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Chlorine in PDB 6xfp: Crystal Structure of Braf Kinase Domain Bound to Belvarafenib

Protein crystallography data

The structure of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib, PDB code: 6xfp was solved by J.Yin, J.Sudhamsu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.78 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 48.793, 119.563, 103.934, 90, 90, 90
R / Rfree (%) 20.4 / 25.7

Other elements in 6xfp:

The structure of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib also contains other interesting chemical elements:

Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib (pdb code 6xfp). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib, PDB code: 6xfp:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 1 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl801

b:40.1
occ:1.00
 CL33 A:V1Y801 0.0 40.1 1.0
C30 A:V1Y801 1.7 36.6 1.0
C31 A:V1Y801 2.7 32.3 1.0
C29 A:V1Y801 2.7 30.8 1.0
F32 A:V1Y801 2.9 28.4 1.0
CA A:GLY593 3.7 27.6 1.0
O A:ILE592 3.9 22.3 1.0
C26 A:V1Y801 4.0 32.8 1.0
C28 A:V1Y801 4.0 33.8 1.0
CG2 A:ILE513 4.1 21.9 1.0
C A:GLY593 4.2 31.2 1.0
C A:ILE592 4.3 26.5 1.0
N A:GLY593 4.3 24.0 1.0
CD2 A:HIS574 4.5 33.8 1.0
CG2 A:ILE592 4.5 23.9 1.0
CD1 A:LEU567 4.5 28.8 1.0
C27 A:V1Y801 4.5 28.0 1.0
NE2 A:HIS574 4.5 34.6 1.0
N A:ASP594 4.5 31.4 1.0
CD2 A:LEU567 4.7 23.1 1.0
O A:GLY593 4.8 30.6 1.0
CD2 A:LEU505 4.8 36.9 1.0

Chlorine binding site 2 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 2 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl802

b:52.4
occ:1.00
 CG A:LYS551 3.8 43.3 1.0
CE A:LYS551 3.9 53.4 1.0
CE A:LYS552 4.0 60.9 1.0
CA A:LYS552 4.0 35.9 1.0
CB A:LYS552 4.2 43.7 1.0
N A:LYS552 4.2 40.9 1.0
CD A:LYS551 4.3 55.4 1.0
CB A:ASP555 4.3 30.2 1.0
O A:LYS551 4.3 34.6 1.0
C A:LYS551 4.4 34.8 1.0
NZ A:LYS552 4.5 53.4 1.0
OD2 A:ASP555 4.5 43.3 1.0
CG A:ASP555 4.6 44.1 1.0
CB A:LYS551 4.7 43.0 1.0
CG A:LYS552 4.8 39.1 1.0
CD A:LYS552 4.8 54.2 1.0
NZ A:LYS551 4.9 65.8 1.0
OE2 A:GLU549 5.0 78.5 1.0

Chlorine binding site 3 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 3 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl803

b:48.4
occ:1.00
 O A:HOH909 3.0 54.3 1.0
ND1 A:HIS608 3.6 55.9 1.0
CB A:SER605 4.1 47.6 1.0
CE1 A:HIS608 4.2 55.7 1.0
OG A:SER605 4.2 51.8 1.0
CZ A:PHE610 4.3 49.4 1.0
CE2 A:PHE610 4.5 49.1 1.0
CG A:HIS608 4.5 54.2 1.0
CB A:HIS608 4.9 44.2 1.0

Chlorine binding site 4 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 4 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl804

b:47.9
occ:0.50
 CZ2 A:TRP450 3.2 34.0 1.0
NE A:ARG509 3.6 25.4 1.0
NE1 A:TRP450 3.6 41.1 1.0
CE2 A:TRP450 3.6 36.4 1.0
NH2 A:ARG509 3.7 24.9 1.0
CZ A:ARG509 4.1 23.1 1.0
O A:ARG506 4.1 31.5 1.0
CH2 A:TRP450 4.2 31.6 1.0
CD A:ARG509 4.6 30.5 1.0
CD1 A:TRP450 4.8 41.1 1.0
CD2 A:TRP450 4.9 33.3 1.0
CG A:ARG506 5.0 51.0 1.0

Chlorine binding site 5 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 5 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl805

b:16.8
occ:1.00
 O A:HOH945 3.2 36.8 1.0
N A:ARG603 3.7 31.6 1.0
CB A:ARG603 4.0 31.3 1.0
NE2 A:GLN493 4.1 38.7 0.4
CG A:ARG603 4.2 33.8 1.0
CB A:SER602 4.3 40.4 1.0
CD1 A:PHE468 4.4 40.7 1.0
CA A:ARG603 4.4 31.4 1.0
CA A:SER602 4.5 36.5 1.0
C A:SER602 4.6 37.5 1.0
CD A:ARG603 4.6 32.2 1.0
CB A:PHE468 4.7 36.5 1.0
CD2 A:LEU485 4.7 54.8 1.0
CG A:GLN494 4.8 32.2 1.0
CB A:ALA497 4.8 29.7 1.0
NH1 A:ARG603 4.8 29.6 1.0
CG A:PHE468 4.9 40.8 1.0

Chlorine binding site 6 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 6 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl806

b:60.8
occ:1.00
 OE2 A:GLU715 2.7 58.3 1.0
O A:HOH983 3.2 43.9 1.0
CD A:GLU715 3.5 61.5 1.0
CD2 A:LEU711 3.6 27.9 1.0
CG A:GLU715 3.7 49.2 1.0
CG A:LEU711 3.8 33.5 1.0
NE A:ARG562 4.0 26.8 1.0
CD1 A:LEU711 4.1 27.6 1.0
NH2 A:ARG562 4.5 37.4 1.0
CG A:ARG562 4.5 23.9 1.0
OE1 A:GLU715 4.7 62.4 1.0
CZ A:ARG562 4.7 38.8 1.0
CD A:ARG562 4.8 26.5 1.0
CB A:GLU715 5.0 46.9 1.0

Chlorine binding site 7 out of 7 in 6xfp

Go back to Chlorine Binding Sites List in 6xfp
Chlorine binding site 7 out of 7 in the Crystal Structure of Braf Kinase Domain Bound to Belvarafenib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Braf Kinase Domain Bound to Belvarafenib within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl807

b:13.0
occ:1.00
 O A:HOH932 3.2 37.0 1.0
N A:TRP604 3.8 40.1 1.0
CD2 A:LEU597 3.9 35.9 1.0
CB A:ARG603 3.9 31.3 1.0
CD1 A:TRP604 4.0 42.0 1.0
CG A:ARG603 4.1 33.8 1.0
O A:ALA497 4.3 32.2 1.0
CB A:GLU501 4.3 33.9 1.0
CB A:TRP604 4.3 46.4 1.0
CD A:ARG603 4.4 32.2 1.0
N A:GLU501 4.4 29.9 1.0
CA A:ARG603 4.4 31.4 1.0
CA A:GLU501 4.5 27.3 1.0
CB A:ASN500 4.5 34.5 1.0
CG A:TRP604 4.6 46.5 1.0
C A:ARG603 4.6 42.3 1.0
CG A:LEU597 4.6 36.8 1.0
CA A:TRP604 4.7 44.3 1.0
CD1 A:LEU597 4.7 41.6 1.0
C A:ASN500 4.9 30.1 1.0
CG A:GLU501 4.9 29.8 1.0
NE A:ARG603 5.0 37.5 1.0

Reference:

J.Yin, J.Sudhamsu. Crystal Structure of Braf Kinase Domain Bound to Belvarafenib To Be Published.
Page generated: Mon Jul 29 17:10:31 2024

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