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Cadmium in PDB 1on3: Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound)

Enzymatic activity of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound)

All present enzymatic activity of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound):
2.1.3.1;

Protein crystallography data

The structure of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound), PDB code: 1on3 was solved by P.R.Hall, Y.-F.Wang, R.E.Rivera-Hainaj, X.Zheng, M.Pustai-Carey, P.R.Carey, V.C.Yee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.805, 200.708, 146.347, 90.00, 102.43, 90.00
R / Rfree (%) 16.8 / 21.3

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound) (pdb code 1on3). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound), PDB code: 1on3:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1on3

Go back to Cadmium Binding Sites List in 1on3
Cadmium binding site 1 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd7001

b:20.4
occ:1.00
 NE2 D:HIS388 2.0 5.7 1.0
NE2 A:HIS388 2.4 23.6 1.0
O D:HOH5213 2.4 18.8 1.0
O A:HOH7241 2.4 14.5 1.0
O D:HOH5227 2.4 18.5 1.0
O A:HOH7239 2.4 15.4 1.0
CE1 D:HIS388 2.8 21.2 1.0
CD2 D:HIS388 3.2 17.1 1.0
O D:HOH5491 3.2 73.5 1.0
CE1 A:HIS388 3.3 25.3 1.0
CD2 A:HIS388 3.5 19.2 1.0
ND1 D:HIS388 4.0 12.7 1.0
OD2 D:ASP349 4.2 21.0 1.0
CG D:HIS388 4.2 15.9 1.0
OD2 A:ASP349 4.3 18.6 1.0
O A:HOH7269 4.3 22.0 1.0
O D:HOH5218 4.3 17.7 1.0
ND1 A:HIS388 4.4 21.8 1.0
O A:HOH7069 4.5 22.9 1.0
O A:CYS524 4.5 19.3 1.0
NZ A:LYS391 4.5 18.1 1.0
CG A:HIS388 4.6 18.4 1.0
O D:CYS524 4.6 19.8 1.0
O D:HOH5136 4.6 19.9 1.0
NZ D:LYS391 4.6 14.8 1.0
NH1 D:ARG387 4.7 24.1 1.0
NH1 A:ARG387 4.7 25.4 1.0

Cadmium binding site 2 out of 3 in 1on3

Go back to Cadmium Binding Sites List in 1on3
Cadmium binding site 2 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7002

b:13.6
occ:1.00
 O E:HOH5233 2.3 11.2 1.0
NE2 E:HIS388 2.3 10.5 1.0
O E:HOH5284 2.4 15.5 1.0
NE2 B:HIS388 2.4 13.5 1.0
O B:HOH7255 2.4 14.8 1.0
O E:HOH5189 2.4 8.0 1.0
CE1 E:HIS388 3.2 11.6 1.0
CE1 B:HIS388 3.3 14.7 1.0
CD2 E:HIS388 3.4 13.0 1.0
CD2 B:HIS388 3.4 12.6 1.0
OD2 E:ASP349 4.3 12.3 1.0
ND1 E:HIS388 4.3 13.2 1.0
OD2 B:ASP349 4.4 13.8 1.0
O B:HOH7259 4.4 12.9 1.0
O B:HOH7008 4.4 14.6 1.0
O E:HOH5248 4.4 9.8 1.0
ND1 B:HIS388 4.5 15.4 1.0
O E:HOH5234 4.5 14.3 1.0
CG E:HIS388 4.5 8.8 1.0
O E:CYS524 4.5 15.4 1.0
O B:CYS524 4.5 12.9 1.0
CG B:HIS388 4.6 12.5 1.0
NZ B:LYS391 4.6 7.3 1.0
NZ E:LYS391 4.6 16.2 1.0
NH1 E:ARG387 4.6 16.0 1.0
NH1 B:ARG387 4.7 14.3 1.0

Cadmium binding site 3 out of 3 in 1on3

Go back to Cadmium Binding Sites List in 1on3
Cadmium binding site 3 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Methylmalonyl-Coenzyme A and Methylmalonic Acid Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd7003

b:16.2
occ:1.00
 O F:HOH6235 2.2 18.2 1.0
NE2 C:HIS388 2.3 15.3 1.0
NE2 F:HIS388 2.4 18.6 1.0
O C:HOH7258 2.4 16.9 1.0
O F:HOH6234 2.4 12.4 1.0
O C:HOH7255 2.4 10.6 1.0
CE1 C:HIS388 3.2 16.0 1.0
CE1 F:HIS388 3.3 10.6 1.0
CD2 C:HIS388 3.4 14.3 1.0
CD2 F:HIS388 3.4 12.9 1.0
OD2 F:ASP349 4.3 18.6 1.0
OD2 C:ASP349 4.3 18.0 1.0
O C:HOH7261 4.4 12.9 1.0
ND1 C:HIS388 4.4 17.8 1.0
O F:HOH6237 4.4 18.3 1.0
ND1 F:HIS388 4.4 11.3 1.0
O F:HOH6252 4.5 17.2 1.0
O F:CYS524 4.5 16.5 1.0
O C:CYS524 4.5 15.5 1.0
O C:HOH7263 4.5 14.7 1.0
CG C:HIS388 4.5 18.4 1.0
CG F:HIS388 4.5 9.6 1.0
NZ F:LYS391 4.6 14.4 1.0
NH1 C:ARG387 4.6 15.2 1.0
NZ C:LYS391 4.6 15.7 1.0
NH1 F:ARG387 4.6 13.5 1.0

Reference:

P.R.Hall, Y.-F.Wang, R.E.Rivera-Hainaj, X.Zheng, M.Pustai-Carey, P.R.Carey, V.C.Yee. Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core Embo J. V. 22 2334 2003.
ISSN: ISSN 0261-4189
PubMed: 12743028
DOI: 10.1093/EMBOJ/CDG244
Page generated: Thu Jul 10 11:12:17 2025

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