Chlorine in PDB 8cwg: 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

Enzymatic activity of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose

All present enzymatic activity of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose:
3.2.1.17;

Protein crystallography data

The structure of 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwg 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 (%) 12.9 / 16.7

Other elements in 8cwg:

The structure of 200US 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 200US Temperature-Jump (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose (pdb code 8cwg). 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 (DARK1) Xfel Structure of Lysozyme Bound to N, N'-Diacetylchitobiose, PDB code: 8cwg:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 8cwg

Go back to Chlorine Binding Sites List in 8cwg
Chlorine binding site 1 out of 5 in the 200US 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 200US 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:31.8
occ:1.00
 H A:THR69 2.4 21.3 1.0
O A:HOH348 3.0 18.3 1.0
O A:HOH385 3.1 37.4 1.0
H A:GLY67 3.1 21.4 1.0
O A:THR69 3.2 19.7 1.0
N A:THR69 3.2 17.8 1.0
HA2 A:GLY67 3.2 24.9 1.0
H A:ARG68 3.4 20.7 1.0
OD1 A:ASN65 3.5 26.3 1.0
C A:THR69 3.5 18.0 1.0
N A:ARG68 3.5 17.2 1.0
N A:GLY67 3.6 17.9 1.0
C A:GLY67 3.6 19.7 1.0
CA A:GLY67 3.6 20.8 1.0
HB A:THR69 3.6 17.9 1.0
OG A:SER72 3.8 21.0 1.0
CA A:THR69 3.8 18.2 1.0
O A:HOH380 3.9 20.8 1.0
HA A:PRO70 3.9 29.8 1.0
H A:ASP66 4.0 18.2 1.0
OD1 A:ASP66 4.1 15.5 1.0
N A:PRO70 4.2 20.0 1.0
CB A:THR69 4.2 15.0 1.0
C A:ARG68 4.2 20.4 1.0
O A:GLY67 4.3 26.2 1.0
CA A:ARG68 4.3 17.6 1.0
HG1 A:THR69 4.4 18.9 1.0
HA A:ARG68 4.5 21.1 1.0
CA A:PRO70 4.5 24.8 1.0
HA3 A:GLY67 4.6 24.9 1.0
HA A:ASN65 4.6 18.9 1.0
H A:SER72 4.6 26.7 1.0
C A:ASP66 4.6 15.6 1.0
CG A:ASN65 4.7 24.8 1.0
N A:ASP66 4.7 15.2 1.0
NA A:NA201 4.7 17.8 1.0
HA A:THR69 4.7 21.8 1.0
OG1 A:THR69 4.8 15.8 1.0
HD3 A:PRO70 4.8 30.5 1.0
CB A:SER72 5.0 20.3 1.0

Chlorine binding site 2 out of 5 in 8cwg

Go back to Chlorine Binding Sites List in 8cwg
Chlorine binding site 2 out of 5 in the 200US 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 200US 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:81.0
occ:1.00
 H A:ILE88 2.3 22.4 1.0
HG12 A:ILE88 2.6 24.7 1.0
HE1 A:HIS15 2.8 39.1 1.0
HA A:ASP87 2.9 24.1 1.0
N A:ILE88 3.1 18.7 1.0
HH21 A:ARG14 3.2 35.7 0.4
HH22 A:ARG14 3.3 35.7 0.4
CG1 A:ILE88 3.5 20.6 1.0
CE1 A:HIS15 3.5 32.6 1.0
OD1 A:ASP87 3.5 28.6 1.0
NH2 A:ARG14 3.6 29.8 0.4
HH12 A:ARG14 3.7 43.5 0.6
HB1 A:ALA11 3.8 24.7 1.0
CA A:ASP87 3.8 20.1 1.0
HG23 A:ILE88 3.8 22.7 1.0
HG13 A:ILE88 3.8 24.7 1.0
O A:HOH331 3.8 34.0 1.0
HZ A:PHE3 3.8 22.9 1.0
C A:ASP87 3.9 19.7 1.0
H A:THR89 4.0 21.2 1.0
HG1 A:THR89 4.1 30.1 1.0
CA A:ILE88 4.1 16.3 1.0
CG A:ASP87 4.2 31.2 1.0
CB A:ILE88 4.2 17.1 1.0
O A:SER86 4.3 25.5 1.0
NH1 A:ARG14 4.3 36.3 0.6
HB2 A:ALA11 4.3 24.7 1.0
ND1 A:HIS15 4.4 31.9 1.0
HD1 A:HIS15 4.4 38.3 1.0
NE2 A:HIS15 4.4 33.4 1.0
HD11 A:ILE88 4.4 28.1 1.0
CD1 A:ILE88 4.5 23.4 1.0
N A:THR89 4.5 17.7 1.0
CG2 A:ILE88 4.5 19.0 1.0
CB A:ALA11 4.5 20.6 1.0
CB A:ASP87 4.5 24.5 1.0
HD13 A:ILE88 4.5 28.1 1.0
HH22 A:ARG14 4.6 44.0 0.6
HH11 A:ARG14 4.7 43.5 0.6
C A:ILE88 4.7 15.4 1.0
CZ A:PHE3 4.7 19.1 1.0
OG1 A:THR89 4.8 25.1 1.0
N A:ASP87 4.8 22.9 1.0
HE2 A:PHE3 4.8 24.2 1.0
HB2 A:ASP87 4.8 29.4 1.0
CZ A:ARG14 4.9 28.4 0.4
HA A:ILE88 4.9 19.5 1.0
C A:SER86 5.0 20.9 1.0

