Atomistry » Chlorine » PDB 8cvu-8d1l » 8cwh
Atomistry »
  Chlorine »
    PDB 8cvu-8d1l »
      8cwh »

Chlorine in PDB 8cwh: 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

Enzymatic activity of 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

All present enzymatic activity of 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose:
3.2.1.17;

Protein crystallography data

The structure of 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwh 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 (%) 13.2 / 16.8

Other elements in 8cwh:

The structure of 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwh). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwh:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cwh

Go back to Chlorine Binding Sites List in 8cwh
Chlorine binding site 1 out of 5 in the 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:30.5
occ:1.00
 H A:THR69 2.4 19.8 1.0
O A:HOH350 3.0 18.2 1.0
H A:GLY67 3.1 21.3 1.0
O A:THR69 3.2 19.6 1.0
O A:HOH388 3.2 35.5 1.0
N A:THR69 3.2 16.5 1.0
HA2 A:GLY67 3.2 23.5 1.0
H A:ARG68 3.4 21.8 1.0
C A:THR69 3.4 18.2 1.0
OD1 A:ASN65 3.5 25.7 1.0
N A:ARG68 3.5 18.2 1.0
HB A:THR69 3.6 18.7 1.0
N A:GLY67 3.6 17.8 1.0
CA A:GLY67 3.6 19.6 1.0
C A:GLY67 3.6 19.9 1.0
OG A:SER72 3.8 20.1 1.0
CA A:THR69 3.8 17.2 1.0
O A:HOH383 3.9 21.7 1.0
HA A:PRO70 3.9 28.5 1.0
H A:ASP66 4.0 18.1 1.0
OD1 A:ASP66 4.1 15.2 1.0
N A:PRO70 4.1 20.1 1.0
CB A:THR69 4.1 15.7 1.0
C A:ARG68 4.2 19.1 1.0
O A:GLY67 4.3 24.6 1.0
CA A:ARG68 4.3 18.6 1.0
HG1 A:THR69 4.4 19.0 1.0
HA A:ARG68 4.5 22.3 1.0
CA A:PRO70 4.5 23.8 1.0
H A:SER72 4.5 26.7 1.0
HA3 A:GLY67 4.6 23.5 1.0
HA A:ASN65 4.6 18.2 1.0
C A:ASP66 4.7 16.6 1.0
NA A:NA201 4.7 17.7 1.0
CG A:ASN65 4.7 23.2 1.0
N A:ASP66 4.7 15.2 1.0
HA A:THR69 4.7 20.7 1.0
OG1 A:THR69 4.8 15.8 1.0
HD3 A:PRO70 4.8 29.4 1.0
CB A:SER72 5.0 19.7 1.0

