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Cadmium in PDB 4dzi: Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10

Protein crystallography data

The structure of Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi was solved by Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo, Enzyme Function Initiative (Efi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.106, 136.131, 93.229, 90.00, 113.09, 90.00
R / Rfree (%) 16.6 / 20.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 (pdb code 4dzi). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10, PDB code: 4dzi:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cadmium binding site 1 out of 8 in 4dzi

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Cadmium binding site 1 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:16.0
occ:1.00
OE2 A:GLU360 2.3 21.8 1.0
ND1 A:HIS358 2.3 13.8 1.0
OD2 A:ASP355 2.3 15.4 1.0
OE1 A:GLU292 2.3 13.5 1.0
O A:HOH659 2.4 13.8 1.0
OE2 A:GLU292 2.5 15.1 1.0
CD A:GLU292 2.7 15.6 1.0
OD1 A:ASP355 2.8 16.6 1.0
CG A:ASP355 2.9 13.5 1.0
CD A:GLU360 3.2 16.6 1.0
CE1 A:HIS358 3.2 16.8 1.0
CG A:HIS358 3.3 15.7 1.0
CG A:GLU360 3.6 20.1 1.0
CB A:HIS358 3.6 16.0 1.0
CD A:CD502 3.8 14.0 1.0
NE2 A:HIS14 4.0 10.3 1.0
O A:HOH1027 4.2 39.7 1.0
O A:HOH756 4.2 35.2 1.0
CG A:GLU292 4.2 13.1 1.0
OE1 A:GLU360 4.3 19.6 1.0
CD2 A:HIS14 4.3 19.4 1.0
CB A:ASP355 4.4 14.3 1.0
NE2 A:HIS358 4.4 14.7 1.0
CD2 A:HIS358 4.4 17.1 1.0
O A:HOH675 4.6 24.6 1.0
O A:ASP355 4.9 16.4 1.0
O A:HOH920 4.9 29.1 1.0
CE1 A:HIS14 4.9 11.7 1.0
CE1 A:HIS229 5.0 14.9 1.0

Cadmium binding site 2 out of 8 in 4dzi

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Cadmium binding site 2 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:14.0
occ:1.00
OE2 A:GLU292 2.2 15.1 1.0
NE2 A:HIS14 2.2 10.3 1.0
OD1 A:ASP12 2.3 15.8 1.0
OD1 A:ASP355 2.3 16.6 1.0
NE2 A:HIS229 2.4 11.6 1.0
OD2 A:ASP12 2.5 12.7 1.0
CG A:ASP12 2.7 15.1 1.0
CE1 A:HIS14 3.2 11.7 1.0
CD2 A:HIS14 3.2 19.4 1.0
CE1 A:HIS229 3.2 14.9 1.0
CD A:GLU292 3.3 15.6 1.0
CG A:ASP355 3.3 13.5 1.0
CD2 A:HIS229 3.5 10.6 1.0
CB A:GLU292 3.7 10.6 1.0
CD A:CD501 3.8 16.0 1.0
CG A:GLU292 3.9 13.1 1.0
OD2 A:ASP355 4.1 15.4 1.0
CB A:ASP355 4.1 14.3 1.0
CB A:ASP12 4.2 13.1 1.0
OE1 A:GLU292 4.3 13.5 1.0
ND1 A:HIS14 4.3 14.5 1.0
CA A:ASP355 4.3 15.1 1.0
CG A:HIS14 4.3 16.0 1.0
ND1 A:HIS229 4.4 13.9 1.0
CG A:HIS229 4.6 11.5 1.0
O A:HOH659 4.6 13.8 1.0
ND1 A:HIS358 4.7 13.8 1.0
CG2 A:ILE291 4.7 11.8 1.0
CD1 A:LEU120 4.8 12.4 1.0
CE1 A:HIS358 4.8 16.8 1.0
CA A:ASP12 4.9 14.3 1.0

Cadmium binding site 3 out of 8 in 4dzi

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Cadmium binding site 3 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:14.5
occ:1.00
OE2 B:GLU360 2.3 17.7 1.0
OD2 B:ASP355 2.3 16.4 1.0
ND1 B:HIS358 2.3 16.4 1.0
OE2 B:GLU292 2.4 12.9 1.0
O B:HOH659 2.4 14.8 1.0
OE1 B:GLU292 2.5 15.4 1.0
CD B:GLU292 2.7 14.5 1.0
OD1 B:ASP355 2.7 13.9 1.0
CG B:ASP355 2.9 19.0 1.0
CE1 B:HIS358 3.2 10.7 1.0
CD B:GLU360 3.3 19.2 1.0
CG B:HIS358 3.4 14.6 1.0
CB B:HIS358 3.7 12.8 1.0
CG B:GLU360 3.8 20.2 1.0
CD B:CD502 3.8 12.5 1.0
NE2 B:HIS14 4.0 12.1 1.0
O B:HOH886 4.1 34.4 1.0
CG B:GLU292 4.2 16.8 1.0
CD2 B:HIS14 4.3 11.2 1.0
OE1 B:GLU360 4.4 21.7 1.0
NE2 B:HIS358 4.4 15.9 1.0
CB B:ASP355 4.4 10.8 1.0
CD2 B:HIS358 4.5 13.4 1.0
O B:HOH738 4.6 21.5 1.0
O B:HOH805 4.7 24.7 1.0
O B:HOH705 4.8 22.1 1.0
O B:ASP355 4.8 14.3 1.0
CE1 B:HIS229 4.9 13.6 1.0
CE1 B:HIS14 4.9 11.8 1.0

