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: Tue Jul 30 08:18:21 2024

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