Chlorine in PDB 8cwd: 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

Enzymatic activity of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

All present enzymatic activity of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose:
3.2.1.17;

Protein crystallography data

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwd 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 / 1.48
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 (%) 13 / 16.3

Other elements in 8cwd:

The structure of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwd). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwd:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cwd

Go back to Chlorine Binding Sites List in 8cwd
Chlorine binding site 1 out of 5 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:32.2
occ:1.00
 H A:THR69 2.4 19.6 1.0
O A:HOH350 3.0 18.1 1.0
H A:GLY67 3.2 20.0 1.0
O A:THR69 3.2 18.8 1.0
O A:HOH384 3.2 36.3 1.0
N A:THR69 3.2 16.3 1.0
HA2 A:GLY67 3.2 23.2 1.0
H A:ARG68 3.4 19.7 1.0
C A:THR69 3.5 17.0 1.0
OD1 A:ASN65 3.5 25.0 1.0
N A:ARG68 3.5 16.4 1.0
N A:GLY67 3.6 16.7 1.0
HB A:THR69 3.6 17.8 1.0
C A:GLY67 3.6 18.5 1.0
CA A:GLY67 3.6 19.3 1.0
OG A:SER72 3.7 18.9 1.0
CA A:THR69 3.8 16.4 1.0
O A:HOH380 3.9 20.5 1.0
HA A:PRO70 3.9 25.3 1.0
H A:ASP66 4.0 17.1 1.0
OD1 A:ASP66 4.1 13.9 1.0
N A:PRO70 4.1 18.2 1.0
CB A:THR69 4.2 14.9 1.0
C A:ARG68 4.2 18.5 1.0
O A:GLY67 4.3 22.6 1.0
CA A:ARG68 4.3 17.4 1.0
HG1 A:THR69 4.4 18.1 1.0
HA A:ARG68 4.5 20.8 1.0
CA A:PRO70 4.5 21.1 1.0
HA3 A:GLY67 4.6 23.2 1.0
HA A:ASN65 4.6 17.6 1.0
H A:SER72 4.6 25.2 1.0
C A:ASP66 4.6 15.9 1.0
N A:ASP66 4.7 14.3 1.0
NA A:NA201 4.7 16.6 1.0
CG A:ASN65 4.7 23.0 1.0
HA A:THR69 4.7 19.7 1.0
OG1 A:THR69 4.8 15.1 1.0
HD3 A:PRO70 4.8 26.1 1.0
CB A:SER72 5.0 18.7 1.0

Chlorine binding site 2 out of 5 in 8cwd

Go back to Chlorine Binding Sites List in 8cwd
Chlorine binding site 2 out of 5 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:87.1
occ:1.00
 H A:ILE88 2.3 21.3 1.0
HG12 A:ILE88 2.6 21.6 1.0
HE1 A:HIS15 2.7 35.1 1.0
HA A:ASP87 2.9 25.2 1.0
N A:ILE88 3.1 17.8 1.0
HH21 A:ARG14 3.2 33.4 0.4
HH22 A:ARG14 3.4 33.4 0.4
OD1 A:ASP87 3.5 28.3 1.0
CE1 A:HIS15 3.5 29.3 1.0
CG1 A:ILE88 3.6 18.0 1.0
NH2 A:ARG14 3.6 27.9 0.4
CA A:ASP87 3.7 21.0 1.0
HH12 A:ARG14 3.7 40.4 0.6
HG23 A:ILE88 3.8 22.6 1.0
HG13 A:ILE88 3.8 21.6 1.0
HB1 A:ALA11 3.8 21.9 1.0
C A:ASP87 3.9 18.4 1.0
HZ A:PHE3 3.9 21.8 1.0
O A:HOH339 3.9 34.3 1.0
H A:THR89 4.0 19.4 1.0
HG1 A:THR89 4.0 26.9 1.0
CA A:ILE88 4.1 15.6 1.0
CG A:ASP87 4.1 29.9 1.0
CB A:ILE88 4.2 16.1 1.0
O A:SER86 4.3 24.4 1.0
NE2 A:HIS15 4.3 31.1 1.0
ND1 A:HIS15 4.3 28.8 1.0
NH1 A:ARG14 4.4 33.7 0.6
HD1 A:HIS15 4.4 34.5 1.0
HB2 A:ALA11 4.4 21.9 1.0
N A:THR89 4.4 16.2 1.0
CG2 A:ILE88 4.5 18.9 1.0
CB A:ASP87 4.5 24.2 1.0
HH22 A:ARG14 4.6 40.0 0.6
CB A:ALA11 4.6 18.3 1.0
HD11 A:ILE88 4.6 25.1 1.0
CD1 A:ILE88 4.6 21.0 1.0
C A:ILE88 4.7 15.2 1.0
HD13 A:ILE88 4.7 25.1 1.0
HH11 A:ARG14 4.7 40.4 0.6
OG1 A:THR89 4.7 22.4 1.0
CZ A:PHE3 4.8 18.2 1.0
N A:ASP87 4.8 21.3 1.0
HB2 A:ASP87 4.9 29.1 1.0
HA A:ILE88 4.9 18.7 1.0
HE2 A:PHE3 4.9 22.2 1.0
CZ A:ARG14 4.9 27.4 0.4

