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Cadmium in PDB 6rei: Crystal Structure of PIZZA6-S with CD2+

Protein crystallography data

The structure of Crystal Structure of PIZZA6-S with CD2+, PDB code: 6rei was solved by H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.73 / 1.50
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.018, 72.018, 167.855, 90.00, 90.00, 90.00
R / Rfree (%) 15.1 / 17.8

Other elements in 6rei:

The structure of Crystal Structure of PIZZA6-S with CD2+ also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of PIZZA6-S with CD2+ (pdb code 6rei). 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 PIZZA6-S with CD2+, PDB code: 6rei:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6;

Cadmium binding site 1 out of 6 in 6rei

Go back to Cadmium Binding Sites List in 6rei
Cadmium binding site 1 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd301

b:9.8
occ:1.00
 NE2 B:HIS241 2.3 10.2 1.0
NE2 A:HIS157 2.4 10.1 1.0
O B:HOH608 2.5 18.3 1.0
O A:HOH616 2.5 21.7 1.0
CL B:CL301 2.6 9.9 1.0
CL A:CL309 2.6 10.3 1.0
CD2 B:HIS241 3.2 10.3 1.0
CE1 B:HIS241 3.3 10.8 1.0
CE1 A:HIS157 3.3 10.0 1.0
CD2 A:HIS157 3.3 7.7 1.0
O A:HOH614 4.2 23.0 1.0
O B:HOH613 4.2 21.5 1.0
O B:HOH617 4.2 20.0 1.0
O A:HOH619 4.2 19.3 1.0
ND1 B:HIS241 4.4 11.2 1.0
CG B:HIS241 4.4 9.2 1.0
O A:HOH568 4.4 29.0 1.0
ND1 A:HIS157 4.4 10.3 1.0
CG A:HIS157 4.5 9.4 1.0
CG2 B:THR14 4.5 21.6 1.0
CD A:CD306 4.5 9.7 1.0
CD A:CD302 4.6 9.8 1.0
O A:HOH593 5.0 32.6 1.0

Cadmium binding site 2 out of 6 in 6rei

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Cadmium binding site 2 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd302

b:9.8
occ:1.00
 NE2 A:HIS115 2.3 9.8 1.0
NE2 B:HIS31 2.3 9.3 1.0
O A:HOH614 2.6 23.0 1.0
O B:HOH613 2.6 21.5 1.0
CL B:CL302 2.6 9.6 1.0
CL A:CL309 2.6 10.3 1.0
CE1 B:HIS31 3.3 12.8 1.0
CE1 A:HIS115 3.3 10.3 1.0
CD2 A:HIS115 3.3 9.7 1.0
CD2 B:HIS31 3.3 8.5 1.0
O A:HOH616 4.1 21.7 1.0
O B:HOH619 4.1 19.8 1.0
O A:HOH624 4.1 26.1 1.0
O B:HOH608 4.2 18.3 1.0
ND1 B:HIS31 4.4 10.8 1.0
ND1 A:HIS115 4.4 11.7 1.0
CG A:HIS115 4.4 10.4 1.0
CG B:HIS31 4.4 10.1 1.0
CD A:CD303 4.5 9.9 1.0
CD A:CD301 4.6 9.8 1.0
O A:HOH402 4.6 32.9 1.0
O A:HOH568 4.9 29.0 1.0

Cadmium binding site 3 out of 6 in 6rei

Go back to Cadmium Binding Sites List in 6rei
Cadmium binding site 3 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd303

b:9.9
occ:1.00
 NE2 B:HIS73 2.3 9.8 1.0
NE2 A:HIS73 2.3 9.8 1.0
O B:HOH619 2.5 19.8 1.0
O A:HOH624 2.6 26.1 1.0
CL A:CL310 2.6 10.3 1.0
CL B:CL302 2.6 9.6 1.0
CD2 A:HIS73 3.3 9.7 1.0
CE1 B:HIS73 3.3 12.2 1.0
CD2 B:HIS73 3.3 10.4 1.0
CE1 A:HIS73 3.3 12.9 1.0
O A:HOH613 4.1 18.6 1.0
O A:HOH614 4.2 23.0 1.0
O B:HOH615 4.2 19.8 1.0
O B:HOH613 4.4 21.5 1.0
ND1 B:HIS73 4.4 11.3 1.0
CG B:HIS73 4.4 11.8 1.0
ND1 A:HIS73 4.4 11.4 1.0
CG A:HIS73 4.4 9.0 1.0
CD A:CD302 4.5 9.8 1.0
CD A:CD304 4.5 9.6 1.0
O B:HOH407 4.9 34.4 1.0
O A:HOH602 5.0 34.0 1.0

