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Zinc in PDB 6xhb: 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 II)

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 II)

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 II):
2.7.11.1;

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 II), PDB code: 6xhb 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) 48.65 / 2.50
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 133.984, 133.984, 89.275, 90, 90, 120
R / Rfree (%) 18.6 / 22.1

Other elements in 6xhb:

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 II) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Arsenic (As) 1 atom
Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 II) (pdb code 6xhb). 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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form II), PDB code: 6xhb:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6xhb

Go back to Zinc Binding Sites List in 6xhb
Zinc binding site 1 out of 2 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 II)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn203

b:46.2
occ:1.00
 ND1 B:HIS139 2.2 38.8 1.0
SG B:CYS184 2.4 48.7 1.0
SG B:CYS168 2.4 47.6 1.0
SG B:CYS165 2.4 46.5 1.0
CE1 B:HIS139 3.0 40.5 1.0
CB B:CYS184 3.1 40.9 1.0
CG B:HIS139 3.2 39.1 1.0
CB B:CYS165 3.3 36.0 1.0
CB B:CYS168 3.4 35.2 1.0
CB B:HIS139 3.6 44.0 1.0
N B:CYS168 3.7 48.7 1.0
CA B:HIS139 3.7 40.8 1.0
CA B:CYS184 4.0 39.8 1.0
CA B:CYS168 4.2 44.8 1.0
NE2 B:HIS139 4.2 39.6 1.0
CD2 B:HIS139 4.3 41.4 1.0
CB B:THR167 4.4 49.9 1.0
N B:HIS139 4.6 41.8 1.0
N B:ASN140 4.7 46.5 1.0
C B:THR167 4.7 52.9 1.0
CA B:CYS165 4.8 42.7 1.0
C B:HIS139 4.8 43.4 1.0
C B:CYS184 4.9 43.8 1.0
CA B:THR167 5.0 53.0 1.0
N B:THR167 5.0 54.6 1.0
C B:CYS168 5.0 41.7 1.0

Zinc binding site 2 out of 2 in 6xhb

Go back to Zinc Binding Sites List in 6xhb
Zinc binding site 2 out of 2 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 II)


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 Wild-Type Kras (Gmppnp-Bound) in Complex with Ras-Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn204

b:54.4
occ:1.00
 ND1 B:HIS173 2.1 55.4 1.0
SG B:CYS155 2.4 50.8 1.0
SG B:CYS152 2.4 47.7 1.0
SG B:CYS176 2.4 57.2 1.0
CE1 B:HIS173 3.1 58.1 1.0
CB B:CYS152 3.1 40.1 1.0
CG B:HIS173 3.2 55.1 1.0
CB B:CYS155 3.4 44.2 1.0
CB B:CYS176 3.5 48.5 1.0
CB B:HIS173 3.5 48.8 1.0
N B:HIS173 3.8 51.1 1.0
N B:CYS155 3.8 52.3 1.0
CA B:CYS155 4.2 47.3 1.0
NE2 B:HIS173 4.2 55.5 1.0
CE1 B:HIS175 4.2 74.7 1.0
CD2 B:HIS173 4.3 57.9 1.0
CA B:HIS173 4.3 47.3 1.0
CB B:ILE154 4.5 45.0 1.0
CA B:CYS152 4.6 52.4 1.0
NE2 B:HIS175 4.6 78.1 1.0
C B:ILE154 4.8 53.5 1.0
ND1 B:HIS175 4.9 75.7 1.0
C B:PHE172 4.9 46.4 1.0
CA B:CYS176 4.9 46.9 1.0
C B:CYS155 4.9 48.4 1.0
CA B:PHE172 5.0 45.3 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 II) To Be Published.
Page generated: Tue Oct 29 10:56:03 2024

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