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Potassium in PDB 5ftb: Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp

Enzymatic activity of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp

All present enzymatic activity of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp, PDB code: 5ftb was solved by W.-F.Chen, Y.-X.Dai, X.-L.Duan, N.-N.Liu, W.Shi, M.Li, S.-X.Dou, N.Li, Y.-H.Dong, S.Rety, X.-G.Xi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.038 / 1.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.238, 74.930, 107.729, 90.00, 90.00, 90.00
R / Rfree (%) 16.68 / 18.28

Other elements in 5ftb:

The structure of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp (pdb code 5ftb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 9 binding sites of Potassium where determined in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp, PDB code: 5ftb:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Potassium binding site 1 out of 9 in 5ftb

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Potassium binding site 1 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


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Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1432

b:24.7
occ:1.00
 O A:HOH2288 2.2 42.4 1.0
O A:HOH2054 2.3 41.0 1.0
O A:HOH2287 2.4 40.3 1.0
O A:GLY134 2.4 17.2 1.0
O A:HOH2053 2.4 25.9 1.0
O A:HOH2295 2.6 41.6 1.0
O A:HOH2052 2.7 33.1 1.0
C A:GLY134 3.5 16.0 1.0
O A:HOH2225 3.5 42.0 1.0
HA3 A:GLY134 3.8 19.7 1.0
HA2 A:GLY134 3.9 19.7 1.0
CA A:GLY134 4.0 16.4 1.0
HG2 A:GLU21 4.2 29.2 1.0
HA A:GLU21 4.3 20.3 1.0
OE2 A:GLU130 4.3 39.2 1.0
O A:ASP20 4.4 18.7 1.0
HA A:VAL135 4.6 17.5 1.0
O A:HOH2294 4.6 23.6 1.0
N A:VAL135 4.6 13.7 1.0
O A:HOH2058 4.7 30.8 1.0
O A:HOH2289 4.7 56.1 1.0
OD1 A:ASP20 4.8 28.1 1.0
H A:GLN136 4.8 15.7 1.0
HB2 A:GLN136 4.8 16.7 1.0
N A:GLN136 4.9 13.0 1.0
C A:VAL135 5.0 12.9 1.0
CA A:VAL135 5.0 14.6 1.0
CD A:GLU130 5.0 38.3 1.0

Potassium binding site 2 out of 9 in 5ftb

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Potassium binding site 2 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1433

b:58.2
occ:1.00
 HA A:MET4 3.1 32.8 1.0
HB3 A:ASP3 3.4 53.6 1.0
HB2 A:MET4 3.5 46.7 1.0
HG22 A:THR36 3.6 17.4 1.0
H2' A:ANP1434 3.7 37.0 1.0
CA A:MET4 3.8 27.3 1.0
N3 A:ANP1434 3.8 20.0 1.0
C4 A:ANP1434 3.8 16.7 1.0
N A:MET4 3.9 30.9 1.0
HG3 A:MET4 3.9 41.4 1.0
C2 A:ANP1434 4.0 20.4 1.0
C5 A:ANP1434 4.1 15.1 1.0
CB A:MET4 4.1 38.9 1.0
C A:ASP3 4.2 28.4 1.0
HB2 A:ASP3 4.2 53.6 1.0
CB A:ASP3 4.2 44.6 1.0
H A:MET4 4.2 37.0 1.0
N1 A:ANP1434 4.2 19.4 1.0
C6 A:ANP1434 4.2 16.2 1.0
N9 A:ANP1434 4.3 16.5 1.0
O A:ASP3 4.3 32.9 1.0
H2 A:ANP1434 4.4 24.4 1.0
CG2 A:THR36 4.4 14.5 1.0
HG21 A:THR36 4.4 17.4 1.0
CG A:MET4 4.5 34.5 1.0
C2' A:ANP1434 4.6 30.8 1.0
N7 A:ANP1434 4.7 15.1 1.0
C8 A:ANP1434 4.8 14.5 1.0
HG23 A:THR36 4.8 17.4 1.0
HG1 A:THR36 4.8 18.3 1.0
CA A:ASP3 4.9 35.7 1.0
H A:ILE5 4.9 22.8 1.0
C1' A:ANP1434 4.9 18.2 1.0
HB3 A:MET4 4.9 46.7 1.0