Cadmium binding site 4 out of 8 in 4dzi

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Cadmium binding site 4 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:12.5
occ:1.00
NE2 B:HIS14 2.2 12.1 1.0
OD1 B:ASP12 2.3 11.5 1.0
NE2 B:HIS229 2.3 10.9 1.0
OE2 B:GLU292 2.3 12.9 1.0
OD1 B:ASP355 2.4 13.9 1.0
OD2 B:ASP12 2.6 12.1 1.0
CG B:ASP12 2.8 10.1 1.0
CE1 B:HIS229 3.1 13.6 1.0
CE1 B:HIS14 3.2 11.8 1.0
CD2 B:HIS14 3.2 11.2 1.0
CD B:GLU292 3.3 14.5 1.0
CG B:ASP355 3.3 19.0 1.0
CD2 B:HIS229 3.4 13.2 1.0
CB B:GLU292 3.7 14.5 1.0
CD B:CD501 3.8 14.5 1.0
CG B:GLU292 3.9 16.8 1.0
OD2 B:ASP355 4.1 16.4 1.0
CB B:ASP355 4.1 10.8 1.0
CB B:ASP12 4.3 10.5 1.0
ND1 B:HIS14 4.3 13.2 1.0
ND1 B:HIS229 4.3 14.2 1.0
CG B:HIS14 4.3 12.5 1.0
CA B:ASP355 4.4 11.3 1.0
OE1 B:GLU292 4.4 15.4 1.0
CG B:HIS229 4.5 12.6 1.0
O B:HOH659 4.6 14.8 1.0
ND1 B:HIS358 4.8 16.4 1.0
CG2 B:ILE291 4.8 12.9 1.0
CD1 B:LEU120 4.8 17.1 1.0
O B:HOH738 4.9 21.5 1.0
CE1 B:HIS358 5.0 10.7 1.0
CA B:ASP12 5.0 8.2 1.0

Cadmium binding site 5 out of 8 in 4dzi

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Cadmium binding site 5 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:14.2
occ:1.00
OE2 C:GLU360 2.3 15.6 1.0
ND1 C:HIS358 2.3 11.5 1.0
OD2 C:ASP355 2.3 16.4 1.0
OE1 C:GLU292 2.4 14.5 1.0
O C:HOH615 2.5 15.8 1.0
OE2 C:GLU292 2.5 12.2 1.0
OD1 C:ASP355 2.7 14.7 1.0
CD C:GLU292 2.7 19.0 1.0
CG C:ASP355 2.9 11.9 1.0
CD C:GLU360 3.2 16.5 1.0
CE1 C:HIS358 3.3 11.4 1.0
CG C:HIS358 3.3 11.6 1.0
CB C:HIS358 3.6 12.2 1.0
CG C:GLU360 3.7 15.3 1.0
CD C:CD502 3.8 12.1 1.0
NE2 C:HIS14 4.1 11.3 1.0
CG C:GLU292 4.2 12.1 1.0
O C:HOH849 4.3 31.7 1.0
OE1 C:GLU360 4.3 18.9 1.0
O C:HOH879 4.3 38.4 1.0
CB C:ASP355 4.4 15.0 1.0
CD2 C:HIS14 4.4 13.7 1.0
NE2 C:HIS358 4.4 14.5 1.0
CD2 C:HIS358 4.5 11.9 1.0
O C:HOH816 4.6 22.4 1.0
O C:HOH812 4.7 23.6 1.0
O C:HOH707 4.8 28.8 1.0
O C:ASP355 4.9 14.9 1.0
CE1 C:HIS14 5.0 8.3 1.0
CE1 C:HIS229 5.0 11.7 1.0

Cadmium binding site 6 out of 8 in 4dzi

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Cadmium binding site 6 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd502

