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Cadmium in PDB 5veg: Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment

Protein crystallography data

The structure of Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment, PDB code: 5veg was solved by M.Sutter, J.S.Plegaria, C.A.Kerfeld, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.90 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 47.301, 95.807, 102.378, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 25

Other elements in 5veg:

The structure of Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment (pdb code 5veg). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment, PDB code: 5veg:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 5veg

Go back to Cadmium Binding Sites List in 5veg
Cadmium binding site 1 out of 3 in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd202

b:33.2
occ:1.00
OD2 A:ASP74 2.4 32.7 1.0
OD1 A:ASP70 2.5 29.0 1.0
O A:HOH361 2.6 39.9 1.0
OD2 A:ASP70 2.6 32.4 1.0
CG A:ASP70 2.9 27.9 1.0
CG A:ASP74 3.2 32.1 1.0
OD1 A:ASP74 3.2 35.4 1.0
NA A:NA203 3.8 29.8 1.0
O A:HOH308 3.9 30.7 1.0
O A:HOH314 4.0 37.4 1.0
O A:HOH339 4.3 44.7 1.0
CB A:ASP70 4.4 28.8 1.0
CB A:ASP74 4.6 30.6 1.0
O A:HOH342 4.7 48.0 1.0
O A:ASP70 4.7 32.3 1.0
C A:ASP70 4.9 27.1 1.0

Cadmium binding site 2 out of 3 in 5veg

Go back to Cadmium Binding Sites List in 5veg
Cadmium binding site 2 out of 3 in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd202

b:40.8
occ:0.82
O B:HOH310 2.5 45.0 1.0
OD2 B:ASP74 2.6 46.7 1.0
OD1 B:ASP70 2.6 49.9 1.0
OD1 B:ASP74 2.6 40.8 1.0
CG B:ASP74 2.9 48.5 1.0
OD2 B:ASP70 3.2 49.3 1.0
CG B:ASP70 3.3 46.4 1.0
O B:HOH301 3.7 41.8 1.0
O B:HOH306 3.8 38.1 1.0
CB B:ASP74 4.4 40.9 1.0
O B:ASP70 4.5 45.2 1.0
CB B:ASP70 4.7 46.1 1.0
O B:HOH305 4.8 44.4 1.0

Cadmium binding site 3 out of 3 in 5veg

Go back to Cadmium Binding Sites List in 5veg
Cadmium binding site 3 out of 3 in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd203

b:46.9
occ:0.66
OE1 B:GLU16 2.4 36.3 1.0
OE1 C:GLU97 2.6 35.8 1.0
OE2 C:GLU97 2.7 44.3 1.0
CD C:GLU97 3.0 37.8 1.0
CD B:GLU16 3.2 39.4 1.0
OE2 B:GLU16 3.3 44.3 1.0
OH B:TYR8 4.0 43.8 1.0
CG C:GLU97 4.4 40.2 1.0
O C:HOH307 4.5 34.3 1.0
CE1 B:TYR8 4.6 35.8 1.0
CG B:GLU16 4.6 33.8 1.0
CZ B:TYR8 4.7 40.4 1.0
CG2 B:THR10 4.9 28.7 1.0

Reference:

J.S.Plegaria, M.Sutter, B.Ferlez, C.Aussignargues, J.Niklas, O.G.Poluektov, C.Fromwiller, M.Teravest, L.M.Utschig, D.M.Tiede, C.A.Kerfeld. Structural and Functional Characterization of A Short-Chain Flavodoxin Associated with A Noncanonical 1,2-Propanediol Utilization Bacterial Microcompartment. Biochemistry V. 56 5679 2017.
ISSN: ISSN 1520-4995
PubMed: 28956602
DOI: 10.1021/ACS.BIOCHEM.7B00682
Page generated: Sat Dec 12 08:27:44 2020

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