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Zinc in PDB 6xgv: Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

Enzymatic activity of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

All present enzymatic activity of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf:
2.7.11.1; 3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgv was solved by T.H.Tran, A.H.Chan, S.Dharmaiah, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.36 / 2.11
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.75, 132.75, 89.48, 90, 90, 120
R / Rfree (%) 18.4 / 20.4

Other elements in 6xgv:

The structure of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Arsenic (As) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (pdb code 6xgv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgv:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6xgv

Go back to Zinc Binding Sites List in 6xgv
Zinc binding site 1 out of 3 in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn203

b:68.9
occ:0.41
 NE2 A:HIS95 2.3 71.6 1.0
OD1 A:ASP92 2.8 65.7 1.0
CD2 A:HIS95 2.8 68.5 1.0
CE1 A:HIS95 3.6 65.8 1.0
CG A:ASP92 3.9 65.2 1.0
CG A:HIS95 4.1 69.3 1.0
ND1 A:HIS95 4.4 69.5 1.0
NZ A:LYS88 4.5 74.2 1.0
CA A:ASP92 4.6 55.9 1.0
OD2 A:ASP92 4.7 76.4 1.0
CB A:ASP92 4.9 56.1 1.0

Zinc binding site 2 out of 3 in 6xgv

Go back to Zinc Binding Sites List in 6xgv
Zinc binding site 2 out of 3 in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:40.2
occ:1.00
 ND1 B:HIS139 2.1 36.1 1.0
SG B:CYS168 2.3 39.9 1.0
SG B:CYS184 2.3 39.4 1.0
SG B:CYS165 2.3 37.8 1.0
CE1 B:HIS139 2.9 37.8 1.0
CB B:CYS184 3.1 38.5 1.0
CG B:HIS139 3.2 38.5 1.0
CB B:CYS168 3.2 38.8 1.0
CB B:CYS165 3.2 39.1 1.0
CB B:HIS139 3.6 38.1 1.0
N B:CYS168 3.7 39.4 1.0
CA B:HIS139 3.8 37.6 1.0
CA B:CYS184 4.0 41.6 1.0
CA B:CYS168 4.0 39.0 1.0
NE2 B:HIS139 4.1 36.4 1.0
O B:HOH346 4.2 38.2 1.0
CD2 B:HIS139 4.2 36.5 1.0
CB B:THR167 4.5 46.6 1.0
CA B:CYS165 4.7 39.1 1.0
N B:HIS139 4.7 38.3 1.0
C B:THR167 4.7 44.8 1.0
N B:ASN140 4.7 40.9 1.0
C B:CYS168 4.8 40.6 1.0
C B:HIS139 4.9 41.7 1.0
C B:CYS184 4.9 44.1 1.0
CA B:THR167 5.0 45.8 1.0

Zinc binding site 3 out of 3 in 6xgv

Go back to Zinc Binding Sites List in 6xgv
Zinc binding site 3 out of 3 in the Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Kras-G13D (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn205

b:46.0
occ:1.00
 ND1 B:HIS173 2.1 43.0 1.0
SG B:CYS176 2.3 47.2 1.0
SG B:CYS155 2.3 44.5 1.0
SG B:CYS152 2.4 42.0 1.0
CE1 B:HIS173 3.0 49.5 1.0
CB B:CYS152 3.1 39.2 1.0
CG B:HIS173 3.1 48.1 1.0
CB B:CYS155 3.4 44.9 1.0
CB B:CYS176 3.5 42.7 1.0
CB B:HIS173 3.5 44.5 1.0
N B:CYS155 3.7 40.5 1.0
N B:HIS173 3.9 42.3 1.0
CA B:CYS155 4.1 41.1 1.0
NE2 B:HIS173 4.2 48.7 1.0
CD2 B:HIS173 4.2 43.9 1.0
CE1 B:HIS175 4.3 55.4 1.0
CA B:HIS173 4.4 44.6 1.0
CB B:ILE154 4.4 39.6 1.0
CA B:CYS152 4.6 44.6 1.0
C B:ILE154 4.7 43.6 1.0
CA B:CYS176 4.8 45.1 1.0
C B:CYS155 4.8 48.0 1.0
CA B:ILE154 4.9 40.0 1.0
NE2 B:HIS175 4.9 60.8 1.0
ND1 B:HIS175 4.9 57.2 1.0
N B:ILE154 5.0 39.1 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: Tue Oct 29 10:56:03 2024

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