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Cadmium in PDB 3qpx: Crystal Structure of Fab C2507

Protein crystallography data

The structure of Crystal Structure of Fab C2507, PDB code: 3qpx was solved by J.Luo, A.Teplyakov, O.Obmolova, T.Malia, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.150, 87.050, 100.310, 90.00, 90.00, 90.00
R / Rfree (%) 22.5 / 26.4

Other elements in 3qpx:

The structure of Crystal Structure of Fab C2507 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Fab C2507 (pdb code 3qpx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 6 binding sites of Cadmium where determined in the Crystal Structure of Fab C2507, PDB code: 3qpx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 1 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd226

b:45.5
occ:0.62
ND1 L:HIS188 2.4 47.4 1.0
OD2 L:ASP150 2.5 41.1 1.0
CE1 L:HIS188 3.3 53.4 1.0
CG L:ASP150 3.4 41.8 1.0
CG L:HIS188 3.4 49.1 1.0
CB L:ASP150 3.6 45.1 1.0
CB L:HIS188 3.7 45.0 1.0
CA L:HIS188 4.2 42.6 1.0
O L:VAL149 4.3 37.4 1.0
O L:LYS187 4.4 40.8 1.0
NE2 L:HIS188 4.4 54.3 1.0
CD2 L:HIS188 4.5 52.9 1.0
OD1 L:ASP150 4.6 39.5 1.0
CG1 L:VAL149 4.6 37.9 1.0
O L:HOH272 4.6 47.2 1.0
C L:VAL149 4.8 40.2 1.0
CA L:ASP150 4.9 42.1 1.0
N L:ASP150 5.0 39.8 1.0

Cadmium binding site 2 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 2 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd227

b:62.2
occ:0.54
O H:HOH410 2.4 40.3 1.0
O L:HOH264 2.4 45.1 1.0
NE2 H:HIS170 2.5 45.5 1.0
ND2 L:ASN137 2.5 55.7 1.0
OD1 L:ASN136 2.8 47.6 1.0
ND2 L:ASN136 3.0 53.6 1.0
CG L:ASN137 3.0 52.8 1.0
OD1 L:ASN137 3.0 58.7 1.0
CD2 H:HIS170 3.1 42.4 1.0
CG L:ASN136 3.3 50.0 1.0
CE1 H:HIS170 3.6 41.7 1.0
OG1 H:THR189 4.1 36.3 1.0
O H:GLY168 4.2 34.1 1.0
CB L:ASN137 4.3 45.0 1.0
CG H:HIS170 4.4 38.6 1.0
CA H:GLY168 4.5 33.8 1.0
OG L:SER173 4.5 33.7 1.0
ND1 H:HIS170 4.6 41.2 1.0
C H:GLY168 4.6 36.3 1.0
CB L:ASN136 4.7 40.1 1.0
CG2 H:THR189 4.8 28.3 1.0
O L:HOH282 4.8 28.4 1.0
N L:ASN137 4.8 30.9 1.0
O H:HOH400 5.0 51.0 1.0

Cadmium binding site 3 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 3 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cd228

b:40.9
occ:1.00
O L:ASP1 2.4 29.4 1.0
N L:ASP1 2.4 41.2 1.0
OD1 L:ASP1 2.5 42.7 1.0
O L:HOH326 2.5 40.4 1.0
C L:ASP1 3.1 32.3 1.0
CA L:ASP1 3.2 39.5 1.0
CG L:ASP1 3.5 41.4 1.0
CB L:ASP1 3.9 40.8 1.0
OE1 L:GLN3 4.2 40.0 1.0
N L:ILE2 4.4 31.1 1.0
O L:HOH331 4.5 55.8 1.0
O L:HOH274 4.6 33.4 1.0
OD2 L:ASP1 4.6 40.2 1.0
CD L:GLN3 4.9 37.1 1.0
CG L:GLN3 5.0 33.2 1.0
O4 L:SO4217 5.0 0.0 1.0

Cadmium binding site 4 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 4 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd238

b:43.3
occ:0.51
NE2 H:HIS224 2.5 45.1 1.0
CD2 H:HIS224 3.2 47.0 1.0
CE1 H:HIS224 3.7 48.3 1.0
O L:GLU212 4.4 38.0 1.0
CG H:HIS224 4.5 47.9 1.0
O H:SER221 4.6 37.2 1.0
ND1 H:HIS224 4.7 46.2 1.0

Cadmium binding site 5 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 5 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd239

b:40.1
occ:1.00
NE2 H:HIS227 2.4 39.4 1.0
OE1 L:GLU212 2.5 34.1 1.0
O H:HOH267 2.6 29.4 1.0
O H:HOH305 2.6 38.9 1.0
OE2 L:GLU212 2.6 34.4 1.0
O L:HOH371 2.7 38.2 1.0
NZ H:LYS135 2.7 41.8 1.0
CD L:GLU212 2.9 40.7 1.0
CE H:LYS135 3.3 41.0 1.0
CD2 H:HIS227 3.3 46.3 1.0
CE1 H:HIS227 3.5 39.9 1.0
O H:CYS222 4.1 40.2 1.0
O1 H:SO4232 4.1 55.6 1.0
CA L:PHE208 4.3 40.2 1.0
N L:ASN209 4.4 36.5 1.0
CG L:GLU212 4.4 42.9 1.0
OD1 L:ASN209 4.5 35.9 1.0
CG H:HIS227 4.5 46.5 1.0
ND1 H:HIS227 4.5 43.8 1.0
O L:SER207 4.6 35.8 1.0
ND1 H:HIS224 4.6 46.2 1.0
O H:HOH359 4.7 67.9 1.0
O H:HIS224 4.7 46.2 1.0
CD H:LYS135 4.7 37.0 1.0
CB L:PHE208 4.8 40.7 1.0
C L:PHE208 4.9 36.6 1.0
CB H:HIS224 4.9 43.6 1.0

Cadmium binding site 6 out of 6 in 3qpx

Go back to Cadmium Binding Sites List in 3qpx
Cadmium binding site 6 out of 6 in the Crystal Structure of Fab C2507


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 Fab C2507 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cd240

b:36.7
occ:1.00
O H:HOH268 2.4 36.7 1.0
NE2 H:HIS225 2.4 43.9 1.0
NE2 H:HIS223 2.4 37.3 1.0
O H:HOH274 2.7 30.0 1.0
CD2 H:HIS225 3.3 43.6 1.0
CD2 H:HIS223 3.3 31.7 1.0
CE1 H:HIS225 3.4 47.2 1.0
CE1 H:HIS223 3.4 36.2 1.0
ND1 H:HIS225 4.5 50.0 1.0
CG H:HIS225 4.5 47.9 1.0
CG H:HIS223 4.5 36.5 1.0
ND1 H:HIS223 4.5 39.2 1.0

Reference:

J.Luo, A.Teplyakov, O.Obmolova, T.Malia, G.L.Gilliland. Crystal Structure of Fab C2507 To Be Published.
Page generated: Sat Dec 12 08:22:59 2020

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