Atomistry » Sodium » PDB 5vb8-5vwn » 5veg
Atomistry »
  Sodium »
    PDB 5vb8-5vwn »
      5veg »

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

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