Zinc in PDB 8t75: Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)

Enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)

All present enzymatic activity of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd):
2.7.11.1; 3.6.5.2;

Protein crystallography data

The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75 was solved by M.J.Whitley, D.K.Simanshu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.45 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.409, 199.509, 113.428, 90, 112.28, 90
R / Rfree (%) 17.8 / 21.9

Other elements in 8t75:

The structure of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) also contains other interesting chemical elements:

Arsenic (As) 4 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) (pdb code 8t75). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd), PDB code: 8t75:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 8t75

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Zinc binding site 1 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:63.9
occ:1.00
 ND1 B:HIS139 2.1 59.4 1.0
SG B:CYS168 2.3 62.3 1.0
SG B:CYS184 2.3 70.5 1.0
SG B:CYS165 2.3 67.0 1.0
CE1 B:HIS139 2.6 52.2 1.0
CB B:CYS165 3.2 52.4 1.0
CB B:CYS168 3.2 55.6 1.0
CB B:CYS184 3.3 61.5 1.0
CG B:HIS139 3.3 54.8 1.0
N B:CYS168 3.6 58.9 1.0
NE2 B:HIS139 3.9 69.5 1.0
CB B:HIS139 4.0 67.1 1.0
CA B:CYS168 4.0 57.5 1.0
CA B:HIS139 4.0 62.8 1.0
CA B:CYS184 4.0 58.7 1.0
CD2 B:HIS139 4.2 51.9 1.0
CB B:THR167 4.5 80.2 1.0
CA B:CYS165 4.7 65.9 1.0
C B:THR167 4.7 75.9 1.0
C B:CYS168 4.8 63.6 1.0
N B:HIS139 4.9 70.9 1.0
N B:GLY169 4.9 64.8 1.0
N B:ASN140 4.9 71.0 1.0
C B:CYS184 4.9 62.1 1.0
CA B:THR167 5.0 74.1 1.0

Zinc binding site 2 out of 8 in 8t75

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Zinc binding site 2 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:73.9
occ:1.00
 ND1 B:HIS173 2.1 71.3 1.0
SG B:CYS152 2.3 69.8 1.0
SG B:CYS155 2.3 65.2 1.0
SG B:CYS176 2.3 79.1 1.0
CB B:CYS152 3.0 59.0 1.0
CE1 B:HIS173 3.1 69.8 1.0
CG B:HIS173 3.1 59.1 1.0
CB B:HIS173 3.4 54.1 1.0
CB B:CYS176 3.5 61.6 1.0
CB B:CYS155 3.6 64.4 1.0
N B:HIS173 3.9 75.9 1.0
N B:CYS155 3.9 53.3 1.0
NE2 B:HIS173 4.2 71.3 1.0
CD2 B:HIS173 4.2 55.5 1.0
CA B:HIS173 4.3 57.0 1.0
CE1 B:HIS175 4.3 93.9 1.0
CA B:CYS155 4.3 54.9 1.0
CB B:ILE154 4.5 52.0 1.0
CA B:CYS152 4.5 48.5 1.0
C B:ILE154 4.9 61.7 1.0
CA B:CYS176 4.9 73.1 1.0
ND1 B:HIS175 4.9 101.9 1.0
C B:PHE172 4.9 70.3 1.0
NE2 B:HIS175 5.0 91.5 1.0
N B:ILE154 5.0 66.2 1.0

Zinc binding site 3 out of 8 in 8t75

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Zinc binding site 3 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


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 KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:57.9
occ:1.00
 ND1 D:HIS139 2.1 50.1 1.0
SG D:CYS168 2.3 56.7 1.0
SG D:CYS165 2.3 56.2 1.0
SG D:CYS184 2.3 63.8 1.0
CE1 D:HIS139 2.8 56.6 1.0
CB D:CYS168 3.2 55.8 1.0
CB D:CYS184 3.2 49.1 1.0
CB D:CYS165 3.2 54.6 1.0
CG D:HIS139 3.2 52.2 1.0
N D:CYS168 3.7 56.4 1.0
CB D:HIS139 3.8 54.5 1.0
CA D:HIS139 3.9 50.9 1.0
NE2 D:HIS139 3.9 55.1 1.0
CA D:CYS184 4.0 53.9 1.0
CA D:CYS168 4.0 56.0 1.0
CD2 D:HIS139 4.2 47.8 1.0
O D:HOH312 4.5 59.1 1.0
CB D:THR167 4.5 64.9 1.0
CA D:CYS165 4.7 56.4 1.0
C D:THR167 4.7 59.0 1.0
N D:HIS139 4.7 55.6 1.0
N D:ASN140 4.8 60.0 1.0
C D:CYS168 4.8 54.0 1.0
C D:CYS184 4.9 60.8 1.0
N D:GLY169 4.9 54.5 1.0
C D:HIS139 4.9 53.4 1.0
CA D:THR167 5.0 62.8 1.0

Zinc binding site 4 out of 8 in 8t75

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Zinc binding site 4 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:63.5
occ:1.00
 ND1 D:HIS173 2.1 60.8 1.0
SG D:CYS155 2.3 64.0 1.0
SG D:CYS152 2.3 67.2 1.0
SG D:CYS176 2.3 60.8 1.0
CB D:CYS152 3.0 50.4 1.0
CE1 D:HIS173 3.0 51.1 1.0
CG D:HIS173 3.2 54.6 1.0
CB D:CYS176 3.4 57.3 1.0
CB D:HIS173 3.5 55.1 1.0
CB D:CYS155 3.5 48.0 1.0
N D:CYS155 3.8 57.4 1.0
N D:HIS173 3.9 55.2 1.0
NE2 D:HIS173 4.2 56.7 1.0
CD2 D:HIS173 4.2 50.1 1.0
CA D:CYS155 4.3 62.1 1.0
CA D:HIS173 4.3 51.9 1.0
CB D:ILE154 4.4 61.2 1.0
NE2 D:HIS175 4.4 65.8 1.0
CA D:CYS152 4.5 42.7 1.0
C D:ILE154 4.8 55.2 1.0
CE1 D:HIS175 4.8 62.0 1.0
CA D:CYS176 4.8 51.5 1.0
N D:ILE154 4.9 57.7 1.0
C D:PHE172 4.9 58.3 1.0
CA D:ILE154 4.9 54.0 1.0

Zinc binding site 5 out of 8 in 8t75

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Zinc binding site 5 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:56.5
occ:1.00
 ND1 F:HIS139 2.1 58.1 1.0
SG F:CYS165 2.3 62.2 1.0
SG F:CYS168 2.3 62.9 1.0
SG F:CYS184 2.3 68.1 1.0
CE1 F:HIS139 2.8 57.8 1.0
CB F:CYS165 3.2 52.2 1.0
CG F:HIS139 3.3 63.1 1.0
CB F:CYS168 3.3 52.5 1.0
CB F:CYS184 3.3 57.9 1.0
N F:CYS168 3.7 62.1 1.0
CB F:HIS139 3.9 61.2 1.0
CA F:HIS139 4.0 58.5 1.0
NE2 F:HIS139 4.0 67.3 1.0
CA F:CYS168 4.1 57.9 1.0
CA F:CYS184 4.1 51.5 1.0
CD2 F:HIS139 4.2 61.0 1.0
CB F:THR167 4.3 72.7 1.0
CA F:CYS165 4.7 53.3 1.0
C F:THR167 4.7 64.0 1.0
N F:HIS139 4.8 60.4 1.0
C F:CYS168 4.9 62.8 1.0
CA F:THR167 4.9 67.0 1.0
N F:ASN140 4.9 61.6 1.0
N F:THR167 4.9 62.0 1.0
CG2 F:THR167 5.0 62.1 1.0
CB F:TYR170 5.0 49.0 1.0
N F:GLY169 5.0 58.3 1.0

Zinc binding site 6 out of 8 in 8t75

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Zinc binding site 6 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:64.6
occ:1.00
 ND1 F:HIS173 2.1 62.4 1.0
SG F:CYS155 2.3 79.7 1.0
SG F:CYS152 2.3 71.0 1.0
SG F:CYS176 2.3 64.1 1.0
CB F:CYS152 2.9 58.3 1.0
CE1 F:HIS173 3.0 62.0 1.0
CG F:HIS173 3.1 63.9 1.0
CB F:CYS176 3.5 66.2 1.0
CB F:CYS155 3.5 60.4 1.0
CB F:HIS173 3.5 58.9 1.0
N F:HIS173 3.8 47.0 1.0
N F:CYS155 3.9 62.8 1.0
NE2 F:HIS173 4.2 61.3 1.0
CD2 F:HIS173 4.2 54.8 1.0
CA F:CYS155 4.3 64.6 1.0
CA F:HIS173 4.3 60.1 1.0
CA F:CYS152 4.4 57.3 1.0
CB F:ILE154 4.6 60.9 1.0
NE2 F:HIS175 4.6 78.1 1.0
CA F:CYS176 4.9 60.6 1.0
C F:ILE154 4.9 61.9 1.0
C F:PHE172 4.9 55.8 1.0
C F:CYS152 5.0 56.7 1.0
C F:CYS155 5.0 55.1 1.0
CE1 F:HIS175 5.0 75.2 1.0