Chlorine binding site 3 out of 5 in 8cwd

Go back to Chlorine Binding Sites List in 8cwd
Chlorine binding site 3 out of 5 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:20.5
occ:1.00
 HH A:TYR23 2.1 16.6 1.0
OH A:TYR23 2.9 13.8 1.0
O A:HOH382 3.0 30.3 1.0
HE2 A:TYR23 3.0 15.2 1.0
HA3 A:GLY104 3.2 16.9 1.0
CE2 A:TYR23 3.5 12.7 1.0
CZ A:TYR23 3.6 12.7 1.0
HA2 A:GLY104 3.9 16.9 1.0
CA A:GLY104 4.0 14.1 1.0
O A:ARG21 4.4 21.2 1.0
O A:HOH305 4.4 28.3 1.0
N A:GLY104 4.5 15.9 1.0
H A:MET105 4.6 13.4 1.0
H A:GLY104 4.7 19.0 1.0
CD2 A:TYR23 4.7 11.7 1.0
CE1 A:TYR23 4.7 11.9 1.0
HB3 A:ARG21 4.8 26.0 1.0
O A:HOH358 4.9 29.1 1.0

Chlorine binding site 4 out of 5 in 8cwd

Go back to Chlorine Binding Sites List in 8cwd
Chlorine binding site 4 out of 5 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:32.8
occ:1.00
 H A:GLY26 2.2 14.6 1.0
HG3 A:GLN121 2.6 38.0 1.0
HA A:GLN121 2.7 22.8 1.0
HB2 A:SER24 2.8 21.2 1.0
HD13 A:ILE124 2.9 32.5 1.0
HE22 A:GLN121 2.9 41.4 1.0
HA3 A:GLY26 2.9 13.2 1.0
N A:GLY26 3.0 12.2 1.0
OG A:SER24 3.0 20.4 1.0
HG A:SER24 3.3 24.5 1.0
CB A:SER24 3.3 17.7 1.0
CG A:GLN121 3.4 31.7 1.0
HG23 A:VAL120 3.4 21.5 1.0
NE2 A:GLN121 3.4 34.6 1.0
CA A:GLY26 3.5 11.1 1.0
HG12 A:ILE124 3.5 27.5 1.0
CA A:GLN121 3.5 19.0 1.0
CD1 A:ILE124 3.7 27.1 1.0
CD A:GLN121 3.7 36.2 1.0
H A:LEU25 3.8 16.1 1.0
HD11 A:ILE124 3.8 32.5 1.0
N A:LEU25 3.9 13.4 1.0
N A:GLN121 3.9 17.5 1.0
CB A:GLN121 3.9 24.2 1.0
HE21 A:GLN121 4.0 41.4 1.0
HB3 A:SER24 4.0 21.2 1.0
C A:SER24 4.1 12.4 1.0
HA2 A:GLY26 4.1 13.2 1.0
HB3 A:LEU25 4.1 17.3 1.0
CG1 A:ILE124 4.1 22.9 1.0
H A:ASN27 4.1 12.7 1.0
HG2 A:GLN121 4.1 38.0 1.0
C A:LEU25 4.1 12.6 1.0
O A:VAL120 4.2 16.1 1.0
HB3 A:GLN121 4.2 29.1 1.0
H A:GLN121 4.3 21.0 1.0
C A:VAL120 4.3 15.6 1.0
CA A:SER24 4.3 14.9 1.0
CG2 A:VAL120 4.3 17.9 1.0
HD12 A:ILE124 4.5 32.5 1.0
HG23 A:ILE124 4.5 26.4 1.0
CA A:LEU25 4.5 13.7 1.0
C A:GLY26 4.5 11.2 1.0
HG21 A:VAL120 4.5 21.5 1.0
O A:SER24 4.6 13.2 1.0
N A:ASN27 4.6 10.6 1.0
HG13 A:ILE124 4.6 27.5 1.0
C A:GLN121 4.7 17.5 1.0
OE1 A:GLN121 4.8 37.6 1.0
HA A:SER24 4.8 17.9 1.0
HB2 A:GLN121 4.8 29.1 1.0
CB A:LEU25 4.8 14.4 1.0
HG22 A:VAL120 4.9 21.5 1.0
HB A:VAL120 4.9 19.7 1.0
O A:GLN121 4.9 20.1 1.0
HG21 A:ILE124 5.0 26.4 1.0

Chlorine binding site 5 out of 5 in 8cwd

Go back to Chlorine Binding Sites List in 8cwd
Chlorine binding site 5 out of 5 in the 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of 20NS Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:113.7
occ:1.00
 O A:HOH389 2.3 37.3 1.0
HZ1 A:LYS33 2.6 33.6 1.0
O A:HOH381 2.8 37.7 1.0
HZ2 A:LYS33 2.9 33.6 1.0
HE2 A:PHE38 3.1 18.6 1.0
NZ A:LYS33 3.2 28.0 1.0
HD2 A:PHE38 3.5 17.6 1.0
HZ3 A:LYS33 3.7 33.6 1.0
CE2 A:PHE38 3.8 15.5 1.0
O A:HOH316 3.8 25.2 1.0
HD3 A:LYS33 3.8 25.7 1.0
O A:HOH345 3.8 29.0 1.0
CD2 A:PHE38 4.0 14.7 1.0
CE A:LYS33 4.3 25.1 1.0
HB2 A:ARG5 4.3 21.4 1.0
CD A:LYS33 4.4 21.4 1.0
HE2 A:LYS33 4.5 30.1 1.0
HD2 A:LYS33 4.6 25.7 1.0
OD1 A:ASN37 4.8 24.0 0.9
HZ3 A:TRP123 4.9 26.9 1.0
H A:ARG5 4.9 20.1 1.0
CZ A:PHE38 4.9 14.5 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: Tue Jul 30 08:13:49 2024

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