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Chlorine in PDB 6xi7: Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)

Enzymatic activity of Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)

All present enzymatic activity of Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I):
2.7.11.1; 3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I), PDB code: 6xi7 was solved by A.H.Chan, T.H.Tran, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.95 / 1.95
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.89, 91.89, 154.11, 90, 90, 120
R / Rfree (%) 20.4 / 23.2

Other elements in 6xi7:

The structure of Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) also contains other interesting chemical elements:

Zinc (Zn) 3 atoms
Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) (pdb code 6xi7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I), PDB code: 6xi7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 6xi7

Go back to Chlorine Binding Sites List in 6xi7
Chlorine binding site 1 out of 5 in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl205

b:93.6
occ:1.00
 OD1 A:ASP126 3.0 51.4 0.4
N A:THR127 3.1 50.4 1.0
CG A:ASP126 3.3 52.7 0.4
OD2 A:ASP126 3.6 54.7 0.1
CA A:ASP126 3.7 50.0 1.0
CG2 A:THR127 3.8 50.2 1.0
CD A:ARG123 3.8 59.7 1.0
C A:ASP126 3.9 48.1 1.0
CB A:THR127 4.0 54.0 1.0
CB A:ASP126 4.0 48.6 1.0
NH1 A:ARG123 4.0 58.9 1.0
NE A:ARG123 4.2 61.3 1.0
CA A:THR127 4.2 52.7 1.0
CZ A:ARG123 4.3 59.8 1.0
N A:ASP126 5.0 47.6 1.0
O A:VAL125 5.0 38.6 1.0

Chlorine binding site 2 out of 5 in 6xi7

Go back to Chlorine Binding Sites List in 6xi7
Chlorine binding site 2 out of 5 in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl206

b:88.4
occ:1.00
 O A:HOH318 3.1 47.2 1.0
NZ A:LYS167 3.5 54.0 1.0
CE A:LYS167 3.6 59.5 1.0
NZ A:LYS104 4.1 49.7 1.0
CG A:GLU76 4.6 45.7 1.0
CA A:GLU76 4.7 42.2 1.0
O A:GLY75 4.8 46.0 1.0
CD A:LYS167 4.8 56.1 1.0
CB A:GLU76 4.8 43.2 1.0
CE1 A:HIS166 4.9 49.6 1.0
CE A:LYS104 5.0 49.1 1.0

Chlorine binding site 3 out of 5 in 6xi7

Go back to Chlorine Binding Sites List in 6xi7
Chlorine binding site 3 out of 5 in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl207

b:62.3
occ:1.00
 O A:HOH331 3.0 47.7 1.0
O A:HOH335 3.0 47.9 1.0
N A:ASP154 3.0 39.0 1.0
CB A:ASP153 3.3 42.2 1.0
N A:ASP153 3.4 40.8 1.0
CA A:GLY151 3.4 35.8 1.0
C A:GLY151 3.5 36.3 1.0
N A:GLY151 3.5 34.9 1.0
CA A:ASP153 3.7 41.8 1.0
N A:VAL152 3.7 38.9 1.0
CB A:ASP154 3.7 41.1 1.0
C A:ASP153 3.8 40.5 1.0
CA A:ASP154 4.0 38.8 1.0
O A:GLY151 4.0 37.2 1.0
C A:VAL152 4.2 39.2 1.0
CG A:ASP153 4.5 47.1 1.0
CG A:ASP154 4.6 43.4 0.4
CA A:VAL152 4.6 39.7 1.0
O A:ARG149 4.6 42.0 1.0
OD2 A:ASP154 4.6 46.5 0.8
C A:GLN150 4.8 38.5 1.0
O A:HOH337 4.8 64.1 1.0
O A:HOH353 4.9 51.1 1.0
O A:ASP153 5.0 38.2 1.0

Chlorine binding site 4 out of 5 in 6xi7

Go back to Chlorine Binding Sites List in 6xi7
Chlorine binding site 4 out of 5 in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl203

b:93.7
occ:1.00
 O B:HOH310 3.2 76.8 1.0
N B:LYS148 3.3 80.8 1.0
N B:LEU147 3.4 70.4 1.0
NZ B:LYS148 3.5 94.8 1.0
CB B:LYS148 3.8 86.3 1.0
CE B:LYS148 4.0 95.3 1.0
CA B:PHE146 4.0 64.1 1.0
CA B:LYS148 4.1 84.3 1.0
C B:PHE146 4.1 67.4 1.0
CA B:LEU147 4.2 74.1 1.0
C B:LEU147 4.2 76.6 1.0
CB B:PHE146 4.2 62.2 1.0
CG B:LYS148 4.3 93.9 1.0
O B:LYS148 4.4 74.0 1.0
CD2 B:PHE146 4.4 60.0 1.0
CE B:LYS144 4.4 63.8 1.0
NZ B:LYS144 4.4 71.7 1.0
CB B:LEU147 4.5 74.6 1.0
C B:LYS148 4.6 80.0 1.0
CD1 B:LEU147 4.6 71.3 1.0
CD B:LYS148 4.8 98.0 1.0
CG B:PHE146 4.8 60.2 1.0

Chlorine binding site 5 out of 5 in 6xi7

Go back to Chlorine Binding Sites List in 6xi7
Chlorine binding site 5 out of 5 in the Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl204

b:90.0
occ:1.00
 CE2 B:TYR170 3.7 67.8 1.0
CZ B:TYR170 3.9 67.1 1.0
CD2 B:TYR170 4.0 66.1 1.0
OH B:TYR170 4.3 69.5 1.0
OD2 B:ASP153 4.3 63.9 1.0
CE1 B:TYR170 4.3 65.3 1.0
CG B:TYR170 4.4 64.7 1.0
CD1 B:TYR170 4.5 63.8 1.0
CG B:ASP153 4.6 63.6 1.0
CB B:ASP153 4.8 61.8 1.0

Reference:

T.H.Tran, A.H.Chan, S.Dharmaiah, D.K.Simanshu. Crystal Structure of Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form I) Nat Commun 2020.
ISSN: ESSN 2041-1723
Page generated: Mon Jul 29 17:15:16 2024

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