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Sodium in PDB 8p1d: Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv

Enzymatic activity of Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv

All present enzymatic activity of Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv:
3.2.1.17;

Protein crystallography data

The structure of Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv, PDB code: 8p1d was solved by J.Nan, F.Leonarski, A.Furrer, F.Dworkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 9.93 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.06, 79.06, 38.26, 90, 90, 90
R / Rfree (%) 16.5 / 19

Other elements in 8p1d:

The structure of Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv (pdb code 8p1d). 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 Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv, PDB code: 8p1d:

Sodium binding site 1 out of 1 in 8p1d

Go back to Sodium Binding Sites List in 8p1d
Sodium binding site 1 out of 1 in the Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Lysozyme Structure Solved From Serial Crystallography Data Collected at 100 Hz with Jungfrau Detector at Maxiv within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:34.8
occ:1.00
 OG A:SER72 2.1 44.1 1.0
O A:SER60 2.3 26.0 1.0
O A:CYS64 2.3 21.5 1.0
O A:HOH312 2.5 37.4 1.0
O A:ARG73 2.5 43.0 1.0
O A:HOH369 2.7 27.6 1.0
CB A:SER72 2.9 36.2 1.0
C A:CYS64 3.4 22.5 1.0
C A:SER60 3.5 20.7 1.0
C A:ARG73 3.5 38.1 1.0
C A:SER72 3.9 42.3 1.0
CA A:ASN65 3.9 23.8 1.0
N A:ARG73 3.9 34.5 1.0
CA A:SER72 4.0 38.9 1.0
N A:ASN65 4.0 21.4 1.0
CA A:SER60 4.2 18.7 1.0
N A:CYS64 4.3 18.5 1.0
N A:ASN74 4.3 29.7 1.0
O A:ARG61 4.3 29.4 0.5
O A:SER72 4.3 36.9 1.0
CA A:ARG73 4.4 31.1 1.0
C A:ARG61 4.4 29.4 0.5
CA A:ASN74 4.4 23.2 1.0
O A:ARG61 4.4 29.4 0.5
C A:ARG61 4.4 29.4 0.5
CA A:CYS64 4.5 21.7 1.0
CB A:SER60 4.5 21.0 1.0
N A:ARG61 4.5 20.4 0.5
CB A:ASN74 4.5 24.5 1.0
N A:ARG61 4.6 20.4 0.5
CA A:ARG61 4.7 25.8 0.5
CA A:ARG61 4.7 25.8 0.5
N A:TRP62 4.7 23.1 1.0
CB A:ASN65 4.8 21.7 1.0
OD1 A:ASN65 4.8 36.9 1.0
O A:HOH366 4.8 30.7 1.0
N A:ASP66 4.9 19.7 1.0
N A:TRP63 4.9 21.2 1.0
CB A:THR69 4.9 24.7 1.0
C A:ASN65 4.9 21.7 1.0
C A:TRP62 4.9 22.8 1.0
O A:THR69 5.0 30.1 1.0

Reference:

F.Leonarski, J.Nan, Z.Matej, Q.Bertrand, A.Furrer, I.Gorgisyan, M.Bjelcic, M.Kepa, H.Glover, V.Hinger, T.Eriksson, A.Cehovin, M.Eguiraun, P.Gasparotto, A.Mozzanica, T.Weinert, A.Gonzalez, J.Standfuss, M.Wang, T.Ursby, F.Dworkowski. Kilohertz Serial Crystallography with the Jungfrau Detector at A 4TH Generation Synchrotron Source To Be Published.
Page generated: Mon Aug 18 14:57:38 2025

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