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Zinc in PDB 6xgu: Crystal Structure of Kras-Q61R (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf

Enzymatic activity of Crystal Structure of Kras-Q61R (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-Q61R (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-Q61R (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgu 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) 48.32 / 2.70
Space group P 6 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.32, 132.32, 89.91, 90, 90, 120
R / Rfree (%) 18.7 / 23.6

Other elements in 6xgu:

The structure of Crystal Structure of Kras-Q61R (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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Kras-Q61R (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf (pdb code 6xgu). 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-Q61R (Gmppnp-Bound) in Complex with Ras- Binding Domain (Rbd) and Cysteine-Rich Domain (Crd) of RAF1/Craf, PDB code: 6xgu:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6xgu

Go back to Zinc Binding Sites List in 6xgu
Zinc binding site 1 out of 3 in the Crystal Structure of Kras-Q61R (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-Q61R (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:178.8
occ:0.36
 NE2 A:HIS95 2.7 149.5 1.0
CD2 A:HIS95 3.1 139.2 1.0
OD1 A:ASP92 3.2 143.3 1.0
CE1 A:HIS95 3.8 144.6 1.0
CG A:ASP92 4.1 145.8 1.0
CG A:HIS95 4.3 141.2 1.0
OD2 A:ASP92 4.5 141.9 1.0
ND1 A:HIS95 4.6 146.0 1.0

Zinc binding site 2 out of 3 in 6xgu

Go back to Zinc Binding Sites List in 6xgu
Zinc binding site 2 out of 3 in the Crystal Structure of Kras-Q61R (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-Q61R (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:Zn201

b:66.2
occ:1.00
 ND1 B:HIS139 2.2 61.8 1.0
SG B:CYS184 2.3 62.1 1.0
SG B:CYS165 2.3 72.2 1.0
SG B:CYS168 2.3 65.2 1.0
CE1 B:HIS139 3.0 57.4 1.0
CB B:CYS184 3.1 61.8 1.0
CB B:CYS165 3.2 64.2 1.0
CG B:HIS139 3.2 63.4 1.0
CB B:CYS168 3.3 63.3 1.0
N B:CYS168 3.6 73.3 1.0
CB B:HIS139 3.6 63.0 1.0
CA B:HIS139 3.8 61.8 1.0
CA B:CYS184 3.9 63.7 1.0
CA B:CYS168 4.0 73.8 1.0
NE2 B:HIS139 4.1 62.5 1.0
CD2 B:HIS139 4.2 48.9 1.0
O B:HOH312 4.4 66.1 1.0
CB B:THR167 4.4 66.7 1.0
CA B:CYS165 4.6 71.9 1.0
C B:THR167 4.6 79.2 1.0
N B:HIS139 4.7 66.8 1.0
N B:ASN140 4.7 66.4 1.0
N B:GLY169 4.8 69.1 1.0
C B:CYS184 4.8 62.2 1.0
C B:CYS168 4.8 70.4 1.0
C B:HIS139 4.9 63.6 1.0
N B:THR167 4.9 74.2 1.0
N B:CYS184 4.9 64.7 1.0
CA B:THR167 4.9 68.0 1.0

Zinc binding site 3 out of 3 in 6xgu

Go back to Zinc Binding Sites List in 6xgu
Zinc binding site 3 out of 3 in the Crystal Structure of Kras-Q61R (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-Q61R (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:Zn202

b:83.1
occ:1.00
 ND1 B:HIS173 2.0 100.8 1.0
SG B:CYS176 2.3 87.9 1.0
SG B:CYS155 2.3 92.4 1.0
SG B:CYS152 2.3 82.2 1.0
CE1 B:HIS173 2.9 94.1 1.0
CG B:HIS173 3.0 92.4 1.0
CB B:CYS152 3.1 77.7 1.0
CB B:CYS155 3.3 76.3 1.0
CB B:HIS173 3.4 86.9 1.0
CB B:CYS176 3.4 88.6 1.0
N B:CYS155 3.9 83.8 1.0
N B:HIS173 3.9 98.7 1.0
NE2 B:HIS173 4.0 89.6 1.0
CD2 B:HIS173 4.1 99.6 1.0
CA B:CYS155 4.2 73.7 1.0
CA B:HIS173 4.3 87.3 1.0
CB B:ILE154 4.4 79.7 1.0
CA B:CYS152 4.5 79.5 1.0
NE2 B:HIS175 4.6 114.1 1.0
CE1 B:HIS175 4.6 113.8 1.0
C B:ILE154 4.7 89.8 1.0
CG2 B:ILE154 4.8 79.8 1.0
CA B:CYS176 4.8 77.8 1.0
C B:CYS155 4.9 80.5 1.0
N B:ILE154 4.9 77.3 1.0
CA B:ILE154 4.9 82.5 1.0
C B:PHE172 5.0 93.1 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 10:49:04 2024

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