Chlorine binding site 3 out of 5 in 8cwg

Go back to Chlorine Binding Sites List in 8cwg
Chlorine binding site 3 out of 5 in the 200US 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 200US 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:22.3
occ:1.00
 HH A:TYR23 2.1 18.9 1.0
OH A:TYR23 2.9 15.8 1.0
HE2 A:TYR23 3.0 17.1 1.0
O A:HOH378 3.0 32.1 1.0
HA3 A:GLY104 3.3 19.7 1.0
CE2 A:TYR23 3.5 14.2 1.0
CZ A:TYR23 3.6 13.6 1.0
HA2 A:GLY104 3.9 19.7 1.0
CA A:GLY104 4.0 16.4 1.0
O A:ARG21 4.4 21.9 1.0
O A:HOH306 4.5 28.4 1.0
N A:GLY104 4.6 17.3 1.0
H A:MET105 4.7 14.8 1.0
CD2 A:TYR23 4.7 12.5 1.0
CE1 A:TYR23 4.7 12.6 1.0
H A:GLY104 4.7 20.8 1.0
HB3 A:ARG21 4.8 26.3 1.0
O A:HOH368 4.8 31.1 1.0

Chlorine binding site 4 out of 5 in 8cwg

Go back to Chlorine Binding Sites List in 8cwg
Chlorine binding site 4 out of 5 in the 200US 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 200US 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:33.4
occ:1.00
 H A:GLY26 2.2 16.5 1.0
HG3 A:GLN121 2.5 43.2 1.0
HA A:GLN121 2.7 23.8 1.0
HB2 A:SER24 2.8 22.0 1.0
HD13 A:ILE124 2.9 36.6 1.0
HA3 A:GLY26 2.9 15.0 1.0
HE22 A:GLN121 2.9 47.3 1.0
N A:GLY26 3.0 13.8 1.0
OG A:SER24 3.0 20.7 1.0
HG A:SER24 3.3 24.9 1.0
CB A:SER24 3.4 18.4 1.0
CG A:GLN121 3.4 36.0 1.0
HG23 A:VAL120 3.4 23.3 1.0
NE2 A:GLN121 3.4 39.4 1.0
CA A:GLY26 3.5 12.5 1.0
HG12 A:ILE124 3.5 29.6 1.0
CA A:GLN121 3.5 19.9 1.0
CD1 A:ILE124 3.7 30.5 1.0
CD A:GLN121 3.7 41.4 1.0
H A:LEU25 3.8 18.1 1.0
HD11 A:ILE124 3.8 36.6 1.0
N A:LEU25 3.9 15.1 1.0
N A:GLN121 3.9 18.9 1.0
CB A:GLN121 3.9 25.5 1.0
HE21 A:GLN121 4.0 47.3 1.0
HB3 A:SER24 4.0 22.0 1.0
HA2 A:GLY26 4.1 15.0 1.0
C A:SER24 4.1 14.8 1.0
HB3 A:LEU25 4.1 18.9 1.0
CG1 A:ILE124 4.1 24.7 1.0
HG2 A:GLN121 4.1 43.2 1.0
H A:ASN27 4.1 13.9 1.0
C A:LEU25 4.1 14.0 1.0
HB3 A:GLN121 4.2 30.6 1.0
O A:VAL120 4.2 16.9 1.0
H A:GLN121 4.3 22.7 1.0
C A:VAL120 4.3 16.3 1.0
CA A:SER24 4.3 16.1 1.0
CG2 A:VAL120 4.3 19.5 1.0
HD12 A:ILE124 4.4 36.6 1.0
HG23 A:ILE124 4.5 25.9 1.0
CA A:LEU25 4.5 15.1 1.0
C A:GLY26 4.5 11.6 1.0
HG21 A:VAL120 4.5 23.3 1.0
O A:SER24 4.6 14.9 1.0
N A:ASN27 4.6 11.6 1.0
HG13 A:ILE124 4.6 29.6 1.0
C A:GLN121 4.7 18.0 1.0
OE1 A:GLN121 4.7 41.3 1.0
HB2 A:GLN121 4.8 30.6 1.0
HA A:SER24 4.8 19.4 1.0
CB A:LEU25 4.8 15.7 1.0
HB A:VAL120 4.9 20.9 1.0
HG22 A:VAL120 4.9 23.3 1.0
O A:GLN121 4.9 21.6 1.0

Chlorine binding site 5 out of 5 in 8cwg

Go back to Chlorine Binding Sites List in 8cwg
Chlorine binding site 5 out of 5 in the 200US 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 200US 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:107.2
occ:1.00
 O A:HOH388 2.3 36.4 1.0
HZ1 A:LYS33 2.6 37.8 1.0
HZ2 A:LYS33 2.8 37.8 1.0
O A:HOH383 2.9 42.7 1.0
HE2 A:PHE38 3.1 21.1 1.0
NZ A:LYS33 3.1 31.5 1.0
HZ3 A:LYS33 3.6 37.8 1.0
HD2 A:PHE38 3.6 19.2 1.0
CE2 A:PHE38 3.8 17.6 1.0
HD3 A:LYS33 3.8 26.4 1.0
O A:HOH349 3.9 31.4 1.0
O A:HOH316 3.9 26.2 1.0
CD2 A:PHE38 4.1 16.0 1.0
CE A:LYS33 4.2 27.3 1.0
HB2 A:ARG5 4.3 22.0 1.0
CD A:LYS33 4.4 22.0 1.0
HE2 A:LYS33 4.4 32.7 1.0
HD2 A:LYS33 4.6 26.4 1.0
HZ3 A:TRP123 4.8 29.4 1.0
OD1 A:ASN37 4.8 26.1 0.9
CZ A:PHE38 4.9 16.3 1.0
H A:ARG5 5.0 21.1 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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy