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Cadmium in PDB 1on9: Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Hydrolyzed Methylmalonyl-Coenzyme A Bound)

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

All present enzymatic activity of Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Hydrolyzed Methylmalonyl-Coenzyme A 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 Hydrolyzed Methylmalonyl-Coenzyme A Bound), PDB code: 1on9 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) 29.55 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.810, 200.020, 145.900, 90.00, 102.97, 90.00
R / Rfree (%) 15.2 / 19.8

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 Hydrolyzed Methylmalonyl-Coenzyme A Bound) (pdb code 1on9). 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 Hydrolyzed Methylmalonyl-Coenzyme A Bound), PDB code: 1on9:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1on9

Go back to Cadmium Binding Sites List in 1on9
Cadmium binding site 1 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Hydrolyzed Methylmalonyl-Coenzyme A 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 Hydrolyzed Methylmalonyl-Coenzyme A Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd7001

b:16.4
occ:1.00
 NE2 A:HIS388 2.3 14.4 1.0
NE2 D:HIS388 2.3 11.0 1.0
O D:HOH4368 2.3 18.2 1.0
O A:HOH7407 2.4 13.1 1.0
O A:HOH7009 2.4 11.5 1.0
O A:HOH7006 2.4 14.8 1.0
CE1 D:HIS388 3.1 12.3 1.0
CE1 A:HIS388 3.2 17.9 1.0
CD2 A:HIS388 3.3 16.2 1.0
CD2 D:HIS388 3.4 10.5 1.0
OD2 D:ASP349 4.2 17.3 1.0
OD2 A:ASP349 4.3 14.3 1.0
O A:HOH7034 4.3 17.2 1.0
O A:HOH7253 4.3 14.5 1.0
ND1 D:HIS388 4.3 14.0 1.0
ND1 A:HIS388 4.3 14.1 1.0
O A:CYS524 4.4 25.3 1.0
CG A:HIS388 4.4 16.2 1.0
O A:HOH7331 4.5 13.8 1.0
CG D:HIS388 4.5 14.4 1.0
O D:CYS524 4.5 21.9 1.0
O D:HOH4370 4.5 11.9 1.0
NZ D:LYS391 4.6 13.3 1.0
NZ A:LYS391 4.6 11.8 1.0
NH1 D:ARG387 4.6 15.9 1.0
NH1 A:ARG387 4.6 14.8 1.0

Cadmium binding site 2 out of 3 in 1on9

Go back to Cadmium Binding Sites List in 1on9
Cadmium binding site 2 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Hydrolyzed Methylmalonyl-Coenzyme A 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 Hydrolyzed Methylmalonyl-Coenzyme A Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd7002

b:11.7
occ:1.00
 NE2 E:HIS388 2.3 10.2 1.0
O E:HOH4468 2.3 9.3 1.0
O B:HOH7252 2.3 14.7 1.0
O B:HOH7010 2.3 14.6 1.0
NE2 B:HIS388 2.3 8.6 1.0
O E:HOH4466 2.4 9.8 1.0
CE1 B:HIS388 3.2 7.2 1.0
CE1 E:HIS388 3.3 14.8 1.0
CD2 E:HIS388 3.3 10.5 1.0
CD2 B:HIS388 3.4 5.8 1.0
OD2 E:ASP349 4.3 11.2 1.0
OD2 B:ASP349 4.3 9.6 1.0
O B:HOH7380 4.3 11.3 1.0
O B:HOH7290 4.3 10.5 1.0
O E:CYS524 4.4 13.9 1.0
ND1 E:HIS388 4.4 10.6 1.0
ND1 B:HIS388 4.4 8.4 1.0
O E:HOH4472 4.4 8.4 1.0
O B:CYS524 4.4 16.6 1.0
CG E:HIS388 4.4 9.7 1.0
O E:HOH4478 4.5 11.8 1.0
NH1 E:ARG387 4.5 12.7 1.0
CG B:HIS388 4.5 8.9 1.0
NZ B:LYS391 4.5 8.8 1.0
NZ E:LYS391 4.6 9.6 1.0
NH1 B:ARG387 4.6 14.2 1.0

Cadmium binding site 3 out of 3 in 1on9

Go back to Cadmium Binding Sites List in 1on9
Cadmium binding site 3 out of 3 in the Transcarboxylase 12S Crystal Structure: Hexamer Assembly and Substrate Binding to A Multienzyme Core (with Hydrolyzed Methylmalonyl-Coenzyme A 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 Hydrolyzed Methylmalonyl-Coenzyme A Bound) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd7003

b:14.2
occ:1.00
 O F:HOH6008 2.2 12.4 1.0
NE2 F:HIS388 2.3 12.9 1.0
NE2 C:HIS388 2.3 10.6 1.0
O F:HOH6258 2.4 10.0 1.0
O C:HOH7009 2.4 13.3 1.0
O C:HOH7010 2.4 13.4 1.0
CE1 F:HIS388 3.2 10.1 1.0
CE1 C:HIS388 3.2 11.2 1.0
CD2 F:HIS388 3.3 11.6 1.0
CD2 C:HIS388 3.4 11.6 1.0
OD2 C:ASP349 4.2 13.3 1.0
O F:HOH6424 4.3 14.5 1.0
OD2 F:ASP349 4.3 14.1 1.0
ND1 F:HIS388 4.3 11.0 1.0
O F:HOH6276 4.4 12.0 1.0
O C:HOH7401 4.4 13.1 1.0
ND1 C:HIS388 4.4 11.9 1.0
CG F:HIS388 4.4 14.7 1.0
O C:CYS524 4.4 18.3 1.0
O F:CYS524 4.4 18.1 1.0
CG C:HIS388 4.5 11.7 1.0
O C:HOH7432 4.5 12.2 1.0
NZ F:LYS391 4.5 9.7 1.0
NH1 F:ARG387 4.6 15.4 1.0
NZ C:LYS391 4.6 12.3 1.0
NH1 C:ARG387 4.7 10.8 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: Sun Jan 24 09:42:43 2021

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