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Cadmium in PDB 5gsc: Crystal Structure of A Class C Beta Lactamase of Apo Form

Enzymatic activity of Crystal Structure of A Class C Beta Lactamase of Apo Form

All present enzymatic activity of Crystal Structure of A Class C Beta Lactamase of Apo Form:
3.5.2.6;

Protein crystallography data

The structure of Crystal Structure of A Class C Beta Lactamase of Apo Form, PDB code: 5gsc was solved by Y.J.An, S.S.Cha, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.16 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.511, 90.200, 113.920, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 22.3

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of A Class C Beta Lactamase of Apo Form (pdb code 5gsc). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 24 binding sites of Cadmium where determined in the Crystal Structure of A Class C Beta Lactamase of Apo Form, PDB code: 5gsc:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 24 in 5gsc

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Cadmium binding site 1 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd401

b:27.5
occ:1.00
NE2 A:HIS40 2.6 15.0 1.0
CD2 A:HIS40 3.2 17.5 1.0
CE1 A:HIS40 3.8 20.8 1.0
NZ A:LYS38 4.0 29.7 1.0
CD A:LYS38 4.1 22.8 1.0
CG A:HIS40 4.5 16.8 1.0
CD2 A:LEU9 4.6 33.5 1.0
CE A:LYS38 4.7 28.8 1.0
ND1 A:HIS40 4.7 10.9 1.0
CB A:LEU9 4.8 24.2 1.0
CG A:LEU9 4.8 33.3 1.0
CG A:PRO8 4.9 30.0 1.0

Cadmium binding site 2 out of 24 in 5gsc

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Cadmium binding site 2 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd402

b:82.9
occ:1.00
OD2 A:ASP87 2.9 41.8 1.0
OD1 A:ASP87 3.2 29.6 1.0
OE1 A:GLN85 3.3 21.7 1.0
CG A:ASP87 3.4 26.1 1.0
CD A:GLN85 4.4 23.0 1.0
OD1 A:ASP88 4.7 16.7 1.0
CB A:ASP87 4.7 18.2 1.0

Cadmium binding site 3 out of 24 in 5gsc

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Cadmium binding site 3 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd403

b:17.5
occ:1.00
NE2 B:HIS148 2.4 13.5 1.0
OE1 A:GLU124 2.5 13.4 1.0
OE2 A:GLU124 2.5 16.3 1.0
O A:HOH615 2.6 14.1 1.0
O B:HOH625 2.6 20.1 1.0
O B:HOH627 2.7 24.0 1.0
CD A:GLU124 2.8 17.2 1.0
CD2 B:HIS148 3.3 10.4 1.0
CE1 B:HIS148 3.5 12.0 1.0
CE1 B:TYR143 4.3 12.2 1.0
CG A:GLU124 4.4 14.3 1.0
CG B:HIS148 4.5 8.4 1.0
ND1 B:HIS148 4.6 11.7 1.0
CD1 B:TYR143 4.9 10.7 1.0
CD B:PRO297 5.0 14.3 1.0

Cadmium binding site 4 out of 24 in 5gsc

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Cadmium binding site 4 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd404

b:31.5
occ:1.00
OD1 A:ASP127 2.6 11.2 1.0
OD2 A:ASP127 2.8 23.7 1.0
CG A:ASP127 3.0 20.0 1.0
CE A:LYS131 4.3 26.9 1.0
O A:GLU125 4.3 10.4 1.0
OE2 A:GLU125 4.3 45.0 1.0
CB A:ASP127 4.5 11.2 1.0
NZ A:LYS131 4.5 33.6 1.0
O A:HOH546 4.7 15.5 1.0
CD A:LYS131 4.8 21.8 1.0

Cadmium binding site 5 out of 24 in 5gsc

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Cadmium binding site 5 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd405

b:25.5
occ:1.00
NE2 A:HIS161 2.6 9.9 1.0
O A:HOH596 2.6 8.3 1.0
O A:HOH602 2.6 9.9 1.0
CD2 A:HIS161 3.2 16.0 1.0
CE1 A:HIS161 3.7 17.3 1.0
NH2 A:ARG133 4.1 16.7 1.0
O A:HOH551 4.3 11.2 1.0
CG A:HIS161 4.4 10.6 1.0
O A:HOH620 4.7 21.7 1.0
ND1 A:HIS161 4.7 13.2 1.0
NE A:ARG133 4.9 14.7 1.0

Cadmium binding site 6 out of 24 in 5gsc

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Cadmium binding site 6 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd406

b:30.3
occ:1.00
NE2 A:HIS186 2.5 20.3 1.0
CD2 A:HIS186 3.3 26.5 1.0
CE1 A:HIS186 3.5 25.4 1.0
CG A:HIS186 4.5 20.6 1.0
CA A:GLY184 4.5 17.3 1.0
ND1 A:HIS186 4.6 27.3 1.0
O A:PRO181 5.0 19.6 1.0

Cadmium binding site 7 out of 24 in 5gsc

Go back to Cadmium Binding Sites List in 5gsc
Cadmium binding site 7 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd407

b:34.2
occ:1.00
ND1 A:HIS256 2.5 14.3 1.0
O A:HOH609 2.6 17.3 1.0
O A:HOH595 2.7 24.7 1.0
CE1 A:HIS256 3.4 15.7 1.0
CG A:HIS256 3.5 21.6 1.0
CB A:HIS256 3.8 16.4 1.0
NE2 A:HIS256 4.6 13.0 1.0
CD2 A:HIS256 4.7 13.3 1.0
O A:ASN239 4.7 19.2 1.0
CA A:SER253 4.9 15.7 1.0
OG A:SER253 4.9 28.5 1.0

Cadmium binding site 8 out of 24 in 5gsc

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Cadmium binding site 8 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd408

b:30.8
occ:1.00
ND1 A:HIS259 2.5 14.2 1.0
O A:HOH607 2.7 6.4 1.0
CG A:HIS259 3.5 16.2 1.0
CE1 A:HIS259 3.5 20.6 1.0
CB A:HIS259 3.7 13.1 1.0
O A:HOH512 4.4 14.7 1.0
CA A:HIS259 4.6 11.6 1.0
NE2 A:HIS259 4.6 18.6 1.0
CD2 A:HIS259 4.6 15.8 1.0
O A:HIS259 5.0 13.5 1.0

Cadmium binding site 9 out of 24 in 5gsc

Go back to Cadmium Binding Sites List in 5gsc
Cadmium binding site 9 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd409

b:28.0
occ:1.00
O A:VAL278 2.5 15.0 1.0
NE2 A:HIS351 2.5 17.8 1.0
O A:HOH603 2.5 9.9 1.0
O A:HOH614 2.7 25.9 1.0
O A:HOH611 2.7 20.2 1.0
CD2 A:HIS351 3.4 17.9 1.0
C A:VAL278 3.5 14.0 1.0
CE1 A:HIS351 3.5 20.1 1.0
O A:HOH592 3.9 24.2 1.0
N A:VAL278 4.0 16.6 1.0
CA A:THR279 4.1 19.3 1.0
N A:THR279 4.2 15.3 1.0
CA A:VAL278 4.4 18.3 1.0
CG A:HIS351 4.6 20.0 1.0
ND1 A:HIS351 4.6 18.0 1.0
C A:THR279 4.6 18.3 1.0
O A:HOH553 4.7 12.6 1.0
CB A:PRO277 4.7 19.4 1.0
N A:GLU280 4.7 16.0 1.0
C A:PRO277 4.9 18.9 1.0

Cadmium binding site 10 out of 24 in 5gsc

Go back to Cadmium Binding Sites List in 5gsc
Cadmium binding site 10 out of 24 in the Crystal Structure of A Class C Beta Lactamase of Apo Form


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of A Class C Beta Lactamase of Apo Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd410

b:28.8
occ:1.00
OE2 B:GLU23 2.5 19.1 1.0
OE2 A:GLU23 2.6 18.1 1.0
O B:HOH551 2.6 21.4 1.0
O A:HOH560 2.7 22.2 1.0
O A:HOH605 2.8 19.6 1.0
OE1 A:GLU23 2.9 30.1 1.0
OE1 B:GLU23 2.9 26.9 1.0
CD A:GLU23 3.1 22.0 1.0
CD B:GLU23 3.1 30.1 1.0
NE2 B:HIS24 3.9 12.6 1.0
CE1 B:HIS24 3.9 13.0 1.0
CE1 A:HIS24 4.0 12.4 1.0
O A:HOH502 4.1 25.3 1.0
NE2 A:HIS24 4.1 21.9 1.0
O A:HOH606 4.5 21.6 1.0
CG B:GLU23 4.5 23.3 1.0
CG A:GLU23 4.5 20.7 1.0

Reference:

M.K.Kim, Y.J.An, J.H.Na, S.S.Cha. Crystal Structure of A Class C Beta Lactamase of Apo Form To Be Published.
Page generated: Sat Dec 12 08:26:41 2020

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