Atomistry » Cadmium » PDB 4l8q-4qdp » 4lyc
Atomistry »
  Cadmium »
    PDB 4l8q-4qdp »
      4lyc »

Cadmium in PDB 4lyc: Cd Ions Within A Lysoyzme Single Crystal

Enzymatic activity of Cd Ions Within A Lysoyzme Single Crystal

All present enzymatic activity of Cd Ions Within A Lysoyzme Single Crystal:
3.2.1.17;

Protein crystallography data

The structure of Cd Ions Within A Lysoyzme Single Crystal, PDB code: 4lyc was solved by H.Wei, S.House, J.Wu, J.Zhang, Z.Wang, Y.He, Y.-G.Gao, H.Robinson, W.Li, J.-M.Zuo, I.M.Robertson, Y.Lu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.35
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 78.558, 78.558, 37.179, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Cd Ions Within A Lysoyzme Single Crystal (pdb code 4lyc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Cd Ions Within A Lysoyzme Single Crystal, PDB code: 4lyc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 1 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd201

b:44.2
occ:1.00
OH A:TYR23 3.1 19.0 1.0
O A:HOH4005 3.4 21.5 1.0
CE2 A:TYR23 3.7 14.6 1.0
CZ A:TYR23 3.7 14.9 1.0
CA A:GLY104 4.1 17.9 1.0
O A:HOH4128 4.6 40.4 1.0
O A:ARG21 4.7 21.2 1.0
N A:GLY104 4.7 18.2 1.0
CD2 A:TYR23 4.9 14.8 1.0
CE1 A:TYR23 4.9 15.9 1.0

Cadmium binding site 2 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 2 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:59.1
occ:1.00
N A:THR69 3.0 19.7 1.0
O A:HOH4007 3.2 20.6 1.0
O A:HOH4039 3.2 31.6 1.0
O A:HOH4143 3.3 37.1 1.0
O A:THR69 3.4 21.0 1.0
N A:ARG68 3.4 17.7 1.0
C A:GLY67 3.4 22.4 1.0
O A:HOH4110 3.5 40.5 1.0
C A:THR69 3.5 19.2 1.0
CA A:GLY67 3.6 21.4 1.0
N A:GLY67 3.7 18.8 1.0
CA A:THR69 3.7 21.7 1.0
OD1 A:ASN65 3.8 22.6 1.0
OG A:SER72 3.8 26.8 1.0
O A:HOH4026 4.0 24.9 1.0
C A:ARG68 4.0 23.0 1.0
O A:GLY67 4.1 23.3 1.0
CB A:THR69 4.1 18.9 1.0
CA A:ARG68 4.2 18.4 1.0
N A:PRO70 4.2 22.4 1.0
OD1 A:ASP66 4.2 17.2 1.0
OG1 A:THR69 4.7 18.7 1.0
C A:ASP66 4.8 16.1 1.0
CA A:PRO70 4.9 24.2 1.0
O A:HOH4028 4.9 21.6 0.5
N A:ASP66 4.9 16.0 1.0
CB A:SER72 4.9 30.1 1.0
CG A:ASN65 5.0 19.8 1.0

Cadmium binding site 3 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 3 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd203

b:50.0
occ:1.00
OG A:SER24 3.0 23.8 1.0
N A:GLY26 3.2 19.5 1.0
CB A:SER24 3.5 18.6 1.0
CA A:GLY26 3.6 17.6 1.0
CA A:GLN121 3.6 21.7 1.0
N A:GLN121 3.9 20.4 1.0
CB A:GLN121 4.0 29.5 1.0
CG A:GLN121 4.0 34.6 1.0
CD1 A:ILE124 4.1 37.4 1.0
O A:VAL120 4.2 18.8 1.0
C A:VAL120 4.3 17.9 1.0
CG2 A:VAL120 4.3 22.8 1.0
CG1 A:ILE124 4.3 25.5 1.0
N A:LEU25 4.3 18.7 1.0
C A:LEU25 4.4 19.5 1.0
C A:SER24 4.5 19.9 1.0
C A:GLY26 4.6 19.9 1.0
CA A:SER24 4.6 20.7 1.0
N A:ASN27 4.7 17.4 1.0
C A:GLN121 4.8 21.6 1.0
CA A:LEU25 4.8 19.6 1.0
O A:SER24 5.0 18.6 1.0

Cadmium binding site 4 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 4 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd204

b:59.9
occ:1.00
OG1 A:THR43 2.7 19.9 1.0
O A:GLN41 2.8 19.5 1.0
N A:THR43 3.0 17.2 1.0
CB A:THR43 3.5 16.6 1.0
CG2 A:THR43 3.6 17.5 1.0
C A:ALA42 3.6 15.5 1.0
CA A:THR43 3.7 17.7 1.0
CA A:ALA42 3.8 16.1 1.0
C A:GLN41 3.8 20.0 1.0
O A:THR43 4.1 20.2 1.0
N A:ALA42 4.2 15.4 1.0
C A:THR43 4.4 19.4 1.0
O A:ALA42 4.5 15.1 1.0

Cadmium binding site 5 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 5 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd205

b:58.6
occ:1.00
OD2 A:ASP66 2.6 16.3 1.0
OG1 A:THR51 2.7 17.1 1.0
NE A:ARG68 2.9 19.7 1.0
O A:GLY49 3.0 20.2 1.0
OG1 A:THR69 3.2 18.7 1.0
N A:THR51 3.4 14.4 1.0
CB A:THR51 3.4 14.3 1.0
CG A:ARG68 3.5 18.9 1.0
CG A:ASP66 3.5 16.9 1.0
C A:SER50 3.5 14.2 1.0
NE A:ARG45 3.6 36.2 1.0
CD A:ARG68 3.7 18.6 1.0
OD1 A:ASP66 3.7 17.2 1.0
CA A:SER50 3.8 19.6 1.0
OG A:SER60 3.8 17.5 1.0
CZ A:ARG68 3.8 22.3 1.0
NH2 A:ARG68 3.9 20.1 1.0
C A:GLY49 4.0 18.5 1.0
CA A:THR51 4.0 16.3 1.0
NH2 A:ARG45 4.1 22.7 1.0
O A:SER50 4.2 18.0 1.0
O A:ARG68 4.2 30.2 1.0
CZ A:ARG45 4.2 24.7 1.0
OH A:TYR53 4.2 17.3 1.0
CD A:ARG45 4.2 24.8 1.0
N A:SER50 4.4 19.8 1.0
C A:ARG68 4.5 23.0 1.0
CB A:THR69 4.5 18.9 1.0
O A:HOH4120 4.7 52.9 1.0
CB A:ARG68 4.7 21.3 1.0
CG2 A:THR51 4.7 15.9 1.0
CB A:SER60 4.7 16.9 1.0
N A:THR69 4.8 19.7 1.0
CB A:ASP66 4.9 15.7 1.0
CA A:THR69 4.9 21.7 1.0
CG2 A:THR69 4.9 20.7 1.0

Cadmium binding site 6 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 6 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd206

b:70.2
occ:1.00
OG A:SER91 2.8 17.8 1.0
O A:TYR53 2.9 17.1 1.0
N A:LEU56 3.0 17.7 1.0
N A:ILE55 3.4 15.8 1.0
C A:GLY54 3.5 12.9 1.0
CB A:SER91 3.5 18.4 1.0
CA A:GLY54 3.5 15.8 1.0
O A:HOH4027 3.6 33.6 1.0
N A:GLN57 3.6 16.8 1.0
CA A:LEU56 3.7 17.8 1.0
CD1 A:ILE58 3.8 22.5 1.0
CB A:LEU56 3.8 20.1 1.0
CG1 A:ILE58 3.8 18.8 1.0
C A:LEU56 3.8 19.1 1.0
C A:TYR53 3.8 18.3 1.0
CG1 A:ILE55 3.9 21.4 1.0
C A:ILE55 4.0 16.1 1.0
O A:LEU83 4.0 23.3 1.0
O A:GLY54 4.1 15.5 1.0
N A:ILE58 4.1 15.3 1.0
CA A:ILE55 4.2 17.6 1.0
N A:GLY54 4.2 15.8 1.0
CB A:ILE58 4.3 18.2 1.0
CB A:LEU83 4.3 22.2 1.0
CD2 A:LEU83 4.3 21.9 1.0
CA A:SER91 4.4 17.3 1.0
O A:LEU56 4.6 18.0 1.0
CA A:GLN57 4.7 15.0 1.0
CB A:ILE55 4.7 23.6 1.0
CG A:LEU83 4.8 25.2 1.0
CD1 A:ILE55 4.8 45.9 1.0
CG A:LEU56 4.8 18.9 1.0
CA A:ILE58 4.9 16.4 1.0
C A:GLN57 4.9 16.2 1.0
CD1 A:LEU83 5.0 22.9 1.0
C A:LEU83 5.0 22.1 1.0
CA A:LEU83 5.0 17.6 1.0