Chlorine binding site 2 out of 5 in 8cwh

Go back to Chlorine Binding Sites List in 8cwh
Chlorine binding site 2 out of 5 in the 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:88.5
occ:1.00
 H A:ILE88 2.3 21.1 1.0
HG12 A:ILE88 2.6 23.0 1.0
HE1 A:HIS15 2.7 36.5 1.0
HA A:ASP87 2.9 26.2 1.0
HH21 A:ARG14 3.1 35.7 0.4
N A:ILE88 3.2 17.6 1.0
HH22 A:ARG14 3.4 35.7 0.4
OD1 A:ASP87 3.5 29.0 1.0
CE1 A:HIS15 3.5 30.5 1.0
CG1 A:ILE88 3.5 19.2 1.0
NH2 A:ARG14 3.6 29.8 0.4
HH12 A:ARG14 3.7 42.0 0.6
HG13 A:ILE88 3.8 23.0 1.0
CA A:ASP87 3.8 21.9 1.0
HG23 A:ILE88 3.8 24.5 1.0
HB1 A:ALA11 3.8 23.8 1.0
O A:HOH333 3.9 34.5 1.0
H A:THR89 3.9 20.8 1.0
C A:ASP87 3.9 19.6 1.0
HZ A:PHE3 3.9 22.3 1.0
HG1 A:THR89 4.0 28.1 1.0
CG A:ASP87 4.1 30.7 1.0
CA A:ILE88 4.1 16.2 1.0
CB A:ILE88 4.2 17.1 1.0
NH1 A:ARG14 4.3 35.0 0.6
ND1 A:HIS15 4.3 29.3 1.0
NE2 A:HIS15 4.3 32.2 1.0
HD1 A:HIS15 4.3 35.1 1.0
O A:SER86 4.3 25.2 1.0
HB2 A:ALA11 4.4 23.8 1.0
N A:THR89 4.4 17.3 1.0
HH22 A:ARG14 4.5 41.9 0.6
CG2 A:ILE88 4.5 20.4 1.0
CB A:ASP87 4.5 25.9 1.0
CB A:ALA11 4.5 19.8 1.0
HD11 A:ILE88 4.5 26.4 1.0
CD1 A:ILE88 4.6 22.0 1.0
HH11 A:ARG14 4.6 42.0 0.6
HD13 A:ILE88 4.7 26.4 1.0
C A:ILE88 4.7 15.6 1.0
OG1 A:THR89 4.7 23.5 1.0
CZ A:PHE3 4.8 18.6 1.0
HB2 A:ASP87 4.8 31.0 1.0
N A:ASP87 4.9 22.1 1.0
CZ A:ARG14 4.9 28.2 0.4
HE2 A:PHE3 4.9 22.9 1.0
HA A:ILE88 4.9 19.4 1.0
OD2 A:ASP87 5.0 37.1 1.0

Chlorine binding site 3 out of 5 in 8cwh

Go back to Chlorine Binding Sites List in 8cwh
Chlorine binding site 3 out of 5 in the 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:21.8
occ:1.00
 HH A:TYR23 2.1 18.7 1.0
OH A:TYR23 2.9 15.6 1.0
O A:HOH387 2.9 32.6 1.0
HE2 A:TYR23 3.0 16.6 1.0
HA3 A:GLY104 3.3 18.4 1.0
CE2 A:TYR23 3.5 13.8 1.0
CZ A:TYR23 3.6 13.9 1.0
HA2 A:GLY104 3.8 18.4 1.0
CA A:GLY104 4.0 15.4 1.0
O A:ARG21 4.4 22.4 1.0
O A:HOH307 4.5 29.6 1.0
N A:GLY104 4.6 16.4 1.0
H A:MET105 4.7 15.0 1.0
CD2 A:TYR23 4.7 12.5 1.0
H A:GLY104 4.7 19.7 1.0
CE1 A:TYR23 4.7 12.7 1.0
HB3 A:ARG21 4.8 27.2 1.0
O A:HOH361 4.9 31.7 1.0

