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Cadmium in PDB 5ac3: Crystal Structure of PAM12A

Enzymatic activity of Crystal Structure of PAM12A

All present enzymatic activity of Crystal Structure of PAM12A:
3.5.1.4;

Protein crystallography data

The structure of Crystal Structure of PAM12A, PDB code: 5ac3 was solved by B.Wu, H.J.Wijma, L.Song, H.J.Rozeboom, C.Poloni, Y.Tian, M.I.Arif, T.Nuijens, P.J.L.M.Quadflieg, W.Szymanski, B.L.Feringa, D.B.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.77 / 1.80
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 82.870, 82.870, 112.891, 90.00, 90.00, 120.00
R / Rfree (%) 16 / 19.6

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of PAM12A (pdb code 5ac3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of PAM12A, PDB code: 5ac3:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 5ac3

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Cadmium binding site 1 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1532

b:20.5
occ:1.00
 O A:HOH2124 2.3 16.9 1.0
OD1 A:ASP156 2.3 19.7 1.0
OD2 A:ASP156 2.5 19.8 1.0
O A:HOH2114 2.5 19.1 1.0
CG A:ASP156 2.8 19.3 1.0
CB A:ASP156 4.3 18.7 1.0
O A:HOH2340 4.4 32.4 1.0
O A:ARG152 4.6 18.1 1.0
O A:HOH2115 4.6 32.4 1.0
O A:HOH2111 4.7 33.3 1.0
CA A:ASP156 5.0 18.6 1.0

Cadmium binding site 2 out of 9 in 5ac3

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Cadmium binding site 2 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1533

b:30.1
occ:0.75
 O A:ACY1544 2.2 31.6 1.0
O A:HOH2230 2.4 33.7 1.0
NE2 A:HIS445 2.5 30.9 1.0
O A:HOH2302 2.6 35.5 1.0
O A:HOH2337 2.6 40.1 1.0
C A:ACY1544 2.9 33.7 1.0
OXT A:ACY1544 3.0 32.6 1.0
CD2 A:HIS445 3.5 29.7 1.0
CE1 A:HIS445 3.5 31.2 1.0
CH3 A:ACY1544 4.4 32.1 1.0
O A:GLU348 4.5 31.0 1.0
N A:GLU348 4.5 28.1 1.0
ND1 A:HIS445 4.6 30.4 1.0
CG A:HIS445 4.6 28.9 1.0
CB A:ALA444 4.7 27.5 1.0
CB A:GLU348 5.0 34.0 1.0

Cadmium binding site 3 out of 9 in 5ac3

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Cadmium binding site 3 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1534

b:29.6
occ:0.75
 O A:HOH2055 2.0 38.0 1.0
O A:ACY1545 2.3 36.5 1.0
NE2 A:HIS86 2.3 20.4 1.0
O A:HOH2338 2.4 23.0 0.5
O A:HOH2052 2.5 32.6 1.0
O A:HOH2053 2.7 42.8 1.0
OXT A:ACY1545 2.8 34.9 1.0
C A:ACY1545 2.9 36.5 1.0
CE1 A:HIS86 3.1 20.2 1.0
CD2 A:HIS86 3.5 19.8 1.0
O A:HOH2054 4.0 27.1 1.0
CD A:ARG80 4.3 31.4 1.0
ND1 A:HIS86 4.3 19.2 1.0
NE A:ARG80 4.4 32.4 1.0
CH3 A:ACY1545 4.4 35.2 1.0
CG A:HIS86 4.5 18.7 1.0

Cadmium binding site 4 out of 9 in 5ac3

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Cadmium binding site 4 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1535

b:36.0
occ:0.50
 NE2 A:HIS197 2.4 21.4 1.0
O A:HOH2307 2.7 27.7 1.0
CD2 A:HIS197 3.4 20.7 1.0
CE1 A:HIS197 3.4 21.6 1.0
CD A:CD1536 3.5 46.1 0.5
CD A:PRO460 4.3 22.9 1.0
CG A:PRO460 4.4 23.7 1.0
ND1 A:HIS197 4.5 21.1 1.0
CG A:HIS197 4.5 20.1 1.0
O A:ALA458 4.6 18.2 1.0
CD1 A:LEU494 4.7 18.4 1.0

