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Sodium in PDB 8cwg: 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

Enzymatic activity of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

All present enzymatic activity of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose:
3.2.1.17;

Protein crystallography data

The structure of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwg was solved by A.M.Wolff, M.C.Thompson, J.S.Fraser, E.Nango, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.74 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 77.061, 77.061, 37.223, 90, 90, 90
R / Rfree (%) 12.9 / 16.7

Other elements in 8cwg:

The structure of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwg:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 8cwg

Go back to Sodium Binding Sites List in 8cwg
Sodium binding site 1 out of 2 in the 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:17.8
occ:1.00
O A:SER60 2.3 15.4 1.0
O A:CYS64 2.3 13.5 1.0
O A:ARG73 2.3 20.3 1.0
O A:HOH380 2.3 20.8 1.0
OG A:SER72 2.4 21.0 1.0
O A:HOH348 2.5 18.3 1.0
HA A:ASN65 2.9 18.9 1.0
HB2 A:SER72 2.9 24.3 1.0
CB A:SER72 3.2 20.3 1.0
C A:SER60 3.4 12.8 1.0
C A:CYS64 3.4 14.0 1.0
C A:ARG73 3.4 22.0 1.0
HB2 A:SER60 3.4 14.7 1.0
HA A:SER60 3.7 13.5 1.0
HB A:THR69 3.7 17.9 1.0
HB2 A:ASN74 3.8 21.4 1.0
CA A:ASN65 3.8 15.8 1.0
H A:CYS64 3.8 17.0 1.0
HB3 A:SER72 3.9 24.3 1.0
N A:ARG73 3.9 19.2 1.0
H A:ARG73 3.9 23.1 1.0
CA A:SER60 3.9 11.3 1.0
HA A:ASN74 4.0 22.0 1.0
H A:ASP66 4.0 18.2 1.0
N A:ASN65 4.0 15.5 1.0
C A:SER72 4.0 20.7 1.0
CB A:SER60 4.2 12.2 1.0
CA A:SER72 4.3 21.3 1.0
N A:ASN74 4.3 20.0 1.0
CA A:ARG73 4.3 22.2 1.0
N A:CYS64 4.3 14.2 1.0
CA A:ASN74 4.4 18.4 1.0
HB2 A:ASN65 4.5 22.0 1.0
O A:ARG61 4.5 15.9 1.0
C A:ARG61 4.5 14.4 1.0
HA A:ARG61 4.5 18.6 1.0
N A:ARG61 4.5 13.9 1.0
CA A:CYS64 4.5 13.1 1.0
CB A:ASN74 4.6 17.9 1.0
O A:SER72 4.6 23.8 1.0
N A:ASP66 4.6 15.2 1.0
CB A:THR69 4.6 15.0 1.0
HG21 A:THR69 4.6 19.6 1.0
OD1 A:ASN65 4.7 26.3 1.0
CB A:ASN65 4.7 18.4 1.0
CL A:CL204 4.7 31.8 1.0
HA A:ARG73 4.7 26.6 1.0
CA A:ARG61 4.7 15.5 1.0
HG A:SER60 4.7 15.1 1.0
C A:ASN65 4.8 15.8 1.0
O A:THR69 4.8 19.7 1.0
H A:TRP63 4.8 16.5 1.0
N A:TRP62 4.8 14.4 1.0
HB3 A:SER60 4.8 14.7 1.0
H A:ASN65 4.8 18.6 1.0
O A:HOH385 4.9 37.4 1.0
HA A:SER72 4.9 25.6 1.0
H A:SER72 5.0 26.7 1.0
OG A:SER60 5.0 12.6 1.0
N A:TRP63 5.0 13.8 1.0

Sodium binding site 2 out of 2 in 8cwg

Go back to Sodium Binding Sites List in 8cwg
Sodium binding site 2 out of 2 in the 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:83.0
occ:1.00
O A:HOH338 2.1 26.2 1.0
O A:HOH315 2.1 20.7 1.0
H21 A:VY5202 2.1 27.7 1.0
OE1 A:GLU35 2.3 14.7 1.0
O8 A:VY5202 2.4 23.1 1.0
O3 A:VY5202 2.4 13.8 1.0
H20 A:VY5202 3.0 16.1 1.0
H10 A:VY5202 3.2 15.2 1.0
C6 A:VY5202 3.2 14.1 1.0
C11 A:VY5202 3.2 17.7 1.0
C10 A:VY5202 3.2 12.7 1.0
HB3 A:GLN57 3.3 15.1 1.0
O A:HOH355 3.4 35.0 1.0
CD A:GLU35 3.4 12.2 1.0
H11 A:VY5202 3.4 21.2 1.0
H6 A:VY5202 3.4 16.9 1.0
HG3 A:GLN57 3.5 14.0 1.0
O7 A:VY5202 3.6 13.4 1.0
HB2 A:GLN57 3.7 15.1 1.0
OE2 A:GLU35 3.8 14.8 1.0
CB A:GLN57 3.8 12.6 1.0
O A:HOH311 3.9 27.7 1.0
HA A:GLU35 4.0 12.5 1.0
CG A:GLN57 4.1 11.7 1.0
H12 A:VY5202 4.2 21.2 1.0
OE1 A:GLN57 4.2 14.1 1.0
HB A:VAL109 4.3 15.6 1.0
HB3 A:GLU35 4.3 13.2 1.0
OD2 A:ASP52 4.5 19.0 1.0
C1 A:VY5202 4.6 14.4 1.0
HB2 A:ALA110 4.6 15.6 1.0
H A:ALA110 4.6 13.4 1.0
C7 A:VY5202 4.6 12.3 1.0
HB3 A:ASP52 4.6 14.7 1.0
CD A:GLN57 4.6 12.3 1.0
CG A:GLU35 4.7 12.5 1.0
O A:GLU35 4.7 15.6 1.0
HB2 A:ASP52 4.7 14.7 1.0
CA A:GLU35 4.7 10.4 1.0
CG A:ASP52 4.8 14.4 1.0
CB A:GLU35 4.8 11.0 1.0
H1 A:VY5202 4.8 17.2 1.0
H7 A:VY5202 4.8 14.7 1.0
HG2 A:GLN57 4.9 14.0 1.0
O A:GLN57 4.9 13.1 1.0
CB A:ASP52 5.0 12.2 1.0
HD22 A:ASN44 5.0 24.3 1.0

Reference:

A.M.Wolff, E.Nango, I.D.Young, A.S.Brewster, M.Kubo, T.Nomura, M.Sugahara, S.Owada, B.A.Barad, K.Ito, A.Bhowmick, S.Carbajo, T.Hino, J.M.Holton, D.Im, L.J.O'riordan, T.Tanaka, R.Tanaka, R.G.Sierra, F.Yumoto, K.Tono, S.Iwata, N.K.Sauter, J.S.Fraser, M.C.Thompson. Mapping Protein Dynamics at High-Resolution with Temperature-Jump X-Ray Crystallography Biorxiv 2022.
DOI: 10.1101/2022.06.10.495662
Page generated: Wed Oct 9 11:19:37 2024

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