A:SER72 4.0 18.7 1.0
H A:CYS64 4.0 10.1 1.0
N A:ASN65 4.1 8.7 1.0
HA A:SER60 4.1 8.4 1.0
H A:ASP66 4.1 8.2 1.0
CA A:SER72 4.1 18.7 1.0
HA A:ASN74 4.2 20.5 1.0
CA A:ARG73 4.3 19.6 1.0
HB2 A:ASN74 4.3 20.1 1.0
CA A:SER60 4.3 8.3 1.0
HB2 A:ASN65 4.4 18.1 1.0
C A:ARG61 4.5 14.9 1.0
HA A:ARG61 4.5 17.2 1.0
N A:ASN74 4.5 18.2 1.0
CB A:SER60 4.5 8.1 1.0
O A:ARG61 4.5 15.1 1.0
N A:CYS64 4.5 8.6 1.0
O A:HOH392 4.6 6.2 1.0
O A:SER72 4.6 19.0 1.0
HA A:ARG73 4.6 24.3 1.0
N A:ARG61 4.6 9.5 1.0
CB A:ASN65 4.7 14.4 1.0
CA A:CYS64 4.7 8.3 1.0
CA A:ASN74 4.7 17.4 1.0
HA A:SER72 4.7 20.6 1.0
CB A:THR69 4.7 18.0 1.0
N A:TRP62 4.7 14.4 1.0
N A:ASP66 4.7 7.5 1.0
CA A:ARG61 4.8 13.7 1.0
HG21 A:THR69 4.8 20.3 1.0
O A:THR69 4.8 18.8 1.0
C A:ASN65 4.9 8.1 1.0
H A:ASN65 4.9 11.2 1.0
OD1 A:ASN65 4.9 18.9 1.0
H A:SER72 4.9 21.4 1.0
H A:TRP62 4.9 18.1 1.0
CB A:ASN74 5.0 17.5 1.0

Reference:

I.I.Mathews, K.Allison, T.Robbins, A.Y.Lyubimov, M.Uervirojnangkoorn, A.T.Brunger, C.Khosla, H.Demirci, S.E.Mcphillips, M.Hollenbeck, M.Soltis, A.E.Cohen. The Conformational Flexibility of the Acyltransferase From the Disorazole Polyketide Synthase Is Revealed By An X-Ray Free-Electron Laser Using A Room-Temperature Sample Delivery Method For Serial Crystallography. Biochemistry V. 56 4751 2017.
ISSN: ISSN 1520-4995
PubMed: 28832129
DOI: 10.1021/ACS.BIOCHEM.7B00711
Page generated: Tue Oct 8 01:53:43 2024

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