Zinc binding site 7 out of 8 in 8t75

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Zinc binding site 7 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:60.7
occ:1.00
 ND1 H:HIS139 2.1 61.3 1.0
SG H:CYS184 2.3 67.0 1.0
SG H:CYS165 2.3 53.2 1.0
SG H:CYS168 2.3 93.4 1.0
CB H:CYS168 2.7 53.8 1.0
CE1 H:HIS139 2.8 39.8 1.0
CB H:CYS184 3.1 56.7 1.0
CG H:HIS139 3.2 58.7 1.0
N H:CYS168 3.3 79.7 1.0
CA H:CYS168 3.5 60.2 1.0
CB H:CYS165 3.5 65.2 1.0
CB H:HIS139 3.7 61.8 1.0
CA H:HIS139 3.8 54.5 1.0
CA H:CYS184 3.8 50.9 1.0
NE2 H:HIS139 4.0 56.4 1.0
CD2 H:HIS139 4.2 49.4 1.0
C H:THR167 4.4 62.0 1.0
N H:HIS139 4.5 65.2 1.0
CB H:THR167 4.6 67.3 1.0
C H:CYS184 4.7 64.5 1.0
N H:ASN140 4.9 55.5 1.0
C H:CYS168 4.9 60.0 1.0
C H:HIS139 4.9 59.0 1.0
N H:VAL185 4.9 60.8 1.0
CA H:CYS165 4.9 57.9 1.0
N H:CYS184 4.9 59.3 1.0
CA H:THR167 4.9 62.6 1.0

Zinc binding site 8 out of 8 in 8t75

Go back to Zinc Binding Sites List in 8t75
Zinc binding site 8 out of 8 in the Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of KRAS4A (Gmppnp) in Complex with RAF1 (Rbd-Crd) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:64.0
occ:1.00
 ND1 H:HIS173 2.1 56.3 1.0
SG H:CYS155 2.3 72.9 1.0
SG H:CYS176 2.3 64.8 1.0
SG H:CYS152 2.3 72.4 1.0
CB H:CYS152 3.0 55.6 1.0
CE1 H:HIS173 3.0 52.9 1.0
CG H:HIS173 3.1 58.1 1.0
CB H:CYS176 3.4 66.3 1.0
CB H:HIS173 3.4 63.3 1.0
CB H:CYS155 3.5 67.3 1.0
N H:CYS155 3.8 73.2 1.0
N H:HIS173 3.8 69.8 1.0
NE2 H:HIS173 4.2 59.0 1.0
CD2 H:HIS173 4.2 50.4 1.0
CA H:CYS155 4.2 71.3 1.0
CA H:HIS173 4.3 62.3 1.0
CB H:ILE154 4.4 67.2 1.0
CA H:CYS152 4.5 58.8 1.0
NE2 H:HIS175 4.6 78.1 1.0
C H:ILE154 4.8 69.7 1.0
CA H:CYS176 4.8 66.3 1.0
C H:PHE172 4.9 68.2 1.0
CE1 H:HIS175 4.9 85.2 1.0
CA H:ILE154 4.9 61.2 1.0
N H:ILE154 4.9 61.4 1.0
CG2 H:ILE154 5.0 63.4 1.0
C H:CYS155 5.0 66.7 1.0

Reference:

M.J.Whitley, T.H.Tran, M.Yi, S.Dharmaiah, G.Cornilescu, D.K.Simanshu. Comparative Analysis of KRAS4A and KRAS4B Splice Variants Reveals Distinctive Structural and Functional Properties Sci Adv 2024.
ISSN: ESSN 2375-2548
DOI: 10.1126/SCIADV.ADJ4137
Page generated: Thu Oct 31 11:28:06 2024

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