Chlorine in PDB 9gcv: Identification of Chloride Ions in Lysozyme at Long Wavelengths

Enzymatic activity of Identification of Chloride Ions in Lysozyme at Long Wavelengths

All present enzymatic activity of Identification of Chloride Ions in Lysozyme at Long Wavelengths:
3.2.1.17;

Protein crystallography data

The structure of Identification of Chloride Ions in Lysozyme at Long Wavelengths, PDB code: 9gcv was solved by K.El Omari, I.Forsyth, C.M.Orr, A.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.88 / 2.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 79.031, 79.031, 36.897, 90, 90, 90
R / Rfree (%) 18.8 / 21.7

Other elements in 9gcv:

The structure of Identification of Chloride Ions in Lysozyme at Long Wavelengths also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Identification of Chloride Ions in Lysozyme at Long Wavelengths (pdb code 9gcv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Identification of Chloride Ions in Lysozyme at Long Wavelengths, PDB code: 9gcv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 9gcv

Go back to Chlorine Binding Sites List in 9gcv
Chlorine binding site 1 out of 5 in the Identification of Chloride Ions in Lysozyme at Long Wavelengths


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Identification of Chloride Ions in Lysozyme at Long Wavelengths within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl201

b:29.5
occ:1.00
 OG A:SER24 3.1 11.1 1.0
N A:GLY26 3.2 13.4 1.0
CA A:GLY26 3.5 12.7 1.0
CB A:SER24 3.5 11.6 1.0
CA A:GLN121 3.8 27.2 1.0
CD1 A:ILE124 3.9 16.9 1.0
N A:LEU25 4.1 13.0 1.0
CB A:GLN121 4.2 33.8 1.0
N A:GLN121 4.2 24.8 1.0
CG1 A:ILE124 4.2 18.0 1.0
C A:SER24 4.4 12.7 1.0
O A:VAL120 4.4 23.6 1.0
C A:LEU25 4.4 14.3 1.0
CG2 A:VAL120 4.4 18.5 1.0
C A:VAL120 4.4 22.9 1.0
CG A:GLN121 4.5 40.6 1.0
CA A:SER24 4.6 12.6 1.0
C A:GLY26 4.7 12.0 1.0
CA A:LEU25 4.7 13.8 1.0
N A:ASN27 4.8 10.9 1.0
O A:SER24 4.8 12.6 1.0
C A:GLN121 5.0 23.9 1.0
CB A:LEU25 5.0 14.2 1.0

Chlorine binding site 2 out of 5 in 9gcv

Go back to Chlorine Binding Sites List in 9gcv
Chlorine binding site 2 out of 5 in the Identification of Chloride Ions in Lysozyme at Long Wavelengths


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Identification of Chloride Ions in Lysozyme at Long Wavelengths within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl202

b:34.2
occ:1.00
 NZ A:LYS33 3.7 17.1 1.0
CE2 A:PHE38 3.8 10.8 1.0
CZ3 A:TRP123 4.1 19.7 1.0
CE A:LYS33 4.1 16.2 1.0
CD A:ARG5 4.2 22.2 1.0
CB A:ARG5 4.3 20.0 1.0
CD A:LYS33 4.3 15.2 1.0
CZ A:PHE38 4.5 10.8 1.0
CD2 A:PHE38 4.7 10.9 1.0
CG A:ARG5 4.8 20.4 1.0
CE3 A:TRP123 4.9 20.0 1.0
NE A:ARG5 4.9 22.6 1.0
CH2 A:TRP123 5.0 20.6 1.0

Chlorine binding site 3 out of 5 in 9gcv

Go back to Chlorine Binding Sites List in 9gcv
Chlorine binding site 3 out of 5 in the Identification of Chloride Ions in Lysozyme at Long Wavelengths


