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Zinc in PDB 1tnb: Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21

Enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21

All present enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21:
2.5.1.59;

Protein crystallography data

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21, PDB code: 1tnb 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) 27.66 / 2.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.130, 266.720, 185.141, 90.00, 131.68, 90.00
R / Rfree (%) 18.9 / 21

Other elements in 1tnb:

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21 (pdb code 1tnb). 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 Substrate Kksktkcvif Peptide Derived From TC21, PDB code: 1tnb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1tnb

Go back to Zinc Binding Sites List in 1tnb
Zinc binding site 1 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:33.4
occ:1.00
 NE2 B:HIS321 2.1 38.6 1.0
SG B:CYS271 2.2 39.8 1.0
OD2 B:ASP269 2.2 35.0 1.0
SG M:CYS7 2.3 38.6 1.0
OD1 B:ASP269 2.5 38.2 1.0
CG B:ASP269 2.7 35.7 1.0
CD2 B:HIS321 3.1 36.5 1.0
CE1 B:HIS321 3.1 37.6 1.0
CB B:CYS271 3.4 38.0 1.0
CB M:CYS7 3.5 38.2 1.0
CB B:LYS311 4.1 47.5 1.0
CB B:ASP269 4.1 35.3 1.0
N B:CYS271 4.2 36.9 1.0
ND1 B:HIS321 4.2 37.3 1.0
CG B:HIS321 4.2 38.3 1.0
CD2 B:LEU320 4.4 30.2 1.0
CA B:CYS271 4.4 37.2 1.0
CE2 B:TYR272 4.5 36.7 1.0
CE B:LYS311 4.5 53.2 1.0
O B:HOH414 4.6 45.8 1.0
CD2 B:TYR272 4.8 36.5 1.0
CA M:CYS7 4.9 39.4 1.0
CA B:LYS311 5.0 46.5 1.0

Zinc binding site 2 out of 6 in 1tnb

Go back to Zinc Binding Sites List in 1tnb
Zinc binding site 2 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:31.9
occ:1.00
 NE2 D:HIS321 2.1 32.5 1.0
OD2 D:ASP269 2.2 36.8 1.0
SG D:CYS271 2.3 32.1 1.0
SG N:CYS7 2.4 38.5 1.0
OD1 D:ASP269 2.5 36.7 1.0
CG D:ASP269 2.7 34.9 1.0
CD2 D:HIS321 3.0 32.1 1.0
CE1 D:HIS321 3.1 33.0 1.0
CB D:CYS271 3.4 29.4 1.0
CB N:CYS7 3.5 40.2 1.0
CB D:LYS311 4.1 42.1 1.0
N D:CYS271 4.1 29.1 1.0
CB D:ASP269 4.1 33.0 1.0
ND1 D:HIS321 4.1 33.6 1.0
CG D:HIS321 4.2 33.3 1.0
CA D:CYS271 4.3 29.4 1.0
CD2 D:LEU320 4.4 29.7 1.0
CE D:LYS311 4.5 46.8 1.0
CE2 D:TYR272 4.5 36.2 1.0
O D:HOH428 4.6 38.0 1.0
CA N:CYS7 4.8 41.8 1.0
CD2 D:TYR272 4.9 35.0 1.0
CA D:LYS311 4.9 42.3 1.0
CD D:LYS311 5.0 45.6 1.0

Zinc binding site 3 out of 6 in 1tnb

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Zinc binding site 3 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:32.5
occ:1.00
 NE2 F:HIS321 2.1 29.2 1.0
OD2 F:ASP269 2.2 29.4 1.0
SG O:CYS7 2.3 40.9 1.0
SG F:CYS271 2.3 31.4 1.0
OD1 F:ASP269 2.5 32.5 1.0
CG F:ASP269 2.6 29.3 1.0
CD2 F:HIS321 3.0 29.5 1.0
CE1 F:HIS321 3.1 31.2 1.0
CB F:CYS271 3.5 27.4 1.0
CB O:CYS7 3.5 40.7 1.0
CB F:LYS311 4.0 42.1 1.0
CB F:ASP269 4.1 29.7 1.0
ND1 F:HIS321 4.2 31.9 1.0
CG F:HIS321 4.2 32.4 1.0
N F:CYS271 4.2 27.0 1.0
CE F:LYS311 4.4 50.0 1.0
CA F:CYS271 4.4 27.7 1.0
CD2 F:LEU320 4.4 31.7 1.0
CE2 F:TYR272 4.5 32.9 1.0
O F:HOH434 4.6 27.4 1.0
CA O:CYS7 4.8 40.6 1.0
CD2 F:TYR272 4.9 33.4 1.0
CA F:LYS311 4.9 40.5 1.0
CD F:LYS311 4.9 49.3 1.0
NZ F:LYS311 5.0 50.5 1.0

Zinc binding site 4 out of 6 in 1tnb

Go back to Zinc Binding Sites List in 1tnb
Zinc binding site 4 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:43.3
occ:1.00
 NE2 H:HIS321 2.1 46.0 1.0
OD2 H:ASP269 2.2 35.3 1.0
SG H:CYS271 2.3 40.5 1.0
SG P:CYS7 2.4 44.9 1.0
OD1 H:ASP269 2.5 41.0 1.0
CG H:ASP269 2.6 38.3 1.0
CD2 H:HIS321 3.0 46.8 1.0
CE1 H:HIS321 3.1 46.2 1.0
CB H:CYS271 3.4 40.7 1.0
CB P:CYS7 3.5 46.1 1.0
CB H:LYS311 4.1 55.3 1.0
CB H:ASP269 4.1 39.1 1.0
ND1 H:HIS321 4.2 48.2 1.0
N H:CYS271 4.2 39.5 1.0
CG H:HIS321 4.2 47.2 1.0
CD2 H:LEU320 4.4 38.2 1.0
CA H:CYS271 4.4 39.3 1.0
CE H:LYS311 4.5 55.1 1.0
CE2 H:TYR272 4.5 38.0 1.0
O H:HOH401 4.8 31.9 1.0
CA P:CYS7 4.9 47.2 1.0
O H:HOH384 4.9 45.5 1.0
CD2 H:TYR272 4.9 38.1 1.0
CA H:LYS311 4.9 55.2 1.0
CD H:LYS311 5.0 55.7 1.0

Zinc binding site 5 out of 6 in 1tnb

Go back to Zinc Binding Sites List in 1tnb
Zinc binding site 5 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:33.3
occ:1.00
 NE2 J:HIS321 2.1 36.8 1.0
OD2 J:ASP269 2.2 28.8 1.0
SG J:CYS271 2.3 33.4 1.0
SG Q:CYS7 2.4 38.2 1.0
OD1 J:ASP269 2.4 34.1 1.0
CG J:ASP269 2.6 32.5 1.0
CD2 J:HIS321 3.1 35.2 1.0
CE1 J:HIS321 3.1 35.7 1.0
CB J:CYS271 3.4 32.8 1.0
CB Q:CYS7 3.5 39.8 1.0
CB J:ASP269 4.1 31.1 1.0
CB J:LYS311 4.1 43.9 1.0
N J:CYS271 4.1 33.5 1.0
CG J:HIS321 4.2 35.5 1.0
ND1 J:HIS321 4.2 36.4 1.0
CA J:CYS271 4.3 33.6 1.0
CD2 J:LEU320 4.4 25.0 1.0
CE2 J:TYR272 4.5 35.1 1.0
O J:HOH425 4.5 40.7 1.0
CE J:LYS311 4.5 53.2 1.0
CD2 J:TYR272 4.8 33.5 1.0
CA Q:CYS7 4.9 42.2 1.0
CA J:LYS311 4.9 41.5 1.0
C J:ASP269 5.0 32.8 1.0

Zinc binding site 6 out of 6 in 1tnb

Go back to Zinc Binding Sites List in 1tnb
Zinc binding site 6 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Substrate Kksktkcvif Peptide Derived From TC21


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 Substrate Kksktkcvif Peptide Derived From TC21 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:29.1
occ:1.00
 NE2 L:HIS321 2.1 26.4 1.0
OD2 L:ASP269 2.2 30.3 1.0
SG L:CYS271 2.3 24.2 1.0
SG R:CYS7 2.3 38.4 1.0
OD1 L:ASP269 2.4 28.3 1.0
CG L:ASP269 2.6 28.2 1.0
CD2 L:HIS321 3.0 27.3 1.0
CE1 L:HIS321 3.1 28.5 1.0
CB L:CYS271 3.4 22.1 1.0
CB R:CYS7 3.5 38.3 1.0
CB L:LYS311 4.0 31.3 1.0
CB L:ASP269 4.1 25.7 1.0
N L:CYS271 4.1 22.9 1.0
CG L:HIS321 4.2 29.9 1.0
ND1 L:HIS321 4.2 30.5 1.0
CA L:CYS271 4.3 22.4 1.0
CD2 L:LEU320 4.4 23.9 1.0
CE L:LYS311 4.5 43.0 1.0
CE2 L:TYR272 4.5 24.9 1.0
O L:HOH450 4.7 33.3 1.0
CD2 L:TYR272 4.8 25.8 1.0
CA L:LYS311 4.9 28.8 1.0
CA R:CYS7 4.9 39.2 1.0
C L:ASP269 5.0 25.7 1.0
CD L:LYS311 5.0 40.4 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 Dec 16 03:05:05 2020

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