Cadmium binding site 7 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 7 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd207

b:66.1
occ:1.00
ND2 A:ASN65 3.0 22.3 1.0
CA A:GLY67 3.5 21.4 1.0
N A:GLY67 4.0 18.8 1.0
CG A:ASN65 4.1 19.8 1.0
O A:HOH4110 4.1 40.5 1.0
OD1 A:ASN65 4.3 22.6 1.0
C A:ASP66 4.6 16.1 1.0
C A:GLY67 4.8 22.4 1.0
O A:ASP66 4.9 18.6 1.0

Cadmium binding site 8 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 8 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd208

b:61.5
occ:1.00
N A:LYS1 2.7 20.1 1.0
OD1 A:ASN39 2.8 16.6 1.0
NE2 A:GLN41 3.1 17.4 1.0
CA A:LYS1 3.4 18.1 1.0
C A:LYS1 3.5 21.0 1.0
CG A:ASN39 3.7 18.8 1.0
CG A:GLN41 3.7 14.1 1.0
CD A:GLN41 3.9 16.2 1.0
O A:LYS1 3.9 19.6 1.0
CG2 A:VAL2 3.9 21.4 1.0
N A:VAL2 4.0 22.9 1.0
ND2 A:ASN39 4.0 20.6 1.0
CB A:GLN41 4.1 16.0 1.0
N A:GLN41 4.5 16.1 1.0
OG1 A:THR40 4.7 19.4 1.0
O A:HOH4100 4.8 28.8 1.0
CA A:VAL2 4.8 19.9 1.0
N A:THR40 4.8 15.7 1.0
CB A:LYS1 4.9 22.1 1.0
CB A:ASN39 4.9 16.8 1.0
CB A:VAL2 5.0 19.7 1.0
CA A:GLN41 5.0 14.1 1.0

Cadmium binding site 9 out of 9 in 4lyc

Go back to Cadmium Binding Sites List in 4lyc
Cadmium binding site 9 out of 9 in the Cd Ions Within A Lysoyzme Single Crystal


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Cd Ions Within A Lysoyzme Single Crystal within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd209

b:73.0
occ:1.00
O A:HOH4056 2.7 25.4 1.0
OG1 A:THR118 2.7 17.9 1.0
O A:HOH4085 2.8 23.1 1.0
NE1 A:TRP123 2.9 19.7 1.0
CB A:THR118 3.6 20.2 1.0
CD1 A:TRP123 3.7 22.1 1.0
O A:HOH4109 3.8 30.1 1.0
SG A:CYS30 3.8 16.7 1.0
O A:ASP119 4.0 24.5 1.0
CE2 A:TRP123 4.0 18.9 1.0
C A:ASP119 4.2 22.1 1.0
CA A:VAL120 4.3 18.1 1.0
CG1 A:VAL120 4.3 20.1 1.0
CG2 A:THR118 4.4 18.7 1.0
O A:ARG114 4.4 19.4 1.0
N A:VAL120 4.4 19.5 1.0
N A:ASP119 4.5 19.9 1.0
O A:HOH4103 4.5 27.5 1.0
CZ2 A:TRP123 4.5 18.8 1.0
O A:HOH4009 4.6 22.9 1.0
C A:THR118 4.7 18.4 1.0
CB A:CYS30 4.8 13.7 1.0
CA A:THR118 4.8 19.6 1.0
CA A:CYS115 4.8 18.2 1.0
CB A:VAL120 4.9 20.1 1.0
O A:CYS115 4.9 17.7 1.0
CG A:TRP123 5.0 20.0 1.0
CA A:ASP119 5.0 23.9 1.0

Reference:

H.Wei, S.House, J.Wu, J.Zhang, Z.Wang, Y.He, Y.-G.Gao, H.Robinson, W.Li, J.-M.Zuo, I.M.Robertson, Y.Lu. Enhanced and Tunable Fluorescent Quantum Dots Within A Single Crystal of Protein To Be Published.
Page generated: Thu Jul 10 13:46:54 2025

Last articles

Cl in 2GM1
Cl in 2GLP
Cl in 2GLM
Cl in 2GLL
Cl in 2GJT
Cl in 2GJV
Cl in 2GHW
Cl in 2GKR
Cl in 2GJ4
Cl in 2GIV
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy