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Sodium in PDB 5mim: Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N

Enzymatic activity of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N

All present enzymatic activity of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N:
3.4.21.75;

Protein crystallography data

The structure of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N, PDB code: 5mim was solved by S.O.Dahms, J.Guan-Sheng, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.69 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.204, 132.204, 155.727, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.4

Other elements in 5mim:

The structure of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N (pdb code 5mim). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N, PDB code: 5mim:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5mim

Go back to Sodium Binding Sites List in 5mim
Sodium binding site 1 out of 4 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:14.0
occ:1.00
O A:THR309 2.4 12.6 1.0
O A:SER311 2.4 10.5 1.0
O A:THR314 2.4 13.2 1.0
OG1 A:THR314 2.4 12.0 1.0
O A:HOH867 2.5 12.4 1.0
OG A:SER316 2.6 21.4 1.0
C A:THR314 3.2 13.7 1.0
C A:THR309 3.4 14.8 1.0
CB A:THR314 3.6 12.6 1.0
C A:SER311 3.6 13.8 1.0
O A:HOH911 3.6 19.0 1.0
CB A:SER316 3.7 16.2 1.0
CA A:THR314 3.7 13.9 1.0
N A:SER311 3.9 13.1 1.0
N A:THR314 3.9 12.7 1.0
N A:SER316 4.0 13.8 1.0
CA A:THR309 4.2 13.4 1.0
N A:LEU315 4.2 12.8 1.0
CA A:SER311 4.2 13.9 1.0
C A:ASN310 4.3 16.3 1.0
CE A:MET534 4.3 16.6 1.0
O A:TYR308 4.3 14.5 1.0
N A:ASN310 4.4 12.2 1.0
CA A:SER316 4.4 15.7 1.0
O A:SER335 4.4 13.0 1.0
CA A:LEU315 4.6 14.4 1.0
C A:LEU315 4.6 18.9 1.0
N A:ILE312 4.6 11.2 1.0
CA A:ASN310 4.7 10.8 1.0
CB A:SER311 4.7 11.6 1.0
OG1 A:THR309 4.7 18.1 1.0
CG2 A:THR314 4.8 12.6 1.0
O A:ASN310 4.8 16.1 1.0
CA A:ILE312 4.8 12.3 1.0
C A:ILE312 4.9 13.7 1.0

Sodium binding site 2 out of 4 in 5mim

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Sodium binding site 2 out of 4 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:31.1
occ:1.00
O A:SER279 2.4 17.4 1.0
O A:HOH1121 2.5 33.8 1.0
O A:HOH1104 2.5 36.4 1.0
O A:HOH757 2.5 22.9 1.0
O A:GLY284 2.6 21.7 1.0
C A:SER279 3.5 20.7 1.0
C A:GLY284 3.6 20.2 1.0
CA A:GLY284 3.8 22.0 1.0
CA A:SER279 3.9 19.2 1.0
O A:HOH1090 4.1 28.8 1.0
O A:VAL278 4.3 14.3 1.0
O A:HOH1092 4.3 37.1 1.0
O A:HOH748 4.5 29.1 1.0
O A:HOH1129 4.6 35.7 1.0
N A:GLN280 4.7 21.3 1.0
CB A:SER279 4.8 17.0 1.0
N A:LEU285 4.8 16.0 1.0

Sodium binding site 3 out of 4 in 5mim

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Sodium binding site 3 out of 4 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:30.2
occ:0.50
O A:SER544 2.2 15.7 1.0
O A:HOH804 2.4 17.9 1.0
C A:SER544 3.2 13.8 1.0
N A:GLY545 3.9 15.8 1.0
CA A:GLY545 3.9 18.5 1.0
CB A:PRO508 4.0 17.0 1.0
OG A:SER544 4.0 23.5 1.0
CB A:SER544 4.1 18.4 1.0
CA A:SER544 4.1 16.3 1.0
N A:SER544 4.4 13.1 1.0
O A:ASP542 4.6 14.4 1.0
CG A:PRO508 4.8 16.2 1.0
OD1 A:ASP542 5.0 16.1 1.0

Sodium binding site 4 out of 4 in 5mim

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Sodium binding site 4 out of 4 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:33.1
occ:0.50
OE2 A:GLU546 2.5 31.6 1.0
O A:HOH1074 2.5 24.8 1.0
O A:HOH1089 2.5 28.5 1.0
CD A:GLU546 3.7 30.9 1.0
O A:HOH765 4.0 27.3 1.0
O A:HOH1156 4.2 25.2 1.0
O A:HOH725 4.3 20.6 1.0
O A:HOH1106 4.4 29.2 1.0
OE1 A:GLU546 4.4 29.3 1.0
O A:HOH906 4.5 22.4 1.0
CB A:GLU546 4.6 17.3 1.0
O A:HOH1072 4.7 40.4 1.0
CG A:GLU546 4.7 21.7 1.0

Reference:

S.O.Dahms, G.S.Jiao, M.E.Than. Structural Studies Revealed Active Site Distortions of Human Furin By A Small Molecule Inhibitor. Acs Chem. Biol. V. 12 1211 2017.
ISSN: ESSN 1554-8937
PubMed: 28402100
DOI: 10.1021/ACSCHEMBIO.6B01110
Page generated: Tue Dec 15 11:18:34 2020

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