Bromine in PDB 6hpq: Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.

Enzymatic activity of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.

All present enzymatic activity of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.:
3.6.4.12;

Protein crystallography data

The structure of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form., PDB code: 6hpq was solved by V.M.Ledikov, S.Dehghani-Tafti, B.Bax, C.M.Sanders, A.A.Antson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.37 / 1.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 73.250, 76.820, 142.540, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.6

Other elements in 6hpq:

The structure of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. (pdb code 6hpq). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form., PDB code: 6hpq:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 6hpq

Go back to Bromine Binding Sites List in 6hpq
Bromine binding site 1 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br803

b:13.4
occ:1.00
 O A:HOH1194 3.3 18.6 1.0
O A:HOH1239 3.3 24.4 1.0
N A:CYS399 3.4 8.8 1.0
O A:GLY397 3.5 13.5 1.0
C A:GLY397 3.7 11.2 1.0
CB A:CYS399 3.7 10.1 1.0
SG A:CYS399 3.8 12.0 1.0
CB A:PRO598 4.0 13.8 1.0
N A:ARG398 4.0 10.9 1.0
CA A:CYS399 4.1 9.7 1.0
CA A:GLY397 4.1 11.0 1.0
C A:ARG398 4.4 9.5 1.0
CA A:ARG398 4.5 11.4 1.0
CG1 A:VAL601 4.6 15.6 1.0
O A:CYS399 4.6 9.6 1.0
O A:PRO598 4.6 11.4 1.0
CB A:VAL601 4.7 12.4 1.0
O A:VAL601 4.8 15.3 1.0
C A:CYS399 4.8 9.4 1.0
CA A:PRO598 4.9 10.3 1.0
O A:HOH1059 5.0 30.1 1.0
CG A:PRO598 5.0 14.4 1.0

Bromine binding site 2 out of 9 in 6hpq

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Bromine binding site 2 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br804

b:15.0
occ:0.30
 NH1 A:ARG571 1.7 37.4 0.5
OG A:SER568 2.7 15.5 1.0
N A:GLY570 2.8 11.1 1.0
NH2 A:ARG571 2.9 20.0 0.5
CZ A:ARG571 3.0 25.9 0.5
O A:SER568 3.3 10.8 1.0
CG A:ARG571 3.4 16.5 0.5
C A:SER568 3.4 10.7 1.0
CA A:GLY570 3.5 13.9 1.0
CB A:SER568 3.6 11.7 1.0
N A:ARG571 3.7 15.1 1.0
C A:GLY570 3.7 14.9 1.0
N A:LEU569 3.7 10.0 1.0
NH2 A:ARG571 3.7 21.3 0.5
CD A:ARG571 3.8 12.9 0.5
C A:LEU569 3.9 9.5 1.0
NE A:ARG571 3.9 26.5 0.5
CG A:ARG571 3.9 11.6 0.5
CZ A:ARG571 4.0 16.9 0.5
CB A:ARG571 4.0 14.4 0.5
CA A:LEU569 4.1 9.8 1.0
CA A:SER568 4.1 10.4 1.0
CD A:ARG571 4.1 19.5 0.5
NE A:ARG571 4.3 18.3 0.5
CB A:ARG571 4.4 12.2 0.5
CA A:ARG571 4.4 13.8 0.5
O A:GLY570 4.5 19.6 1.0
CA A:ARG571 4.7 13.4 0.5
O A:HOH948 4.7 22.8 1.0
CE1 A:PHE573 4.9 25.0 1.0

Bromine binding site 3 out of 9 in 6hpq

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Bromine binding site 3 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br805

b:17.8
occ:0.30
 NE2 A:GLN429 2.8 16.4 1.0
O A:HOH1463 2.8 25.6 1.0
N A:SER553 2.9 9.3 1.0
CG A:LYS556 3.4 28.1 1.0
OG A:SER553 3.6 16.6 1.0
CA A:MET552 3.7 10.1 1.0
CB A:LYS556 3.7 17.4 1.0
CB A:SER553 3.7 12.9 1.0
CG1 A:VAL432 3.7 13.5 1.0
C A:MET552 3.7 9.4 1.0
O A:HOH1184 3.8 22.1 1.0
CD A:GLN429 3.8 18.3 1.0
CG A:MET552 3.8 16.3 1.0
CA A:SER553 3.9 9.7 1.0
CE A:LYS556 4.0 37.1 1.0
OE1 A:GLN429 4.1 21.9 1.0
CG2 A:VAL432 4.2 13.0 1.0
CD A:LYS556 4.3 36.7 1.0
CB A:MET552 4.3 13.2 1.0
CB A:VAL432 4.4 13.0 1.0
O A:HOH1032 4.4 15.8 1.0
NZ A:LYS556 4.5 56.5 1.0
O A:SER553 4.7 10.7 1.0
O A:HOH1276 4.7 60.3 1.0
C A:SER553 4.8 11.1 1.0
N A:MET552 4.8 10.0 1.0
O A:MET552 5.0 11.1 1.0

Bromine binding site 4 out of 9 in 6hpq

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Bromine binding site 4 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br806

b:48.2
occ:1.00
 O A:LYS414 1.8 31.4 0.5
O A:HOH1211 2.7 20.0 1.0
C A:LYS414 2.8 26.1 0.5
N A:GLY416 3.3 26.6 1.0
NH2 A:ARG592 3.5 22.2 1.0
CA A:LYS414 3.6 25.6 0.5
CA A:LYS414 3.8 26.5 0.5
C A:LYS414 3.8 26.4 0.5
N A:VAL415 3.9 26.6 1.0
CA A:GLY416 3.9 25.3 1.0
C A:VAL415 4.2 28.4 1.0
CB A:LYS414 4.2 29.3 0.5
O A:HOH1114 4.3 29.5 1.0
CB A:LYS414 4.3 31.0 0.5
CA A:VAL415 4.4 24.2 0.5
CG2 A:VAL415 4.4 20.9 0.5
CA A:VAL415 4.4 23.1 0.5
CZ A:ARG592 4.5 18.2 1.0
CB A:VAL415 4.5 25.6 0.5
NH1 A:ARG592 4.5 18.4 1.0
O A:LYS414 4.7 36.6 0.5
O A:HIS413 4.8 19.9 1.0
CG A:LYS414 4.9 39.0 0.5
C A:GLY416 4.9 23.9 1.0
N A:LYS414 5.0 22.4 0.5
CB A:VAL415 5.0 21.5 0.5

Bromine binding site 5 out of 9 in 6hpq

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Bromine binding site 5 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br807

b:60.6
occ:1.00
 NZ A:LYS220 2.9 13.1 1.0
O A:HOH1406 3.2 29.1 1.0
NH2 A:ARG216 3.5 21.9 1.0
CD A:LYS220 3.6 11.0 1.0
CE A:LYS220 3.8 12.0 1.0
CG A:LYS220 4.0 11.0 1.0
CZ A:ARG216 4.3 17.4 1.0
O A:HOH1198 4.6 47.0 1.0
NE A:ARG216 4.6 19.2 1.0
O A:HOH1183 4.8 18.6 1.0

Bromine binding site 6 out of 9 in 6hpq

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Bromine binding site 6 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br803

b:13.4
occ:1.00
 N B:CYS399 3.4 9.6 1.0
O B:GLY397 3.5 13.8 1.0
CB B:CYS399 3.7 10.7 1.0
C B:GLY397 3.7 10.7 1.0
SG B:CYS399 3.8 12.4 1.0
CB B:PRO598 4.0 13.6 1.0
N B:ARG398 4.0 10.3 1.0
CA B:CYS399 4.1 10.2 1.0
CA B:GLY397 4.2 9.9 1.0
O B:HOH906 4.2 32.3 1.0
C B:ARG398 4.4 9.7 1.0
CA B:ARG398 4.5 11.1 1.0
CG1 B:VAL601 4.5 14.0 1.0
O B:PRO598 4.6 12.1 1.0
O B:CYS399 4.6 10.5 1.0
CB B:VAL601 4.7 11.7 1.0
O B:VAL601 4.8 15.1 1.0
C B:CYS399 4.8 9.3 1.0
CA B:PRO598 4.9 9.8 1.0
CG B:PRO598 5.0 13.8 1.0

Bromine binding site 7 out of 9 in 6hpq

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Bromine binding site 7 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br804

b:15.2
occ:0.30
 NH1 B:ARG571 2.0 54.6 1.0
OG B:SER568 2.7 14.4 1.0
N B:GLY570 2.9 11.7 1.0
CZ B:ARG571 2.9 31.1 1.0
O B:SER568 3.3 11.0 1.0
C B:SER568 3.4 9.6 1.0
CA B:GLY570 3.5 14.1 1.0
CG B:ARG571 3.5 21.4 1.0
CB B:SER568 3.6 11.9 1.0
NH2 B:ARG571 3.7 33.7 1.0
N B:ARG571 3.7 17.3 1.0
C B:GLY570 3.7 14.7 1.0
N B:LEU569 3.7 10.1 1.0
NE B:ARG571 3.8 30.6 1.0
C B:LEU569 3.9 9.4 1.0
CA B:SER568 4.1 10.8 1.0
CA B:LEU569 4.1 9.7 1.0
CD B:ARG571 4.1 20.4 1.0
CB B:ARG571 4.1 18.7 1.0
CA B:ARG571 4.4 18.3 1.0
O B:GLY570 4.5 19.5 1.0
O B:HOH958 4.7 22.8 1.0
CE1 B:PHE573 4.8 24.5 1.0

Bromine binding site 8 out of 9 in 6hpq

Go back to Bromine Binding Sites List in 6hpq
Bromine binding site 8 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br805

b:40.4
occ:1.00
 O B:HOH958 3.2 22.8 1.0
O B:HOH1436 3.7 45.1 1.0
OD2 B:ASP595 4.8 18.4 1.0
OG B:SER568 4.8 14.4 1.0

Bromine binding site 9 out of 9 in 6hpq

Go back to Bromine Binding Sites List in 6hpq
Bromine binding site 9 out of 9 in the Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form.


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of Crystal Structure of Human PIF1 Helicase in Complex with Amp-Pnp, Brominated Crystal Form. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br806

b:39.7
occ:1.00
 OE1 B:GLN283 2.4 36.6 1.0
O B:HOH1312 2.8 32.1 1.0
NE2 B:GLN283 2.9 46.9 1.0
CD B:GLN283 2.9 29.5 1.0
CB B:PRO280 3.7 12.3 1.0
CG B:PRO280 3.9 13.6 1.0
CB B:ALA282 4.0 21.4 1.0
CG B:GLN283 4.4 24.4 1.0
N B:GLN283 4.5 15.3 1.0
CA B:ALA282 4.8 16.7 1.0
CD B:PRO280 4.9 13.3 1.0
C B:ALA282 5.0 14.6 1.0
CB B:GLN283 5.0 18.9 1.0
N B:ALA282 5.0 14.2 1.0

Reference:

S.Dehghani-Tafti, V.Levdikov, A.A.Antson, B.Bax, C.M.Sanders. Structural and Functional Analysis of the Nucleotide and Dna Binding Activities of the Human PIF1 Helicase. Nucleic Acids Res. V. 47 3208 2019.
ISSN: ESSN 1362-4962
PubMed: 30698796
DOI: 10.1093/NAR/GKZ028
Page generated: Sat Dec 12 02:34:06 2020

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