Chlorine binding site 4 out of 5 in 8cwh

Go back to Chlorine Binding Sites List in 8cwh
Chlorine binding site 4 out of 5 in the 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:32.6
occ:1.00
 H A:GLY26 2.2 16.1 1.0
HG3 A:GLN121 2.5 40.0 1.0
HA A:GLN121 2.7 24.0 1.0
HB2 A:SER24 2.8 21.7 1.0
HD13 A:ILE124 2.9 31.9 1.0
HA3 A:GLY26 2.9 14.7 1.0
N A:GLY26 3.0 13.4 1.0
HE22 A:GLN121 3.0 44.4 1.0
OG A:SER24 3.0 21.3 1.0
HG A:SER24 3.2 25.6 1.0
CB A:SER24 3.4 18.1 1.0
HG23 A:VAL120 3.4 22.7 1.0
CG A:GLN121 3.4 33.4 1.0
CA A:GLY26 3.4 12.2 1.0
NE2 A:GLN121 3.5 37.1 1.0
HG12 A:ILE124 3.5 28.5 1.0
CA A:GLN121 3.5 20.0 1.0
CD1 A:ILE124 3.7 26.6 1.0
CD A:GLN121 3.7 37.4 1.0
H A:LEU25 3.8 17.6 1.0
HD11 A:ILE124 3.9 31.9 1.0
N A:LEU25 3.9 14.7 1.0
CB A:GLN121 3.9 25.3 1.0
N A:GLN121 3.9 18.2 1.0
HB3 A:SER24 4.0 21.7 1.0
HE21 A:GLN121 4.0 44.4 1.0
HA2 A:GLY26 4.1 14.7 1.0
C A:SER24 4.1 13.7 1.0
HB3 A:LEU25 4.1 18.9 1.0
CG1 A:ILE124 4.1 23.8 1.0
HG2 A:GLN121 4.1 40.0 1.0
H A:ASN27 4.1 14.0 1.0
C A:LEU25 4.1 13.6 1.0
HB3 A:GLN121 4.2 30.4 1.0
O A:VAL120 4.2 17.1 1.0
C A:VAL120 4.3 16.2 1.0
H A:GLN121 4.3 21.8 1.0
CG2 A:VAL120 4.3 18.9 1.0
CA A:SER24 4.3 15.8 1.0
CA A:LEU25 4.5 14.4 1.0
HD12 A:ILE124 4.5 31.9 1.0
HG23 A:ILE124 4.5 26.9 1.0
C A:GLY26 4.5 12.1 1.0
HG21 A:VAL120 4.5 22.7 1.0
O A:SER24 4.5 14.4 1.0
N A:ASN27 4.6 11.7 1.0
HG13 A:ILE124 4.7 28.5 1.0
C A:GLN121 4.7 18.3 1.0
HB2 A:GLN121 4.8 30.4 1.0
HA A:SER24 4.8 19.0 1.0
OE1 A:GLN121 4.8 37.9 1.0
CB A:LEU25 4.8 15.8 1.0
HG22 A:VAL120 4.8 22.7 1.0
HB A:VAL120 4.9 20.1 1.0
O A:GLN121 4.9 20.8 1.0

Chlorine binding site 5 out of 5 in 8cwh

Go back to Chlorine Binding Sites List in 8cwh
Chlorine binding site 5 out of 5 in the 200US Temperature-Jump (DARK2) 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 200US Temperature-Jump (DARK2) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:116.1
occ:1.00
 O A:HOH394 2.4 35.6 1.0
HZ1 A:LYS33 2.6 34.6 1.0
HZ2 A:LYS33 2.9 34.6 1.0
HE2 A:PHE38 3.1 19.4 1.0
NZ A:LYS33 3.1 28.9 1.0
HD2 A:PHE38 3.5 18.5 1.0
HZ3 A:LYS33 3.6 34.6 1.0
O A:HOH345 3.7 30.6 1.0
O A:HOH309 3.7 27.9 1.0
CE2 A:PHE38 3.8 16.2 1.0
HD3 A:LYS33 3.8 26.1 1.0
CD2 A:PHE38 4.0 15.4 1.0
CE A:LYS33 4.3 26.2 1.0
CD A:LYS33 4.4 21.8 1.0
HB2 A:ARG5 4.4 21.3 1.0
HE2 A:LYS33 4.5 31.4 1.0
HD2 A:LYS33 4.6 26.1 1.0
OD1 A:ASN37 4.7 25.9 0.9
O A:HOH377 4.9 42.1 1.0
CZ A:PHE38 4.9 15.2 1.0
HZ3 A:TRP123 4.9 28.2 1.0
H A:ARG5 5.0 21.0 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: Sun Jul 13 10:26:34 2025

Last articles

Mg in 7KWK
Mg in 7KWD
Mg in 7KW7
Mg in 7KVU
Mg in 7KW4
Mg in 7KVV
Mg in 7KVT
Mg in 7KUP
Mg in 7KUL
Mg in 7KUN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy