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Manganese in PDB 3kqu: Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism

Enzymatic activity of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism

All present enzymatic activity of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism:
3.4.21.98; 3.6.1.15;

Protein crystallography data

The structure of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism, PDB code: 3kqu was solved by M.Gu, C.M.Rice, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 116.534, 116.467, 71.114, 90.00, 90.00, 119.97
R / Rfree (%) 19.7 / 21.5

Other elements in 3kqu:

The structure of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism (pdb code 3kqu). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism, PDB code: 3kqu:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3kqu

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Manganese binding site 1 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn3

b:25.9
occ:1.00
 O A:HOH4 2.0 20.0 1.0
O A:HOH628 2.1 19.2 1.0
F3 A:BEF1 2.1 24.0 1.0
O3B A:ADP2 2.1 23.4 1.0
OG A:SER211 2.2 27.3 1.0
OE1 A:GLU291 2.4 36.8 1.0
CB A:SER211 3.2 30.8 1.0
PB A:ADP2 3.4 26.3 1.0
CD A:GLU291 3.4 37.3 1.0
BE A:BEF1 3.4 25.9 1.0
O2B A:ADP2 3.5 29.0 1.0
OD1 A:ASP290 3.6 31.9 1.0
OE2 A:GLU291 3.7 38.9 1.0
OD2 A:ASP290 3.8 30.4 1.0
CG A:ASP290 4.1 30.0 1.0
O2A A:ADP2 4.1 31.6 1.0
N A:SER211 4.2 31.5 1.0
O A:HOH626 4.3 16.0 1.0
O3A A:ADP2 4.3 25.9 1.0
CA A:SER211 4.3 31.9 1.0
F1 A:BEF1 4.3 27.7 1.0
CA A:GLY417 4.3 32.4 1.0
O1B A:ADP2 4.4 28.3 1.0
ND2 A:ASN229 4.5 32.2 1.0
F2 A:BEF1 4.6 28.4 1.0
PA A:ADP2 4.7 28.0 1.0
CE A:LYS210 4.8 24.1 1.0
CG A:GLU291 4.8 34.1 1.0
O A:GLY417 4.8 33.1 1.0
O1A A:ADP2 4.8 23.3 1.0
CZ A:PHE238 4.9 32.8 1.0
NZ A:LYS210 4.9 23.0 1.0
CB A:LYS210 4.9 31.0 1.0

Manganese binding site 2 out of 6 in 3kqu

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Manganese binding site 2 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn3

b:23.1
occ:1.00
 O B:HOH9 2.0 17.4 1.0
O B:HOH8 2.1 24.1 1.0
OG B:SER211 2.1 28.6 1.0
F3 B:BEF1 2.2 22.4 1.0
O3B B:ADP2 2.2 26.7 1.0
OE1 B:GLU291 2.4 36.5 1.0
CB B:SER211 3.2 29.8 1.0
CD B:GLU291 3.4 36.9 1.0
PB B:ADP2 3.4 26.1 1.0
BE B:BEF1 3.4 24.6 1.0
O2B B:ADP2 3.5 27.8 1.0
OD1 B:ASP290 3.5 35.7 1.0
OE2 B:GLU291 3.6 36.3 1.0
OD2 B:ASP290 3.8 31.9 1.0
CG B:ASP290 4.0 33.6 1.0
N B:SER211 4.1 30.8 1.0
O2A B:ADP2 4.2 30.7 1.0
CA B:SER211 4.3 31.2 1.0
F1 B:BEF1 4.3 25.2 1.0
O B:HOH6 4.3 12.5 1.0
O3A B:ADP2 4.3 28.7 1.0
CA B:GLY417 4.3 32.1 1.0
O1B B:ADP2 4.4 26.9 1.0
ND2 B:ASN229 4.5 31.7 1.0
F2 B:BEF1 4.7 28.8 1.0
PA B:ADP2 4.7 28.3 1.0
CG B:GLU291 4.7 34.4 1.0
CE B:LYS210 4.8 24.1 1.0
O B:GLY417 4.8 30.9 1.0
O1A B:ADP2 4.8 23.8 1.0
CZ B:PHE238 4.9 35.0 1.0
CB B:LYS210 4.9 30.8 1.0
NZ B:LYS210 4.9 20.9 1.0
C B:LYS210 5.0 31.4 1.0