Cadmium binding site 5 out of 9 in 5ac3

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Cadmium binding site 5 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1536

b:46.1
occ:0.50
 CE1 A:HIS197 2.4 21.6 1.0
NE2 A:HIS197 3.0 21.4 1.0
CD A:CD1535 3.5 36.0 0.5
ND1 A:HIS197 3.6 21.1 1.0
CG A:PRO460 3.9 23.7 1.0
CD2 A:HIS197 4.3 20.7 1.0
OG A:SER196 4.3 20.1 1.0
CB A:PRO460 4.5 23.7 1.0
O A:HOH2156 4.5 34.9 1.0
CG A:HIS197 4.6 20.1 1.0
CD A:ARG194 4.8 28.9 1.0
CD A:PRO460 4.9 22.9 1.0

Cadmium binding site 6 out of 9 in 5ac3

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Cadmium binding site 6 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1537

b:74.2
occ:0.50
 OE2 A:GLU331 2.6 32.1 1.0
OE1 A:GLU331 2.7 32.4 1.0
CD A:GLU331 3.0 30.1 1.0
CG A:GLU331 4.4 26.8 1.0

Cadmium binding site 7 out of 9 in 5ac3

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Cadmium binding site 7 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1538

b:22.9
occ:0.50
 O A:HOH2069 2.1 14.6 1.0
OE1 A:GLU98 2.2 28.9 1.0
OE1 A:GLU101 2.2 24.8 1.0
OXT A:ACY1542 2.2 35.2 1.0
OE2 A:GLU98 2.5 30.2 1.0
CD A:GLU98 2.7 26.9 1.0
C A:ACY1542 3.0 36.0 1.0
O A:ACY1542 3.0 37.4 1.0
CD A:GLU101 3.2 24.0 1.0
OE2 A:GLU101 3.7 25.2 1.0
NH1 A:ARG102 3.9 23.4 1.0
NZ A:LYS97 4.2 27.0 1.0
CG A:GLU98 4.2 23.8 1.0
NH2 A:ARG102 4.3 24.3 1.0
CH3 A:ACY1542 4.4 35.2 1.0
CG A:GLU101 4.5 22.7 1.0
O A:HOH2068 4.5 26.3 1.0
CZ A:ARG102 4.6 23.3 1.0
CB A:GLU101 4.7 21.6 1.0

Cadmium binding site 8 out of 9 in 5ac3

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Cadmium binding site 8 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1539

b:56.1
occ:1.00
 O A:HOH2261 2.2 36.0 1.0
NE2 A:HIS395 2.4 31.0 1.0
O A:HOH2263 2.7 43.0 1.0
O A:HOH2262 2.9 41.3 1.0
CE1 A:HIS395 3.1 30.6 1.0
O A:HOH2339 3.3 39.2 1.0
O A:HOH2264 3.3 45.5 1.0
CD2 A:HIS395 3.6 30.8 1.0
ND1 A:HIS395 4.4 30.2 1.0
CG A:HIS395 4.6 30.2 1.0
CE2 A:PHE391 4.8 26.0 1.0

Cadmium binding site 9 out of 9 in 5ac3

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Cadmium binding site 9 out of 9 in the Crystal Structure of PAM12A


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 PAM12A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1540

b:54.1
occ:0.50
 O A:HOH2107 2.6 28.1 1.0
ND1 A:HIS378 2.6 23.5 1.0
CE1 A:HIS378 3.1 22.9 1.0
O A:HOH2091 3.4 37.4 1.0
CG A:HIS378 3.8 23.1 1.0
CB A:ASP146 4.3 21.9 1.0
NE2 A:HIS378 4.4 23.4 1.0
CB A:HIS378 4.4 23.2 1.0
OD2 A:ASP146 4.4 25.7 1.0
CA A:HIS378 4.5 24.3 1.0
N A:ASP146 4.5 20.2 1.0
CG A:ASP146 4.7 23.6 1.0
O A:ASP146 4.7 18.5 1.0
CD2 A:HIS378 4.8 22.8 1.0
O A:THR377 4.8 24.2 1.0
ND2 A:ASN127 4.8 17.8 1.0
CA A:ASP146 4.9 20.7 1.0
CB A:PRO145 4.9 19.2 1.0

Reference:

B.Wu, H.J.Wijma, L.Song, H.J.Rozeboom, C.Poloni, Y.Tian, M.I.Arif, T.Nuijens, P.J.L.M.Quadflieg, W.Szymanski, B.L.Feringa, D.B.Janssen. Versatile Peptide C-Terminal Functionalization Via A Computationally Peptide Amidase Acs Catalysis 2016.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.6B01062
Page generated: Thu Jul 10 14:08:09 2025

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