Potassium binding site 3 out of 9 in 5ftb

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Potassium binding site 3 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1436

b:53.6
occ:1.00
 H A:GLU9 2.6 13.9 1.0
HB A:THR7 2.7 15.7 1.0
HG3 A:GLU9 3.0 16.0 1.0
O A:HOH2008 3.1 36.6 1.0
HB2 A:GLU8 3.1 18.5 1.0
H A:GLU8 3.1 16.8 1.0
O A:HOH2014 3.3 28.1 1.0
N A:GLU9 3.4 11.6 1.0
CD A:GLU9 3.4 13.4 1.0
OE1 A:GLU9 3.5 12.3 1.0
HB2 A:GLU9 3.5 14.5 1.0
CG A:GLU9 3.5 13.3 1.0
CB A:THR7 3.6 13.0 1.0
N A:GLU8 3.6 14.0 1.0
HG1 A:THR7 3.7 14.9 1.0
O A:HOH2011 3.8 15.4 1.0
OG1 A:THR7 3.9 12.4 1.0
CB A:GLU8 3.9 15.4 1.0
CB A:GLU9 3.9 12.1 1.0
OE2 A:GLU9 4.0 14.8 1.0
O A:HOH2017 4.1 46.3 1.0
CA A:GLU8 4.1 13.3 1.0
O A:HOH2025 4.2 38.6 1.0
C A:GLU8 4.2 12.0 1.0
CA A:GLU9 4.3 11.4 1.0
C A:THR7 4.3 12.6 1.0
HG22 A:THR7 4.3 18.3 1.0
HB2 A:LYS185 4.4 17.7 1.0
HG2 A:GLU9 4.4 16.0 1.0
CA A:THR7 4.5 12.7 1.0
CG2 A:THR7 4.5 15.3 1.0
HB3 A:GLU8 4.5 18.5 1.0
HG1 A:THR184 4.5 17.6 1.0
HA A:THR7 4.6 15.3 1.0
HG23 A:THR7 4.7 18.3 1.0
HG3 A:GLU8 4.7 40.8 1.0
HA A:GLU9 4.8 13.7 1.0
HB3 A:GLU9 4.8 14.5 1.0
CG A:GLU8 4.9 34.0 1.0
H A:MET10 4.9 13.7 1.0
H A:LYS185 5.0 17.2 1.0

Potassium binding site 4 out of 9 in 5ftb

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Potassium binding site 4 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1437

b:60.3
occ:1.00
 H A:HIS236 2.3 17.2 1.0
HB3 A:CYS234 2.5 16.4 1.0
H A:THR235 2.7 17.4 1.0
OD2 A:ASP239 2.7 24.6 1.0
HG1 A:THR235 2.8 29.2 1.0
OG1 A:THR235 3.0 24.4 1.0
O A:HOH2448 3.0 23.8 1.0
HB2 A:HIS236 3.1 21.1 1.0
O A:HOH2452 3.1 49.1 1.0
N A:HIS236 3.1 14.3 1.0
HB2 A:ASP239 3.2 19.8 1.0
N A:THR235 3.2 14.5 1.0
CB A:CYS234 3.4 13.7 1.0
CG A:ASP239 3.6 19.6 1.0
ND1 A:HIS236 3.6 34.4 1.0
CB A:ASP239 3.7 16.5 1.0
CB A:HIS236 3.8 17.6 1.0
HB2 A:CYS234 3.8 16.4 1.0
CA A:THR235 3.9 13.9 1.0
C A:CYS234 3.9 12.9 1.0
HA A:CYS234 3.9 15.5 1.0
HB3 A:ASP239 3.9 19.8 1.0
C A:THR235 3.9 14.6 1.0
CA A:HIS236 4.0 15.7 1.0
CB A:THR235 4.0 16.8 1.0
CA A:CYS234 4.0 12.9 1.0
CG A:HIS236 4.1 26.7 1.0
O A:HOH2647 4.2 47.9 1.0
O A:HIS236 4.3 16.3 1.0
HG21 A:THR235 4.4 19.2 1.0
SG A:CYS234 4.5 17.4 1.0
HG A:CYS234 4.6 20.9 1.0
C A:HIS236 4.6 16.2 1.0
HB3 A:HIS236 4.6 21.1 1.0
CE1 A:HIS236 4.7 31.6 1.0
HB A:THR235 4.7 20.2 1.0
CG2 A:THR235 4.8 16.0 1.0
HA A:THR235 4.8 16.7 1.0
HA A:HIS236 4.8 18.9 1.0
OD1 A:ASP239 4.8 31.8 1.0
O A:CYS234 4.9 13.4 1.0
HB2 A:HIS374 4.9 22.3 1.0
H A:ASP239 4.9 21.5 1.0