Manganese binding site 3 out of 6 in 3kqu

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Manganese binding site 3 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn3

b:25.0
occ:1.00
 O C:HOH14 2.1 25.0 1.0
O C:HOH13 2.1 25.8 1.0
F3 C:BEF1 2.2 25.3 1.0
O3B C:ADP2 2.2 22.8 1.0
OG C:SER211 2.3 29.9 1.0
OE1 C:GLU291 2.3 35.0 1.0
CD C:GLU291 3.3 36.0 1.0
CB C:SER211 3.3 30.4 1.0
PB C:ADP2 3.4 28.1 1.0
BE C:BEF1 3.5 26.1 1.0
OE2 C:GLU291 3.6 37.6 1.0
O2B C:ADP2 3.6 29.0 1.0
OD1 C:ASP290 3.6 32.8 1.0
OD2 C:ASP290 3.9 31.1 1.0
CG C:ASP290 4.1 31.8 1.0
O2A C:ADP2 4.1 30.1 1.0
O C:HOH11 4.2 17.9 1.0
CA C:GLY417 4.2 31.2 1.0
N C:SER211 4.3 32.5 1.0
F1 C:BEF1 4.3 27.5 1.0
O3A C:ADP2 4.4 27.5 1.0
CA C:SER211 4.4 32.4 1.0
ND2 C:ASN229 4.4 32.4 1.0
O1B C:ADP2 4.5 25.0 1.0
CG C:GLU291 4.6 33.9 1.0
F2 C:BEF1 4.7 31.3 1.0
PA C:ADP2 4.7 28.2 1.0
O C:GLY417 4.7 31.8 1.0
CE C:LYS210 4.8 23.3 1.0
CZ C:PHE238 4.9 33.8 1.0
O1A C:ADP2 4.9 26.4 1.0
N C:GLY417 4.9 31.9 1.0
C C:GLY417 5.0 30.7 1.0

Manganese binding site 4 out of 6 in 3kqu

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Manganese binding site 4 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn3

b:24.8
occ:1.00
 O D:HOH19 2.0 18.7 1.0
F3 D:BEF1 2.2 23.3 1.0
O D:HOH18 2.2 20.1 1.0
OG D:SER211 2.2 29.8 1.0
O3B D:ADP2 2.2 23.9 1.0
OE1 D:GLU291 2.4 37.6 1.0
CB D:SER211 3.2 32.2 1.0
CD D:GLU291 3.3 37.7 1.0
PB D:ADP2 3.4 25.1 1.0
BE D:BEF1 3.5 24.4 1.0
O2B D:ADP2 3.5 30.0 1.0
OD1 D:ASP290 3.6 30.2 1.0
OE2 D:GLU291 3.6 38.2 1.0
OD2 D:ASP290 3.8 30.0 1.0
CG D:ASP290 4.0 29.7 1.0
O2A D:ADP2 4.2 30.5 1.0
N D:SER211 4.2 31.5 1.0
O D:HOH16 4.2 18.2 1.0
CA D:GLY417 4.3 32.0 1.0
F1 D:BEF1 4.3 26.1 1.0
CA D:SER211 4.3 31.7 1.0
O3A D:ADP2 4.4 26.2 1.0
ND2 D:ASN229 4.5 32.0 1.0
O1B D:ADP2 4.5 28.1 1.0
F2 D:BEF1 4.7 28.4 1.0
PA D:ADP2 4.7 27.0 1.0
CG D:GLU291 4.7 35.4 1.0
O D:GLY417 4.8 31.4 1.0
CE D:LYS210 4.8 22.1 1.0
O1A D:ADP2 4.8 24.5 1.0
CZ D:PHE238 4.9 33.3 1.0
NZ D:LYS210 5.0 20.0 1.0
CB D:LYS210 5.0 30.1 1.0
N D:GLY417 5.0 34.0 1.0
O D:HOH17 5.0 18.3 1.0

