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Zinc 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:

Chlorine (Cl) 5 atoms
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 I) (pdb code 6xi7). 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 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 Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6xi7

Go back to Zinc Binding Sites List in 6xi7
Zinc binding site 1 out of 3 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 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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:67.5
occ:0.79
 ND1 B:HIS139 2.1 64.8 1.0
SG B:CYS165 2.3 64.4 0.9
SG B:CYS168 2.3 59.4 1.0
SG B:CYS184 2.3 74.2 1.0
CG B:HIS139 3.0 64.4 1.0
CB B:CYS165 3.0 64.1 0.9
CA B:HIS139 3.1 66.4 1.0
CB B:HIS139 3.2 63.8 1.0
CE1 B:HIS139 3.2 63.6 1.0
CB B:CYS184 3.3 71.4 1.0
CB B:CYS168 3.5 69.2 1.0
N B:CYS168 3.7 73.8 1.0
CA B:CYS184 4.0 72.2 1.0
N B:ASN140 4.0 62.6 1.0
N B:HIS139 4.1 68.8 1.0
C B:HIS139 4.1 65.1 1.0
CD2 B:HIS139 4.2 60.1 1.0
CA B:CYS168 4.2 71.3 1.0
NE2 B:HIS139 4.3 62.8 1.0
CB B:THR167 4.4 89.8 1.0
CA B:CYS165 4.5 62.5 0.9
C B:THR167 4.7 90.6 1.0
N B:THR167 4.8 90.0 1.0
CA B:THR167 4.9 91.0 1.0
C B:CYS165 4.9 65.6 0.9
C B:THR138 5.0 83.1 1.0
C B:CYS184 5.0 76.8 1.0

Zinc binding site 2 out of 3 in 6xi7

Go back to Zinc Binding Sites List in 6xi7
Zinc binding site 2 out of 3 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 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 I) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:48.3
occ:0.85
 ND1 B:HIS173 2.1 48.5 1.0
SG B:CYS176 2.3 46.8 0.9
SG B:CYS152 2.3 50.4 1.0
SG B:CYS155 2.3 57.0 1.0
CB B:CYS152 3.0 53.0 1.0
CE1 B:HIS173 3.1 51.2 1.0
CG B:HIS173 3.2 47.5 1.0
CB B:CYS155 3.2 56.9 1.0
CB B:CYS176 3.3 46.2 0.9
CB B:HIS173 3.6 45.4 1.0
O B:HOH321 3.7 54.8 1.0
N B:CYS155 3.7 58.3 1.0
N B:HIS173 4.0 47.3 1.0
CA B:CYS155 4.0 57.8 1.0
NE2 B:HIS173 4.2 50.4 1.0
O B:HOH324 4.2 52.8 1.0
CD2 B:HIS173 4.3 47.8 1.0
CA B:HIS173 4.5 46.9 1.0
CA B:CYS152 4.5 54.5 1.0
CB B:ILE154 4.5 55.3 1.0
CA B:CYS176 4.7 44.9 0.9
C B:CYS155 4.8 59.1 1.0
C B:ILE154 4.8 58.4 1.0
O B:HOH323 4.9 60.5 1.0
N B:GLN156 5.0 64.7 1.0
N B:ILE154 5.0 56.9 1.0

Zinc binding site 3 out of 3 in 6xi7

Go back to Zinc Binding Sites List in 6xi7
Zinc binding site 3 out of 3 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 Zinc with other atoms in the Zn 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
B:Zn205

b:119.0
occ:0.50
 NE2 B:HIS103 2.5 89.0 1.0
OE2 B:GLU125 2.8 93.8 0.9
CE1 B:HIS103 3.2 88.5 1.0
CD2 B:HIS103 3.5 92.5 0.8
CD B:GLU125 3.5 91.5 0.8
OE1 B:GLU125 3.7 93.8 0.8
ND1 B:HIS103 4.3 91.1 0.4
CD1 B:LEU101 4.4 79.4 1.0
CG B:HIS103 4.5 90.8 1.0
CG B:GLU125 4.7 87.2 1.0
CB B:GLU125 4.8 87.7 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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