Potassium binding site 5 out of 9 in 5ftb

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Potassium binding site 5 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1438

b:48.6
occ:1.00
 O A:HOH2039 2.9 13.9 1.0
HA A:GLN11 3.1 14.9 1.0
HB2 A:MET14 3.1 15.3 1.0
HG2 A:GLN11 3.2 16.2 1.0
HG3 A:MET14 3.5 16.8 1.0
HB3 A:MET14 3.8 15.3 1.0
CB A:MET14 3.8 12.7 1.0
HD11 A:LEU6 3.9 30.5 1.0
CA A:GLN11 4.0 12.4 1.0
CG A:GLN11 4.0 13.5 1.0
CG A:MET14 4.1 14.0 1.0
HB3 A:GLN11 4.1 15.6 1.0
CB A:GLN11 4.3 13.0 1.0
HG2 A:MET14 4.3 16.8 1.0
HG3 A:GLN11 4.4 16.2 1.0
O A:GLN11 4.5 12.4 1.0
HH A:TYR40 4.6 32.0 1.0
OD1 A:ASN15 4.6 14.0 1.0
C A:GLN11 4.8 12.3 1.0
HD23 A:LEU6 4.8 31.0 1.0
CD1 A:LEU6 4.9 25.4 1.0
HB3 A:LEU6 4.9 19.4 1.0
N A:GLN11 4.9 12.4 1.0

Potassium binding site 6 out of 9 in 5ftb

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Potassium binding site 6 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1439

b:71.8
occ:1.00
 HB2 A:ASN203 2.5 21.0 1.0
O A:HOH2399 2.7 18.1 1.0
O A:HOH2398 2.9 39.1 1.0
HA A:ASN200 3.1 21.1 1.0
O A:ASN199 3.1 16.6 1.0
CB A:ASN203 3.2 17.5 1.0
HB2 A:GLN205 3.3 33.9 1.0
HB3 A:ASN203 3.3 21.0 1.0
OE1 A:GLN205 3.4 42.4 1.0
O A:HOH2079 3.4 17.4 1.0
CG A:ASN203 3.5 32.5 1.0
CD A:GLN205 3.5 46.3 1.0
OD1 A:ASN200 3.6 24.7 1.0
HD21 A:ASN203 3.7 31.1 1.0
ND2 A:ASN203 3.7 25.9 1.0
NE2 A:GLN205 3.8 47.9 1.0
HG3 A:GLN205 3.9 33.8 1.0
C A:ASN199 3.9 14.3 1.0
HE22 A:GLN205 4.0 57.5 1.0
CA A:ASN200 4.0 17.5 1.0
CG A:GLN205 4.0 28.2 1.0
OD1 A:ASN203 4.1 25.8 1.0
CB A:GLN205 4.1 28.3 1.0
O A:HOH2078 4.2 42.8 1.0
HD22 A:ASN203 4.2 31.1 1.0
HE21 A:GLN205 4.3 57.5 1.0
H A:ASN203 4.3 19.7 1.0
N A:ASN200 4.3 14.9 1.0
HB3 A:ASN199 4.4 17.9 1.0
HB3 A:GLN205 4.5 33.9 1.0
CA A:ASN203 4.6 25.1 1.0
O A:ASN200 4.6 17.7 1.0
H A:GLN205 4.6 27.4 1.0
CG A:ASN200 4.7 24.6 1.0
C A:ASN200 4.7 17.2 1.0
N A:ASN203 4.8 16.4 1.0
CB A:ASN200 4.9 17.9 1.0
HG2 A:GLN205 5.0 33.8 1.0

