Atomistry » Cadmium » PDB 1mws-1qvf » 1on3
Atomistry »
  Cadmium »
    PDB 1mws-1qvf »
      1on3 »

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: Sat Dec 12 08:11:38 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy