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Zinc in PDB 1tno: Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B

Enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B

All present enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B:
2.5.1.59;

Protein crystallography data

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B, PDB code: 1tno was solved by T.S.Reid, K.L.Terry, P.J.Casey, L.S.Beese, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.98 / 2.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 272.531, 268.484, 185.940, 90.00, 131.48, 90.00
R / Rfree (%) 19.4 / 21.1

Other elements in 1tno:

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B (pdb code 1tno). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B, PDB code: 1tno:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1tno

Go back to Zinc Binding Sites List in 1tno
Zinc binding site 1 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:51.3
occ:1.00
 OD2 B:ASP269 2.2 53.4 1.0
NE2 B:HIS321 2.2 59.6 1.0
SG B:CYS271 2.2 60.1 1.0
SG M:CYS8 2.3 54.5 1.0
OD1 B:ASP269 2.5 58.7 1.0
CG B:ASP269 2.7 55.0 1.0
CD2 B:HIS321 3.2 56.2 1.0
CE1 B:HIS321 3.2 56.3 1.0
CB B:CYS271 3.4 53.6 1.0
CB M:CYS8 3.6 56.5 1.0
CB B:ASP269 4.2 52.9 1.0
N B:CYS271 4.2 50.5 1.0
CB B:LYS311 4.2 66.7 1.0
O B:HOH412 4.2 57.9 1.0
ND1 B:HIS321 4.3 57.1 1.0
CG B:HIS321 4.3 56.1 1.0
CA B:CYS271 4.4 51.5 1.0
CD2 B:LEU320 4.5 51.7 1.0
CE B:LYS311 4.5 78.9 1.0
CE2 B:TYR272 4.6 47.5 1.0
CA M:CYS8 4.9 58.3 1.0
CD2 B:TYR272 4.9 48.2 1.0

Zinc binding site 2 out of 6 in 1tno

Go back to Zinc Binding Sites List in 1tno
Zinc binding site 2 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:53.4
occ:1.00
 NE2 D:HIS321 2.2 53.6 1.0
SG D:CYS271 2.3 49.7 1.0
OD2 D:ASP269 2.3 50.5 1.0
SG N:CYS8 2.4 54.6 1.0
OD1 D:ASP269 2.6 51.0 1.0
CG D:ASP269 2.7 48.7 1.0
CD2 D:HIS321 3.1 55.4 1.0
CE1 D:HIS321 3.1 53.4 1.0
CB D:CYS271 3.4 46.5 1.0
CB N:CYS8 3.5 58.3 1.0
N D:CYS271 4.2 44.6 1.0
CB D:LYS311 4.2 65.4 1.0
ND1 D:HIS321 4.2 53.7 1.0
CB D:ASP269 4.2 47.3 1.0
CG D:HIS321 4.2 54.0 1.0
CA D:CYS271 4.4 45.4 1.0
CD2 D:LEU320 4.4 54.0 1.0
O D:HOH428 4.5 55.1 1.0
CE D:LYS311 4.5 75.9 1.0
CE2 D:TYR272 4.6 49.4 1.0
CA N:CYS8 4.8 60.0 1.0
CD2 D:TYR272 5.0 47.7 1.0

Zinc binding site 3 out of 6 in 1tno

Go back to Zinc Binding Sites List in 1tno
Zinc binding site 3 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:48.4
occ:1.00
 NE2 F:HIS321 2.2 49.8 1.0
OD2 F:ASP269 2.2 43.9 1.0
SG O:CYS8 2.2 56.6 1.0
SG F:CYS271 2.3 53.6 1.0
OD1 F:ASP269 2.5 48.3 1.0
CG F:ASP269 2.7 44.7 1.0
CD2 F:HIS321 3.1 48.3 1.0
CE1 F:HIS321 3.2 50.5 1.0
CB F:CYS271 3.4 45.2 1.0
CB O:CYS8 3.5 56.7 1.0
CB F:LYS311 4.2 64.0 1.0
CB F:ASP269 4.2 43.1 1.0
N F:CYS271 4.2 45.3 1.0
O F:HOH423 4.2 50.1 1.0
ND1 F:HIS321 4.2 51.2 1.0
CG F:HIS321 4.3 50.7 1.0
CA F:CYS271 4.4 45.7 1.0
CD2 F:LEU320 4.4 51.9 1.0
CE F:LYS311 4.5 78.1 1.0
CE2 F:TYR272 4.6 47.5 1.0
CA O:CYS8 4.9 58.1 1.0
CD2 F:TYR272 4.9 47.7 1.0
CA F:LYS311 5.0 59.7 1.0

Zinc binding site 4 out of 6 in 1tno

Go back to Zinc Binding Sites List in 1tno
Zinc binding site 4 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:60.8
occ:1.00
 NE2 H:HIS321 2.2 73.3 1.0
OD2 H:ASP269 2.2 49.9 1.0
SG H:CYS271 2.3 64.4 1.0
SG P:CYS8 2.3 65.9 1.0
OD1 H:ASP269 2.5 60.2 1.0
CG H:ASP269 2.7 54.8 1.0
CD2 H:HIS321 3.1 73.3 1.0
CE1 H:HIS321 3.2 72.8 1.0
CB H:CYS271 3.4 59.7 1.0
CB P:CYS8 3.6 68.4 1.0
N H:CYS271 4.1 56.4 1.0
CB H:ASP269 4.2 54.3 1.0
CB H:LYS311 4.2 83.8 1.0
ND1 H:HIS321 4.2 73.4 1.0
CG H:HIS321 4.2 72.3 1.0
CA H:CYS271 4.4 57.3 1.0
CD2 H:LEU320 4.4 67.4 1.0
CE H:LYS311 4.5 90.0 1.0
O H:HOH404 4.5 56.9 1.0
CE2 H:TYR272 4.6 55.6 1.0
CA P:CYS8 4.9 70.1 1.0
O H:HOH392 5.0 61.0 1.0
CD2 H:TYR272 5.0 55.8 1.0
CA H:LYS311 5.0 82.9 1.0

Zinc binding site 5 out of 6 in 1tno

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Zinc binding site 5 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:53.6
occ:1.00
 OD2 J:ASP269 2.2 46.8 1.0
NE2 J:HIS321 2.2 56.3 1.0
SG J:CYS271 2.3 55.1 1.0
SG Q:CYS8 2.4 57.1 1.0
OD1 J:ASP269 2.5 50.6 1.0
CG J:ASP269 2.7 49.1 1.0
CD2 J:HIS321 3.2 55.3 1.0
CE1 J:HIS321 3.2 54.1 1.0
CB J:CYS271 3.4 49.9 1.0
CB Q:CYS8 3.6 61.6 1.0
N J:CYS271 4.1 47.4 1.0
CB J:ASP269 4.2 47.4 1.0
CB J:LYS311 4.2 61.2 1.0
O J:HOH414 4.2 49.5 1.0
ND1 J:HIS321 4.3 55.1 1.0
CG J:HIS321 4.3 54.1 1.0
CA J:CYS271 4.4 48.9 1.0
CD2 J:LEU320 4.5 49.6 1.0
CE J:LYS311 4.5 76.0 1.0
CE2 J:TYR272 4.6 46.2 1.0
CA Q:CYS8 4.9 64.2 1.0
CD2 J:TYR272 4.9 45.9 1.0

Zinc binding site 6 out of 6 in 1tno

Go back to Zinc Binding Sites List in 1tno
Zinc binding site 6 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvim Peptide Derived From K- RAS4B within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:46.9
occ:1.00
 OD2 L:ASP269 2.2 43.0 1.0
NE2 L:HIS321 2.2 46.6 1.0
SG L:CYS271 2.3 43.3 1.0
SG R:CYS8 2.4 57.3 1.0
OD1 L:ASP269 2.5 44.5 1.0
CG L:ASP269 2.6 43.5 1.0
CD2 L:HIS321 3.2 47.1 1.0
CE1 L:HIS321 3.2 46.3 1.0
CB L:CYS271 3.4 38.0 1.0
CB R:CYS8 3.5 59.1 1.0
CB L:ASP269 4.1 41.6 1.0
N L:CYS271 4.2 38.7 1.0
CB L:LYS311 4.2 51.4 1.0
ND1 L:HIS321 4.3 49.9 1.0
CG L:HIS321 4.3 49.1 1.0
O L:HOH460 4.4 48.2 1.0
CA L:CYS271 4.4 37.9 1.0
CE L:LYS311 4.5 71.2 1.0
CD2 L:LEU320 4.5 45.2 1.0
CE2 L:TYR272 4.6 43.0 1.0
CA R:CYS8 4.9 61.1 1.0
CD2 L:TYR272 4.9 40.5 1.0
O L:HOH429 5.0 39.5 1.0

Reference:

T.S.Reid, K.L.Terry, P.J.Casey, L.S.Beese. Crystallographic Analysis of Caax Prenyltransferases Complexed with Substrates Defines Rules of Protein Substrate Selectivity. J.Mol.Biol. V. 343 417 2004.
ISSN: ISSN 0022-2836
PubMed: 15451670
DOI: 10.1016/J.JMB.2004.08.056
Page generated: Wed Oct 16 19:12:12 2024

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