Potassium binding site 7 out of 9 in 5ftb

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Potassium binding site 7 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1440

b:67.0
occ:1.00
 HZ3 A:LYS174 2.4 57.3 1.0
O A:PHE168 2.8 12.1 1.0
HA A:ASN169 2.8 14.3 1.0
O A:HOH2354 3.0 22.5 1.0
NZ A:LYS174 3.1 47.7 1.0
HZ2 A:LYS174 3.3 57.3 1.0
HB2 A:PHE173 3.3 17.0 1.0
HE2 A:TYR428 3.4 19.5 1.0
O A:ALA170 3.4 13.7 1.0
HZ1 A:LYS174 3.4 57.3 1.0
O A:HOH2706 3.5 49.9 1.0
CA A:ASN169 3.6 12.0 1.0
C A:ASN169 3.6 12.2 1.0
OH A:TYR428 3.7 33.9 1.0
O A:ASN169 3.7 13.7 1.0
C A:PHE168 3.9 10.9 1.0
CE2 A:TYR428 4.1 16.3 1.0
N A:ALA170 4.1 12.3 1.0
N A:ASN169 4.2 11.6 1.0
HD2 A:PHE173 4.2 16.1 1.0
HD21 A:ASN169 4.2 16.8 1.0
CB A:PHE173 4.2 14.1 1.0
C A:ALA170 4.2 12.2 1.0
HH A:TYR428 4.3 40.6 1.0
CE A:LYS174 4.4 49.2 1.0
HD3 A:LYS174 4.4 48.3 1.0
HB3 A:PHE173 4.4 17.0 1.0
CZ A:TYR428 4.4 19.1 1.0
H A:ALA170 4.4 14.8 1.0
HE3 A:LYS174 4.5 59.0 1.0
O A:HOH2346 4.5 20.9 1.0
HG2 A:LYS174 4.6 26.1 1.0
HA A:LEU171 4.7 16.0 1.0
H A:PHE173 4.7 15.8 1.0
HD1 A:PHE168 4.7 13.7 1.0
CB A:ASN169 4.8 12.8 1.0
HB3 A:ASN169 4.8 15.4 1.0
CD A:LYS174 4.8 40.2 1.0
CA A:ALA170 4.8 13.2 1.0
ND2 A:ASN169 4.9 14.0 1.0
C A:PHE173 4.9 13.4 1.0
CD2 A:PHE173 5.0 13.4 1.0
CA A:PHE173 5.0 13.4 1.0

Potassium binding site 8 out of 9 in 5ftb

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Potassium binding site 8 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1441

b:75.0
occ:1.00
 HH22 A:ARG324 2.8 24.8 1.0
HA A:ASP307 3.0 23.3 1.0
O A:ASP307 3.1 18.6 1.0
HH21 A:ARG254 3.1 51.7 1.0
O A:HOH2484 3.3 29.1 1.0
HE1 A:TYR256 3.5 17.6 1.0
HD1 A:TYR256 3.5 16.6 1.0
O A:HOH2575 3.6 42.9 1.0
NH2 A:ARG324 3.6 20.7 1.0
HB3 A:ASP307 3.6 28.6 1.0
CA A:ASP307 3.7 19.4 1.0
HH22 A:ARG254 3.8 51.7 1.0
NH2 A:ARG254 3.8 43.1 1.0
C A:ASP307 3.8 17.4 1.0
HH21 A:ARG324 3.9 24.8 1.0
CE1 A:TYR256 4.0 14.7 1.0
CD1 A:TYR256 4.0 13.8 1.0
CB A:ASP307 4.0 23.8 1.0
OD1 A:ASP307 4.2 28.8 1.0
HH12 A:ARG324 4.3 23.3 1.0
O A:HOH2489 4.3 26.8 1.0
CG A:ASP307 4.3 27.2 1.0
O A:HOH2255 4.5 54.7 1.0
CZ A:ARG324 4.7 18.4 1.0
NH1 A:ARG324 4.8 19.4 1.0
N A:ASP307 5.0 17.9 1.0
HB2 A:ASP307 5.0 28.6 1.0