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Identification of Chloride Ions in Lysozyme at Long Wavelengths within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl203

b:18.9
occ:1.00
 O A:HOH310 3.4 10.4 1.0
ND2 A:ASN113 3.4 11.8 1.0
CB A:ASN113 3.7 12.4 1.0
CA A:ALA110 3.8 13.6 1.0
CG A:ASN113 4.1 11.8 1.0
CB A:ALA110 4.1 13.4 1.0
N A:ALA110 4.2 14.6 1.0
O A:VAL109 4.3 17.5 1.0
CD A:ARG114 4.3 11.5 1.0
CG1 A:VAL109 4.3 16.4 1.0
C A:VAL109 4.4 16.1 1.0
CG A:ARG114 4.5 12.4 1.0
C A:ALA110 4.9 13.2 1.0
O A:ALA110 4.9 13.0 1.0

Chlorine binding site 4 out of 5 in 9gcv

Go back to Chlorine Binding Sites List in 9gcv
Chlorine binding site 4 out of 5 in the Identification of Chloride Ions in Lysozyme at Long Wavelengths


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Identification of Chloride Ions in Lysozyme at Long Wavelengths within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl204

b:21.8
occ:1.00
 O A:HOH315 2.9 10.0 1.0
N A:THR69 3.0 21.6 1.0
O A:THR69 3.2 22.6 1.0
N A:ARG68 3.5 20.8 1.0
C A:THR69 3.5 22.7 1.0
OG A:SER72 3.6 21.1 1.0
C A:GLY67 3.6 19.6 1.0
CA A:THR69 3.7 23.0 1.0
CA A:GLY67 3.8 18.7 1.0
N A:GLY67 3.8 18.0 1.0
OD1 A:ASN65 3.9 22.7 1.0
C A:ARG68 4.0 21.4 1.0
CB A:THR69 4.1 23.2 1.0
CA A:ARG68 4.1 20.7 1.0
OD1 A:ASP66 4.2 18.9 1.0
O A:GLY67 4.3 21.6 1.0
N A:PRO70 4.4 22.8 1.0
OG1 A:THR69 4.7 22.5 1.0
NA A:NA200 4.7 36.3 1.0
O A:HOH309 4.8 16.2 0.5
CB A:SER72 4.8 22.4 1.0
C A:ASP66 4.9 17.8 1.0
N A:ASP66 5.0 19.3 1.0

Chlorine binding site 5 out of 5 in 9gcv

Go back to Chlorine Binding Sites List in 9gcv
Chlorine binding site 5 out of 5 in the Identification of Chloride Ions in Lysozyme at Long Wavelengths


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Identification of Chloride Ions in Lysozyme at Long Wavelengths within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:35.8
occ:1.00
 ND2 A:ASN65 3.0 22.2 1.0
CB A:ASN65 3.7 20.8 1.0
CG A:ASN65 3.8 22.1 1.0
CB A:PRO79 3.8 20.8 1.0
CA A:PRO79 3.9 21.6 1.0
N A:PRO79 4.0 22.6 1.0
O A:ASN65 4.3 21.7 1.0
CD A:PRO79 4.3 21.6 1.0
CG A:PRO79 4.5 20.8 1.0
C A:ILE78 4.6 23.4 1.0
O A:ILE78 4.8 25.3 1.0
ND2 A:ASN74 4.8 22.9 1.0
CA A:ASN65 4.8 20.0 1.0
C A:ASN65 4.8 20.8 1.0
OD1 A:ASN65 4.9 22.7 1.0

Reference:

K.El Omari, I.Forsyth, R.Duman, C.M.Orr, V.Mykhaylyk, E.J.Mancini, A.Wagner. Utilizing Anomalous Signals For Element Identification in Macromolecular Crystallography. Acta Crystallogr D Struct 2024BIOL.
ISSN: ISSN 2059-7983
PubMed: 39291627
DOI: 10.1107/S2059798324008659
Page generated: Thu Oct 31 18:12:23 2024

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