Zinc in PDB 6xha: Crystal Structure of Kras-G12V (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

Enzymatic activity of Crystal Structure of Kras-G12V (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-G12V (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-G12V (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xha 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) 48.30 / 2.87
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.1, 132.1, 90.17, 90, 90, 120
R / Rfree (%) 21.7 / 26.9

Other elements in 6xha:

The structure of Crystal Structure of Kras-G12V (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf also contains other interesting chemical elements:

Arsenic (As) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kras-G12V (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (pdb code 6xha). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Kras-G12V (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xha:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6xha

Go back to Zinc Binding Sites List in 6xha
Zinc binding site 1 out of 2 in the Crystal Structure of Kras-G12V (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-G12V (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:66.0
occ:1.00
 SG B:CYS184 2.4 71.2 1.0
SG B:CYS165 2.4 77.9 1.0
ND1 B:HIS139 2.4 60.4 1.0
SG B:CYS168 2.5 61.6 1.0
CB B:CYS184 3.2 50.6 1.0
CE1 B:HIS139 3.3 66.6 1.0
CB B:CYS168 3.4 67.6 1.0
CB B:CYS165 3.4 64.0 1.0
CG B:HIS139 3.5 71.1 1.0
N B:CYS168 3.7 68.7 1.0
CB B:HIS139 3.9 62.0 1.0
CA B:HIS139 3.9 51.3 1.0
CA B:CYS184 4.0 50.5 1.0
CA B:CYS168 4.2 63.7 1.0
CB B:THR167 4.3 70.8 1.0
NE2 B:HIS139 4.5 77.6 1.0
CD2 B:HIS139 4.6 74.1 1.0
C B:THR167 4.7 69.0 1.0
N B:HIS139 4.7 56.9 1.0
N B:ASN140 4.7 69.3 1.0
CA B:THR167 4.9 65.8 1.0
CA B:CYS165 4.9 63.8 1.0
C B:HIS139 4.9 60.3 1.0
C B:CYS184 4.9 53.3 1.0
N B:THR167 4.9 65.2 1.0
CG2 B:THR167 4.9 52.3 1.0

Zinc binding site 2 out of 2 in 6xha

Go back to Zinc Binding Sites List in 6xha
Zinc binding site 2 out of 2 in the Crystal Structure of Kras-G12V (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-G12V (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:87.2
occ:1.00
 ND1 B:HIS173 2.3 98.1 1.0
SG B:CYS152 2.3 99.5 1.0
SG B:CYS176 2.4 104.2 1.0
SG B:CYS155 2.4 78.5 1.0
CG B:HIS173 3.2 99.7 1.0
CB B:CYS152 3.2 87.7 1.0
CB B:CYS176 3.3 85.8 1.0
CE1 B:HIS173 3.3 108.3 1.0
CB B:HIS173 3.4 87.2 1.0
CB B:CYS155 3.5 93.2 1.0
N B:CYS155 3.5 87.7 1.0
N B:HIS173 3.7 105.8 1.0
CB B:ILE154 4.0 78.4 1.0
CA B:CYS155 4.1 81.3 1.0
CA B:HIS173 4.1 96.3 1.0
CD2 B:HIS173 4.3 99.2 1.0
NE2 B:HIS173 4.4 109.2 1.0
C B:ILE154 4.5 88.1 1.0
CA B:ILE154 4.6 82.6 1.0
CE1 B:HIS175 4.6 119.2 1.0
N B:ILE154 4.6 87.3 1.0
CG2 B:ILE154 4.7 77.2 1.0
CA B:CYS152 4.7 81.9 1.0
CA B:CYS176 4.8 86.1 1.0
C B:PHE172 4.8 96.2 1.0
NE2 B:HIS175 4.8 120.7 1.0
C B:CYS155 4.9 92.2 1.0
CA B:PHE172 4.9 86.0 1.0
O B:HIS173 4.9 95.5 1.0
N B:GLN156 5.0 92.0 1.0
CG1 B:ILE154 5.0 78.8 1.0
C B:HIS173 5.0 102.6 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 Jan 25 16:37:29 2021

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