Potassium binding site 9 out of 9 in 5ftb

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Potassium binding site 9 out of 9 in the Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Crystal Structure of PIF1 Helicase From Bacteroides in Complex with Amppnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K1442

b:26.8
occ:1.00
 H A:LEU143 2.1 12.6 1.0
O A:HOH2321 2.7 21.6 1.0
HA A:ASP142 2.8 13.1 1.0
OG1 A:THR27 2.8 12.5 1.0
HZ A:PHE25 2.8 14.2 1.0
HB2 A:LEU143 2.9 12.9 1.0
N A:LEU143 2.9 10.5 1.0
HD13 A:LEU143 3.0 14.1 1.0
HG1 A:THR27 3.0 15.0 1.0
HG22 A:THR27 3.3 14.7 1.0
HG A:LEU143 3.4 12.5 1.0
HB A:THR27 3.5 13.6 1.0
CB A:LEU143 3.5 10.7 1.0
HE2 A:PHE25 3.6 12.8 1.0
CZ A:PHE25 3.6 11.8 1.0
CB A:THR27 3.6 11.3 1.0
CA A:ASP142 3.6 10.9 1.0
HD2 A:PHE144 3.7 21.2 1.0
C A:ASP142 3.7 10.6 1.0
H A:PHE144 3.7 13.5 1.0
CG A:LEU143 3.7 10.4 1.0
CD1 A:LEU143 3.8 11.7 1.0
CA A:LEU143 3.8 10.8 1.0
OD1 A:ASP142 3.8 17.3 1.0
CG2 A:THR27 3.9 12.2 1.0
HH22 A:ARG202 3.9 15.0 1.0
CE2 A:PHE25 4.0 10.6 1.0
HH21 A:ARG202 4.0 15.0 1.0
O A:GLY141 4.2 12.9 1.0
NH2 A:ARG202 4.3 12.5 1.0
O A:HOH2368 4.3 24.1 1.0
CD2 A:PHE144 4.3 17.6 1.0
HG21 A:THR27 4.3 14.7 1.0
HD12 A:LEU143 4.3 14.1 1.0
N A:PHE144 4.4 11.2 1.0
HE2 A:PHE144 4.4 23.4 1.0
HB3 A:LEU143 4.4 12.9 1.0
HD11 A:LEU143 4.4 14.1 1.0
N A:ASP142 4.4 10.3 1.0
O A:HOH2684 4.5 24.7 1.0
CG A:ASP142 4.5 12.5 1.0
HA A:LEU143 4.6 13.0 1.0
C A:GLY141 4.6 10.5 1.0
C A:LEU143 4.6 11.3 1.0
O A:HOH2679 4.7 23.2 1.0
CB A:ASP142 4.7 12.4 1.0
HG23 A:THR27 4.7 14.7 1.0
CE2 A:PHE144 4.7 19.5 1.0
H A:GLY28 4.7 12.0 1.0
CE1 A:PHE25 4.7 11.6 1.0
HE2 A:PHE417 4.8 15.2 1.0
HB3 A:SER108 4.9 15.8 1.0
HE1 A:PHE25 4.9 14.0 1.0
O A:ASP142 4.9 11.0 1.0

Reference:

W.-F.Chen, Y.-X.Dai, X.-L.Duan, N.-N.Liu, W.Shi, N.Li, M.Li, S.-X.Dou, Y.-H.Dong, S.Rety, X.-G.Xi. Crystal Structures of the BSPIF1 Helicase Reveal That A Major Movement of the 2B SH3 Domain Is Required For Dna Unwinding Nucleic Acids Res. V. 44 2949 2016.
ISSN: ISSN 0305-1048
PubMed: 26809678
DOI: 10.1093/NAR/GKW033
Page generated: Mon Aug 12 13:35:17 2024

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