Cadmium binding site 4 out of 6 in 6rei

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Cadmium binding site 4 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd304

b:9.6
occ:1.00
 NE2 A:HIS31 2.3 9.9 1.0
NE2 B:HIS115 2.3 10.7 1.0
O B:HOH615 2.5 19.8 1.0
O A:HOH613 2.5 18.6 1.0
CL A:CL307 2.6 10.2 1.0
CL A:CL310 2.7 10.3 1.0
CE1 A:HIS31 3.3 10.1 1.0
CE1 B:HIS115 3.3 11.0 1.0
CD2 B:HIS115 3.3 9.8 1.0
CD2 A:HIS31 3.3 9.1 1.0
O B:HOH609 4.2 20.3 1.0
O A:HOH624 4.2 26.1 1.0
O A:HOH617 4.2 19.0 1.0
O B:HOH619 4.3 19.8 1.0
ND1 A:HIS31 4.4 11.2 1.0
ND1 B:HIS115 4.4 11.2 1.0
CG A:HIS31 4.4 9.7 1.0
CG B:HIS115 4.5 10.4 1.0
CD A:CD303 4.5 9.9 1.0
CD A:CD305 4.5 9.9 1.0
O B:HOH438 4.9 27.2 1.0

Cadmium binding site 5 out of 6 in 6rei

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Cadmium binding site 5 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd305

b:9.9
occ:1.00
 NE2 A:HIS241 2.3 10.2 1.0
NE2 B:HIS157 2.3 10.0 1.0
O B:HOH609 2.5 20.3 1.0
O A:HOH617 2.5 19.0 1.0
CL A:CL307 2.6 10.2 1.0
CL A:CL308 2.6 9.3 1.0
CD2 A:HIS241 3.3 10.6 1.0
CE1 A:HIS241 3.3 9.1 1.0
CD2 B:HIS157 3.3 9.8 1.0
CE1 B:HIS157 3.3 10.8 1.0
O A:HOH619 4.1 19.3 1.0
O B:HOH615 4.2 19.8 1.0
O A:HOH613 4.3 18.6 1.0
O B:HOH617 4.3 20.0 1.0
ND1 A:HIS241 4.4 10.9 1.0
CG A:HIS241 4.4 11.0 1.0
ND1 B:HIS157 4.4 9.2 1.0
CG B:HIS157 4.5 10.7 1.0
CG2 A:THR14 4.5 19.6 1.0
CD A:CD304 4.5 9.6 1.0
CD A:CD306 4.6 9.7 1.0
O B:HOH438 4.9 27.2 1.0
O A:HOH612 4.9 36.5 1.0

Cadmium binding site 6 out of 6 in 6rei

Go back to Cadmium Binding Sites List in 6rei
Cadmium binding site 6 out of 6 in the Crystal Structure of PIZZA6-S with CD2+


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 PIZZA6-S with CD2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd306

b:9.7
occ:1.00
 NE2 A:HIS199 2.3 8.1 1.0
NE2 B:HIS199 2.3 10.3 1.0
O A:HOH619 2.5 19.3 1.0
CL A:CL308 2.6 9.3 1.0
CL B:CL301 2.6 9.9 1.0
O B:HOH617 2.7 20.0 1.0
CD2 B:HIS199 3.3 9.8 1.0
CE1 A:HIS199 3.3 9.5 1.0
CD2 A:HIS199 3.3 9.7 1.0
CE1 B:HIS199 3.3 9.9 1.0
O A:HOH617 4.2 19.0 1.0
O B:HOH608 4.3 18.3 1.0
O A:HOH616 4.3 21.7 1.0
O B:HOH609 4.3 20.3 1.0
ND1 A:HIS199 4.4 10.4 1.0
ND1 B:HIS199 4.4 11.6 1.0
CG B:HIS199 4.4 7.9 1.0
CG A:HIS199 4.4 9.5 1.0
CD A:CD301 4.5 9.8 1.0
CD A:CD305 4.6 9.9 1.0
O A:HOH593 4.7 32.6 1.0
O A:HOH530 4.9 34.4 1.0

Reference:

H.Noguchi, D.E.Clarke, J.L.Gryspeerdt, S.D.Feyter, A.R.D.Voet. Artificial Beta-Propeller Protein-Based Hydrolases To Be Published.
Page generated: Fri Jul 19 19:36:10 2024

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