b:12.1
occ:1.00
NE2 C:HIS14 2.2 11.3 1.0
OE2 C:GLU292 2.2 12.2 1.0
OD1 C:ASP12 2.2 11.9 1.0
OD1 C:ASP355 2.3 14.7 1.0
NE2 C:HIS229 2.4 14.0 1.0
OD2 C:ASP12 2.6 13.5 1.0
CG C:ASP12 2.7 12.1 1.0
CD2 C:HIS14 3.2 13.7 1.0
CE1 C:HIS14 3.2 8.3 1.0
CE1 C:HIS229 3.3 11.7 1.0
CD C:GLU292 3.3 19.0 1.0
CG C:ASP355 3.3 11.9 1.0
CD2 C:HIS229 3.4 12.2 1.0
CB C:GLU292 3.7 9.6 1.0
CD C:CD501 3.8 14.2 1.0
CG C:GLU292 3.9 12.1 1.0
OD2 C:ASP355 4.1 16.4 1.0
CB C:ASP355 4.1 15.0 1.0
CB C:ASP12 4.2 9.2 1.0
CA C:ASP355 4.3 11.4 1.0
OE1 C:GLU292 4.3 14.5 1.0
ND1 C:HIS14 4.3 13.3 1.0
CG C:HIS14 4.3 11.9 1.0
ND1 C:HIS229 4.5 10.8 1.0
CG C:HIS229 4.5 8.8 1.0
ND1 C:HIS358 4.6 11.5 1.0
O C:HOH615 4.7 15.8 1.0
CG2 C:ILE291 4.7 11.1 1.0
CE1 C:HIS358 4.9 11.4 1.0
CD1 C:LEU120 4.9 15.0 1.0
CA C:ASP12 4.9 10.9 1.0

Cadmium binding site 7 out of 8 in 4dzi

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Cadmium binding site 7 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd501

b:16.2
occ:1.00
OE2 D:GLU360 2.3 21.3 1.0
ND1 D:HIS358 2.3 12.1 1.0
OD2 D:ASP355 2.3 19.3 1.0
OE1 D:GLU292 2.4 17.6 1.0
OE2 D:GLU292 2.4 12.1 1.0
O D:HOH605 2.5 16.2 1.0
CD D:GLU292 2.7 15.4 1.0
OD1 D:ASP355 2.8 16.3 1.0
CG D:ASP355 2.9 17.4 1.0
CE1 D:HIS358 3.2 14.5 1.0
CD D:GLU360 3.2 17.7 1.0
CG D:HIS358 3.3 14.8 1.0
CB D:HIS358 3.6 13.6 1.0
CG D:GLU360 3.7 24.1 1.0
CD D:CD502 3.8 14.5 1.0
O D:HOH952 4.0 42.9 1.0
NE2 D:HIS14 4.0 11.1 1.0
CG D:GLU292 4.2 12.5 1.0
OE1 D:GLU360 4.3 24.0 1.0
NE2 D:HIS358 4.4 13.2 1.0
CD2 D:HIS14 4.4 11.7 1.0
CB D:ASP355 4.4 12.5 1.0
CD2 D:HIS358 4.4 18.4 1.0
O D:HOH801 4.7 25.1 1.0
O D:HOH705 4.7 26.5 1.0
O D:ASP355 4.9 16.2 1.0
O D:HOH709 4.9 29.2 1.0
CE1 D:HIS14 4.9 14.8 1.0
CE1 D:HIS229 4.9 13.6 1.0

Cadmium binding site 8 out of 8 in 4dzi

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Cadmium binding site 8 out of 8 in the Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10


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 Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium Subsp. Paratuberculosis K-10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cd502

b:14.5
occ:1.00
NE2 D:HIS14 2.2 11.1 1.0
OD1 D:ASP355 2.2 16.3 1.0
OE2 D:GLU292 2.2 12.1 1.0
OD1 D:ASP12 2.3 15.5 1.0
NE2 D:HIS229 2.3 15.6 1.0
OD2 D:ASP12 2.5 15.2 1.0
CG D:ASP12 2.7 16.9 1.0
CD2 D:HIS14 3.2 11.7 1.0
CE1 D:HIS14 3.2 14.8 1.0
CE1 D:HIS229 3.2 13.6 1.0
CG D:ASP355 3.3 17.4 1.0
CD D:GLU292 3.4 15.4 1.0
CD2 D:HIS229 3.4 11.0 1.0
CB D:GLU292 3.7 14.7 1.0
CD D:CD501 3.8 16.2 1.0
CG D:GLU292 3.9 12.5 1.0
OD2 D:ASP355 4.1 19.3 1.0
CB D:ASP355 4.1 12.5 1.0
CB D:ASP12 4.2 13.4 1.0
CA D:ASP355 4.3 12.2 1.0
ND1 D:HIS14 4.3 14.6 1.0
CG D:HIS14 4.3 10.1 1.0
OE1 D:GLU292 4.4 17.6 1.0
ND1 D:HIS229 4.4 13.4 1.0
CG D:HIS229 4.5 11.5 1.0
ND1 D:HIS358 4.6 12.1 1.0
O D:HOH605 4.6 16.2 1.0
CG2 D:ILE291 4.7 15.7 1.0
CD1 D:LEU120 4.8 13.9 1.0
CE1 D:HIS358 4.8 14.5 1.0
CA D:ASP12 4.9 11.2 1.0
O D:HOH705 4.9 26.5 1.0

Reference:

Y.Patskovsky, R.Toro, R.Bhosle, B.Hillerich, R.D.Seidel, E.Washington, A.Scott Glenn, S.Chowdhury, B.Evans, J.Hammonds, W.D.Zencheck, H.J.Imker, J.A.Gerlt, F.M.Raushel, S.C.Almo. Crystal Structure of Amidohydrolase MAP2389C (Target Efi-500390) From Mycobacterium Avium To Be Published.
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