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Sodium in PDB 4tpu: Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans

Protein crystallography data

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu was solved by A.K.Kumar, H.P.Yennawar, N.H.Yennawar, J.G.Ferry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.47 / 2.36
Space group P 2 3
Cell size a, b, c (Å), α, β, γ (°) 93.181, 93.181, 93.181, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 26.9

Other elements in 4tpu:

The structure of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans also contains other interesting chemical elements:

Bromine (Br) 7 atoms
Iron (Fe) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans (pdb code 4tpu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans, PDB code: 4tpu:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 4tpu

Go back to Sodium Binding Sites List in 4tpu
Sodium binding site 1 out of 4 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:81.4
occ:1.00
H A:ARG109 2.7 63.3 1.0
HA A:PRO108 3.2 78.0 1.0
HB2 A:ARG109 3.5 69.4 1.0
N A:ARG109 3.5 52.8 1.0
HH12 A:ARG112 3.5 53.5 1.0
HB3 A:PRO108 3.9 66.8 1.0
CA A:PRO108 3.9 65.1 1.0
HH22 A:ARG112 4.1 69.6 1.0
HB3 A:ARG109 4.1 69.4 1.0
HB2 A:PRO108 4.1 66.8 1.0
CB A:ARG109 4.1 57.9 1.0
CB A:PRO108 4.2 55.8 1.0
C A:PRO108 4.2 60.2 1.0
NH1 A:ARG112 4.3 44.6 1.0
CA A:ARG109 4.4 56.1 1.0
HA A:ARG109 4.7 67.3 1.0
HH11 A:ARG112 4.8 53.5 1.0
NH2 A:ARG112 4.8 58.1 1.0

Sodium binding site 2 out of 4 in 4tpu

Go back to Sodium Binding Sites List in 4tpu
Sodium binding site 2 out of 4 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:55.7
occ:1.00
O A:HOH410 3.0 44.8 1.0
HB3 A:LEU76 3.1 43.7 1.0
HA A:ASN77 3.2 53.8 1.0
BR A:BR307 3.5 85.8 0.5
HB2 A:SER89 3.6 65.4 1.0
O A:HOH414 3.7 45.2 1.0
HB2 A:LEU76 3.9 43.7 1.0
C A:LEU76 3.9 50.9 1.0
CA A:ASN77 3.9 44.9 1.0
CB A:LEU76 3.9 36.5 1.0
HB2 A:ASN77 3.9 56.0 1.0
O A:LEU76 3.9 39.5 1.0
N A:ASN77 3.9 50.7 1.0
HB3 A:SER89 4.1 65.4 1.0
CB A:SER89 4.3 54.5 1.0
H A:ASP90 4.3 67.0 1.0
H A:ASN77 4.3 60.7 1.0
HD13 A:LEU76 4.4 42.1 1.0
HA A:SER89 4.5 56.4 1.0
CB A:ASN77 4.5 46.8 1.0
CA A:LEU76 4.6 46.7 1.0
CA A:SER89 4.9 47.1 1.0

Sodium binding site 3 out of 4 in 4tpu

Go back to Sodium Binding Sites List in 4tpu
Sodium binding site 3 out of 4 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:47.6
occ:1.00
HG3 A:PRO74 3.3 56.3 1.0
BR A:BR310 3.4 81.3 1.0
CG A:PRO74 4.3 47.0 1.0
HD3 A:PRO74 4.6 59.7 1.0
HB3 A:PRO74 4.7 45.7 1.0
HG2 A:PRO74 4.7 56.3 1.0

Sodium binding site 4 out of 4 in 4tpu

Go back to Sodium Binding Sites List in 4tpu
Sodium binding site 4 out of 4 in the Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Ferredoxin-Dependent Disulfide Reductase From Methanosarcina Acetivorans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na315

b:55.8
occ:1.00
HD13 A:ILE66 3.0 43.1 1.0
HG21 A:ILE66 3.1 52.0 1.0
HE2 A:LYS59 3.1 79.6 1.0
BR A:BR311 3.3 68.1 0.5
HD12 A:ILE66 3.4 43.1 1.0
CD1 A:ILE66 3.7 36.0 1.0
CE A:LYS59 4.0 66.4 1.0
HZ1 A:LYS59 4.0 94.3 1.0
CG2 A:ILE66 4.0 43.4 1.0
HE3 A:LYS59 4.1 79.6 1.0
HD11 A:ILE66 4.3 43.1 1.0
HG22 A:ILE66 4.4 52.0 1.0
NZ A:LYS59 4.4 78.7 1.0
HD22 A:LEU63 4.4 57.4 1.0
HB A:ILE66 4.5 54.7 1.0
HG23 A:ILE66 4.5 52.0 1.0
HZ3 A:LYS59 4.6 94.3 1.0
CB A:ILE66 4.6 45.6 1.0
HD23 A:LEU63 4.7 57.4 1.0
CG1 A:ILE66 4.7 55.2 1.0
CD2 A:LEU63 4.9 47.9 1.0

Reference:

A.K.Kumar, R.S.Kumar, N.H.Yennawar, H.P.Yennawar, J.G.Ferry. Structural and Biochemical Characterization of A Ferredoxin:Thioredoxin Reductase-Like Enzyme From Methanosarcina Acetivorans. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25915695
DOI: 10.1021/ACS.BIOCHEM.5B00137
Page generated: Tue Dec 15 07:31:32 2020

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