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

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

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

Protein crystallography data

The structure of 20NS Temperature-Jump (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwc 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 (%) 13.2 / 16.9

Other elements in 8cwc:

The structure of 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwc). 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwc:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cwc

Go back to Chlorine Binding Sites List in 8cwc
Chlorine binding site 1 out of 5 in the 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:39.7
occ:1.00
 H A:THR69 2.4 21.6 1.0
O A:HOH341 3.0 19.8 1.0
O A:HOH382 3.1 40.7 1.0
O A:THR69 3.1 20.6 1.0
H A:GLY67 3.1 21.8 1.0
N A:THR69 3.2 18.1 1.0
HA2 A:GLY67 3.2 25.6 1.0
H A:ARG68 3.4 21.9 1.0
C A:THR69 3.4 17.8 1.0
OD1 A:ASN65 3.5 28.2 1.0
N A:ARG68 3.5 18.3 1.0
HB A:THR69 3.6 20.1 1.0
N A:GLY67 3.6 18.2 1.0
CA A:GLY67 3.6 21.3 1.0
C A:GLY67 3.6 20.3 1.0
OG A:SER72 3.7 21.5 1.0
CA A:THR69 3.8 17.6 1.0
O A:HOH380 3.9 23.6 1.0
HA A:PRO70 3.9 28.5 1.0
H A:ASP66 4.1 19.0 1.0
N A:PRO70 4.1 20.4 1.0
OD1 A:ASP66 4.1 15.6 1.0
CB A:THR69 4.2 16.8 1.0
C A:ARG68 4.2 21.2 1.0
CA A:ARG68 4.3 19.0 1.0
O A:GLY67 4.3 25.1 1.0
HG1 A:THR69 4.4 20.1 1.0
HA A:ARG68 4.5 22.8 1.0
CA A:PRO70 4.5 23.8 1.0
HA3 A:GLY67 4.6 25.6 1.0
H A:SER72 4.6 27.5 1.0
HA A:ASN65 4.6 19.6 1.0
C A:ASP66 4.7 17.8 1.0
NA A:NA201 4.7 18.0 1.0
N A:ASP66 4.7 15.9 1.0
CG A:ASN65 4.7 24.8 1.0
HA A:THR69 4.7 21.1 1.0
OG1 A:THR69 4.8 16.8 1.0
HD3 A:PRO70 4.8 29.9 1.0
CB A:SER72 5.0 19.8 1.0

Chlorine binding site 2 out of 5 in 8cwc

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Chlorine binding site 2 out of 5 in the 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:94.1
occ:1.00
 H A:ILE88 2.3 23.3 1.0
HG12 A:ILE88 2.6 25.0 1.0
HE1 A:HIS15 2.8 38.2 1.0
HA A:ASP87 2.9 26.4 1.0
N A:ILE88 3.2 19.5 1.0
HH21 A:ARG14 3.2 37.4 0.4
HH22 A:ARG14 3.3 37.4 0.4
CG1 A:ILE88 3.5 20.9 1.0
CE1 A:HIS15 3.6 31.9 1.0
OD1 A:ASP87 3.6 30.0 1.0
NH2 A:ARG14 3.6 31.1 0.4
HH12 A:ARG14 3.7 43.1 0.6
HG13 A:ILE88 3.7 25.0 1.0
HG23 A:ILE88 3.7 24.8 1.0
CA A:ASP87 3.8 22.0 1.0
HB1 A:ALA11 3.8 24.3 1.0
HZ A:PHE3 3.8 25.8 1.0
O A:HOH333 3.8 37.9 1.0
C A:ASP87 3.9 20.0 1.0
H A:THR89 4.0 20.1 1.0
HG1 A:THR89 4.1 31.2 1.0
CA A:ILE88 4.2 17.2 1.0
CB A:ILE88 4.2 18.3 1.0
O A:SER86 4.2 26.9 1.0
CG A:ASP87 4.3 32.1 1.0
HB2 A:ALA11 4.3 24.3 1.0
NH1 A:ARG14 4.3 35.9 0.6
NE2 A:HIS15 4.4 33.5 1.0
ND1 A:HIS15 4.4 30.9 1.0
HD1 A:HIS15 4.4 37.0 1.0
CG2 A:ILE88 4.5 20.7 1.0
HD11 A:ILE88 4.5 27.3 1.0
CD1 A:ILE88 4.5 22.8 1.0
CB A:ALA11 4.5 20.3 1.0
N A:THR89 4.5 16.8 1.0
HD13 A:ILE88 4.6 27.3 1.0
CB A:ASP87 4.6 26.0 1.0
HH11 A:ARG14 4.6 43.1 0.6
HH22 A:ARG14 4.7 43.5 0.6
CZ A:PHE3 4.7 21.5 1.0
C A:ILE88 4.7 16.4 1.0
OG1 A:THR89 4.8 26.1 1.0
HE2 A:PHE3 4.8 26.4 1.0
N A:ASP87 4.8 22.5 1.0
HB2 A:ASP87 4.9 31.2 1.0
CZ A:ARG14 4.9 30.4 0.4
HA A:ILE88 4.9 20.6 1.0
C A:SER86 5.0 22.4 1.0

Chlorine binding site 3 out of 5 in 8cwc

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Chlorine binding site 3 out of 5 in the 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:22.3
occ:1.00
 HH A:TYR23 2.1 18.7 1.0
OH A:TYR23 2.9 15.6 1.0
HE2 A:TYR23 3.0 17.5 1.0
O A:HOH379 3.0 32.4 1.0
HA3 A:GLY104 3.2 18.9 1.0
O A:HOH349 3.4 23.9 1.0
CE2 A:TYR23 3.5 14.6 1.0
CZ A:TYR23 3.6 13.7 1.0
HA2 A:GLY104 3.8 18.9 1.0
CA A:GLY104 3.9 15.8 1.0
O A:HOH307 4.4 30.0 1.0
O A:ARG21 4.4 22.4 1.0
N A:GLY104 4.5 17.1 1.0
H A:MET105 4.7 15.0 1.0
H A:GLY104 4.7 20.5 1.0
CD2 A:TYR23 4.7 12.7 1.0
HB3 A:ARG21 4.7 27.2 1.0
CE1 A:TYR23 4.8 13.0 1.0
O A:HOH355 4.9 31.1 1.0

Chlorine binding site 4 out of 5 in 8cwc

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Chlorine binding site 4 out of 5 in the 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:38.5
occ:1.00
 H A:GLY26 2.2 16.1 1.0
HG3 A:GLN121 2.6 42.6 1.0
HA A:GLN121 2.7 23.8 1.0
HB2 A:SER24 2.7 22.6 1.0
HA3 A:GLY26 2.9 15.8 1.0
HD13 A:ILE124 2.9 34.1 1.0
HE22 A:GLN121 2.9 47.3 1.0
OG A:SER24 3.0 21.6 1.0
N A:GLY26 3.0 13.5 1.0
CB A:SER24 3.3 18.8 1.0
HG A:SER24 3.4 25.9 1.0
HG23 A:VAL120 3.4 24.2 1.0
CA A:GLY26 3.4 13.2 1.0
CG A:GLN121 3.4 35.5 1.0
NE2 A:GLN121 3.4 39.5 1.0
HG12 A:ILE124 3.5 28.8 1.0
CA A:GLN121 3.6 19.9 1.0
CD1 A:ILE124 3.7 28.4 1.0
H A:LEU25 3.8 17.8 1.0
CD A:GLN121 3.8 40.6 1.0
HD11 A:ILE124 3.8 34.1 1.0
N A:LEU25 3.9 14.9 1.0
N A:GLN121 4.0 18.2 1.0
CB A:GLN121 4.0 26.1 1.0
HB3 A:SER24 4.0 22.6 1.0
HE21 A:GLN121 4.0 47.3 1.0
HB3 A:LEU25 4.1 19.4 1.0
HA2 A:GLY26 4.1 15.8 1.0
C A:SER24 4.1 14.1 1.0
C A:LEU25 4.1 13.6 1.0
H A:ASN27 4.1 14.4 1.0
CG1 A:ILE124 4.1 24.1 1.0
HG2 A:GLN121 4.2 42.6 1.0
O A:VAL120 4.2 17.6 1.0
HB3 A:GLN121 4.3 31.3 1.0
C A:VAL120 4.3 16.7 1.0
CG2 A:VAL120 4.3 20.2 1.0
CA A:SER24 4.3 15.8 1.0
H A:GLN121 4.3 21.8 1.0
CA A:LEU25 4.5 14.8 1.0
HG23 A:ILE124 4.5 27.0 1.0
HG21 A:VAL120 4.5 24.2 1.0
C A:GLY26 4.5 12.6 1.0
HD12 A:ILE124 4.5 34.1 1.0
O A:SER24 4.6 15.1 1.0
N A:ASN27 4.6 12.0 1.0
HG13 A:ILE124 4.7 28.8 1.0
C A:GLN121 4.7 18.8 1.0
CB A:LEU25 4.8 16.2 1.0
HA A:SER24 4.8 18.9 1.0
OE1 A:GLN121 4.8 40.9 1.0
HB2 A:GLN121 4.8 31.3 1.0
HG22 A:VAL120 4.9 24.2 1.0
HB A:VAL120 4.9 22.1 1.0
O A:GLN121 4.9 21.4 1.0
HG21 A:ILE124 5.0 27.0 1.0

Chlorine binding site 5 out of 5 in 8cwc

Go back to Chlorine Binding Sites List in 8cwc
Chlorine binding site 5 out of 5 in the 20NS Temperature-Jump (Light) 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 (Light) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl208

b:110.6
occ:1.00
 O A:HOH386 2.4 38.7 1.0
O A:HOH384 2.7 37.2 1.0
HZ1 A:LYS33 2.7 37.9 1.0
HZ2 A:LYS33 2.9 37.9 1.0
HE2 A:PHE38 3.1 21.6 1.0
NZ A:LYS33 3.2 31.6 1.0
HD2 A:PHE38 3.5 19.7 1.0
O A:HOH319 3.6 26.6 1.0
HZ3 A:LYS33 3.7 37.9 1.0
O A:HOH351 3.7 32.7 1.0
CE2 A:PHE38 3.8 18.1 1.0
HD3 A:LYS33 3.9 28.7 1.0
CD2 A:PHE38 4.0 16.4 1.0
HB2 A:ARG5 4.3 21.4 1.0
CE A:LYS33 4.3 28.9 1.0
CD A:LYS33 4.5 24.0 1.0
HE2 A:LYS33 4.5 34.6 1.0
HD2 A:LYS33 4.6 28.7 1.0
H A:ARG5 4.9 21.1 1.0
OD1 A:ASN37 4.9 27.4 0.9
HZ3 A:TRP123 5.0 28.7 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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