Manganese binding site 5 out of 6 in 3kqu

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Manganese binding site 5 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn3

b:23.7
occ:1.00
 O E:HOH24 2.0 16.4 1.0
O E:HOH23 2.1 16.4 1.0
F3 E:BEF1 2.2 23.9 1.0
O3B E:ADP2 2.2 25.7 1.0
OG E:SER211 2.2 30.3 1.0
OE1 E:GLU291 2.4 36.7 1.0
CB E:SER211 3.2 30.4 1.0
PB E:ADP2 3.4 26.6 1.0
CD E:GLU291 3.4 37.6 1.0
BE E:BEF1 3.4 23.9 1.0
O2B E:ADP2 3.5 27.2 1.0
OD1 E:ASP290 3.6 35.7 1.0
OE2 E:GLU291 3.7 38.2 1.0
OD2 E:ASP290 3.9 32.4 1.0
CG E:ASP290 4.1 33.7 1.0
O2A E:ADP2 4.1 31.9 1.0
N E:SER211 4.2 31.9 1.0
CA E:GLY417 4.3 31.4 1.0
F1 E:BEF1 4.3 25.2 1.0
O E:HOH21 4.3 13.4 1.0
O3A E:ADP2 4.3 26.3 1.0
CA E:SER211 4.3 31.7 1.0
O1B E:ADP2 4.4 24.4 1.0
ND2 E:ASN229 4.5 32.5 1.0
F2 E:BEF1 4.6 27.4 1.0
PA E:ADP2 4.6 29.6 1.0
O E:GLY417 4.7 30.1 1.0
CG E:GLU291 4.8 35.5 1.0
CE E:LYS210 4.8 24.4 1.0
O1A E:ADP2 4.8 23.2 1.0
CZ E:PHE238 4.9 34.9 1.0
NZ E:LYS210 4.9 22.1 1.0
NH2 E:ARG467 5.0 18.9 1.0
CB E:LYS210 5.0 30.8 1.0
N E:GLY417 5.0 32.4 1.0

Manganese binding site 6 out of 6 in 3kqu

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Manganese binding site 6 out of 6 in the Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn3

b:26.6
occ:1.00
 O F:HOH29 2.0 21.0 1.0
O3B F:ADP2 2.1 21.1 1.0
OG F:SER211 2.2 30.7 1.0
O F:HOH28 2.2 29.2 1.0
F3 F:BEF1 2.2 27.5 1.0
OE1 F:GLU291 2.4 38.1 1.0
CB F:SER211 3.2 32.5 1.0
PB F:ADP2 3.4 28.5 1.0
CD F:GLU291 3.4 37.6 1.0
BE F:BEF1 3.4 27.4 1.0
O2B F:ADP2 3.5 29.4 1.0
OD1 F:ASP290 3.6 34.0 1.0
OE2 F:GLU291 3.6 38.3 1.0
OD2 F:ASP290 3.8 30.3 1.0
CG F:ASP290 4.0 31.4 1.0
O2A F:ADP2 4.1 30.0 1.0
N F:SER211 4.2 32.7 1.0
O3A F:ADP2 4.3 26.6 1.0
CA F:SER211 4.3 32.0 1.0
O F:HOH26 4.3 15.3 1.0
F1 F:BEF1 4.3 30.6 1.0
CA F:GLY417 4.3 32.6 1.0
O1B F:ADP2 4.4 24.5 1.0
ND2 F:ASN229 4.5 30.8 1.0
F2 F:BEF1 4.7 33.1 1.0
PA F:ADP2 4.7 29.3 1.0
CE F:LYS210 4.7 24.5 1.0
CG F:GLU291 4.7 34.2 1.0
O1A F:ADP2 4.8 25.3 1.0
O F:GLY417 4.8 31.8 1.0
CZ F:PHE238 4.9 32.4 1.0
CB F:LYS210 4.9 31.3 1.0
NZ F:LYS210 4.9 23.0 1.0

Reference:

M.Gu, C.M.Rice. Inaugural Article: Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal A Ratchet Translocation Mechanism. Proc.Natl.Acad.Sci.Usa V. 107 521 2010.
ISSN: ISSN 0027-8424
PubMed: 20080715
DOI: 10.1073/PNAS.0913380107
Page generated: Sat Oct 5 16:46:05 2024

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