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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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