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

Go back to Chlorine Binding Sites List in 8cwc
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

Go back to Chlorine Binding Sites List in 8cwc
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

Go back to Chlorine Binding Sites List in 8cwc
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 Apr 4 22:39:56 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy