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Sodium 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:

Cadmium (Cd) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of A Short-Chain Flavodoxin Associated with A Non-Canonical Pdu Bacterial Microcompartment, PDB code: 5veg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 1 out of 6 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 Sodium with other atoms in the Na 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:Na203

b:29.8
occ:1.00
O A:HOH308 2.2 30.7 1.0
OD1 A:ASP70 2.3 29.0 1.0
CG A:ASP70 3.5 27.9 1.0
CD A:CD202 3.8 33.2 1.0
CB A:ASP70 4.2 28.8 1.0
OD1 A:ASP74 4.2 35.4 1.0
OD2 A:ASP70 4.4 32.4 1.0
OD2 A:ASP73 4.4 51.2 1.0
CA A:ASP70 4.5 29.4 1.0

Sodium binding site 2 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 2 out of 6 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 Sodium with other atoms in the Na 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:Na204

b:24.8
occ:1.00
O C:HOH322 2.3 43.5 1.0
O B:GLU127 2.4 26.9 1.0
OE2 C:GLU120 2.5 41.9 1.0
O B:ASP125 2.5 29.7 1.0
OD2 B:ASP132 2.5 39.0 1.0
O B:HOH321 2.7 35.3 1.0
O C:HOH333 2.7 39.9 1.0
CD C:GLU120 3.5 45.3 1.0
CG B:ASP132 3.6 36.8 1.0
C B:GLU127 3.6 27.8 1.0
C B:ASP125 3.6 31.3 1.0
OE1 C:GLU120 3.8 43.0 1.0
OD1 B:ASP132 4.0 33.4 1.0
N B:ASP125 4.1 27.6 1.0
N B:GLU127 4.2 29.5 1.0
CG2 B:ILE124 4.2 29.7 1.0
N B:TYR129 4.2 25.6 1.0
CA B:ASP125 4.3 31.7 1.0
CB B:ASP125 4.3 32.7 1.0
CA B:GLU127 4.5 31.0 1.0
CB B:TYR129 4.5 37.8 1.0
O B:HOH341 4.5 48.2 1.0
C B:LEU126 4.5 28.5 1.0
N B:PRO128 4.5 26.7 1.0
CA B:PRO128 4.5 28.0 1.0
O B:TYR129 4.6 39.8 1.0
N B:LEU126 4.7 31.5 1.0
C B:PRO128 4.8 32.0 1.0
CG C:GLU120 4.8 32.6 1.0
O B:LEU126 4.9 28.5 1.0
CB B:ASP132 4.9 30.0 1.0
CA B:TYR129 4.9 32.1 1.0
OD2 B:ASP125 4.9 37.6 1.0
OE1 B:GLU131 4.9 54.7 1.0

Sodium binding site 3 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 3 out of 6 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 Sodium with other atoms in the Na 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
C:Na202

b:28.1
occ:1.00
OE2 C:GLU141 2.5 48.0 1.0
NZ C:LYS138 2.6 66.0 1.0
OD1 A:ASP60 2.9 77.2 1.0
CE C:LYS138 3.3 65.7 1.0
CG A:ASP60 3.4 59.4 1.0
CD C:GLU141 3.4 56.6 1.0
OE1 C:GLU141 3.6 64.8 1.0
OD2 A:ASP60 3.8 71.1 1.0
CD C:LYS138 4.1 61.6 1.0
CB A:ASP60 4.1 59.1 1.0
CG C:GLU141 4.8 50.6 1.0

Sodium binding site 4 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 4 out of 6 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 Sodium with other atoms in the Na binding site number 4 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
C:Na203

b:31.9
occ:1.00
O C:HOH306 2.3 42.5 1.0
OE1 C:GLU16 2.4 41.8 1.0
OE2 C:GLU16 3.0 40.0 1.0
CD C:GLU16 3.0 44.5 1.0
OH C:TYR8 3.8 35.7 1.0
CG C:GLU16 4.4 31.0 1.0
CE1 C:TYR8 4.5 32.5 1.0
CZ C:TYR8 4.5 31.1 1.0
CG2 C:THR10 5.0 29.3 1.0
CB C:GLU16 5.0 26.6 1.0

Sodium binding site 5 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 5 out of 6 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 Sodium with other atoms in the Na binding site number 5 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
C:Na204

b:24.7
occ:1.00
O C:HOH340 2.1 44.8 1.0
OE2 C:GLU127 2.2 34.8 1.0
O C:HOH334 2.2 35.4 1.0
OD1 C:ASN14 2.3 32.9 1.0
OE1 C:GLU17 2.6 40.3 1.0
CD C:GLU127 2.8 38.5 1.0
OE1 C:GLU127 2.9 38.1 1.0
CG C:ASN14 3.5 33.2 1.0
CD C:GLU17 3.8 41.0 1.0
O C:HOH305 3.9 37.3 1.0
CA C:ASN14 4.3 30.2 1.0
CG C:GLU127 4.3 37.9 1.0
OE2 C:GLU17 4.3 40.8 1.0
ND2 C:ASN14 4.3 28.8 1.0
CB C:ASN14 4.5 28.1 1.0
N C:ASN14 4.6 27.3 1.0
CB C:GLU127 4.7 29.4 1.0
C C:GLY13 4.8 29.8 1.0
CD C:PRO128 4.9 28.9 1.0
O C:HOH331 4.9 41.8 1.0
CA C:GLU127 4.9 29.9 1.0
CB C:GLU17 4.9 34.2 1.0
O C:GLY13 4.9 28.0 1.0

Sodium binding site 6 out of 6 in 5veg

Go back to Sodium Binding Sites List in 5veg
Sodium binding site 6 out of 6 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 Sodium with other atoms in the Na binding site number 6 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
C:Na205

b:20.3
occ:1.00
O C:GLU127 2.3 27.1 1.0
O C:HOH347 2.4 32.5 1.0
O C:ASP125 2.5 25.5 1.0
OD2 C:ASP132 2.5 31.6 1.0
O C:HOH309 2.5 32.1 1.0
CG C:ASP132 3.5 36.1 1.0
C C:GLU127 3.6 23.5 1.0
C C:ASP125 3.6 29.9 1.0
OD1 C:ASP132 3.9 31.7 1.0
N C:GLU127 4.1 29.6 1.0
CG2 C:ILE124 4.2 30.0 1.0
N C:ASP125 4.3 26.9 1.0
N C:TYR129 4.3 26.1 1.0
CA C:ASP125 4.3 29.8 1.0
O C:HOH366 4.4 52.0 1.0
CA C:GLU127 4.4 29.9 1.0
C C:LEU126 4.4 28.0 1.0
CB C:ASP125 4.4 29.6 1.0
CB C:TYR129 4.5 30.9 1.0
N C:PRO128 4.5 27.5 1.0
CA C:PRO128 4.5 28.7 1.0
N C:LEU126 4.7 25.3 1.0
O C:TYR129 4.8 39.9 1.0
O C:LEU126 4.8 28.1 1.0
C C:PRO128 4.8 29.2 1.0
CB C:ASP132 4.8 27.5 1.0
CA C:TYR129 4.9 28.9 1.0
OD2 C:ASP125 5.0 45.5 1.0
CA C:LEU126 5.0 33.0 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: Tue Dec 15 11:44:58 2020

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