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Zinc in PDB 1tnz: Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2

Enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2

All present enzymatic activity of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2:
2.5.1.59;

Protein crystallography data

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2, PDB code: 1tnz 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) 29.96 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.262, 266.922, 185.750, 90.00, 131.91, 90.00
R / Rfree (%) 19.9 / 21.8

Other elements in 1tnz:

The structure of Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2 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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 (pdb code 1tnz). 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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2, PDB code: 1tnz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1tnz

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Zinc binding site 1 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:66.9
occ:1.00
SG B:CYS271 2.2 70.6 1.0
NE2 B:HIS321 2.2 69.4 1.0
OD2 B:ASP269 2.3 65.8 1.0
SG M:CYS3 2.3 77.4 1.0
OD1 B:ASP269 2.5 69.1 1.0
CG B:ASP269 2.7 66.5 1.0
CE1 B:HIS321 3.1 68.5 1.0
CD2 B:HIS321 3.3 67.4 1.0
CB B:CYS271 3.4 68.8 1.0
CB M:CYS3 3.5 78.3 1.0
CB B:ASP269 4.1 66.2 1.0
ND1 B:HIS321 4.2 68.1 1.0
N B:CYS271 4.2 67.8 1.0
CB B:LYS311 4.3 78.3 1.0
CD2 B:LEU320 4.3 61.0 1.0
CG B:HIS321 4.3 69.2 1.0
CA B:CYS271 4.4 68.1 1.0
CE2 B:TYR272 4.5 67.6 1.0
CE B:LYS311 4.6 84.1 1.0
CA M:CYS3 4.9 79.1 1.0
CD2 B:TYR272 4.9 67.3 1.0

Zinc binding site 2 out of 6 in 1tnz

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Zinc binding site 2 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:72.8
occ:1.00
NE2 D:HIS321 2.1 65.1 1.0
OD2 D:ASP269 2.2 69.3 1.0
SG D:CYS271 2.2 64.6 1.0
SG N:CYS3 2.4 74.4 1.0
OD1 D:ASP269 2.5 69.3 1.0
CG D:ASP269 2.7 67.5 1.0
CE1 D:HIS321 3.0 65.5 1.0
CD2 D:HIS321 3.1 64.6 1.0
CB D:CYS271 3.2 61.9 1.0
CB N:CYS3 3.5 77.6 1.0
N D:CYS271 4.1 61.6 1.0
ND1 D:HIS321 4.1 66.1 1.0
CG D:HIS321 4.1 65.8 1.0
CB D:ASP269 4.1 65.6 1.0
CD2 D:LEU320 4.2 62.3 1.0
CA D:CYS271 4.2 61.9 1.0
CB D:LYS311 4.2 74.6 1.0
CE2 D:TYR272 4.6 68.7 1.0
CA N:CYS3 4.8 78.9 1.0
CE D:LYS311 4.9 79.4 1.0
CD2 D:TYR272 5.0 67.5 1.0

Zinc binding site 3 out of 6 in 1tnz

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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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:63.7
occ:1.00
NE2 F:HIS321 2.1 60.2 1.0
SG O:CYS3 2.4 71.3 1.0
SG F:CYS271 2.4 62.4 1.0
OD1 F:ASP269 2.4 63.6 1.0
OD2 F:ASP269 2.5 60.4 1.0
CG F:ASP269 2.7 60.4 1.0
CE1 F:HIS321 3.0 62.2 1.0
CD2 F:HIS321 3.1 60.5 1.0
CB F:CYS271 3.4 58.4 1.0
CB O:CYS3 3.6 73.8 1.0
ND1 F:HIS321 4.1 63.0 1.0
CB F:LYS311 4.1 73.1 1.0
CB F:ASP269 4.1 60.8 1.0
CG F:HIS321 4.2 63.4 1.0
N F:CYS271 4.2 58.0 1.0
CD2 F:LEU320 4.3 62.7 1.0
CA F:CYS271 4.4 58.7 1.0
CE2 F:TYR272 4.6 63.9 1.0
CE F:LYS311 4.7 81.1 1.0
O F:HOH383 4.9 53.0 1.0
CA O:CYS3 4.9 75.5 1.0
CA F:LYS311 4.9 71.5 1.0

Zinc binding site 4 out of 6 in 1tnz

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Zinc binding site 4 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:82.1
occ:1.00
NE2 H:HIS321 2.2 80.7 1.0
OD2 H:ASP269 2.2 70.0 1.0
SG P:CYS3 2.4 90.6 1.0
OD1 H:ASP269 2.4 75.8 1.0
SG H:CYS271 2.5 75.2 1.0
CG H:ASP269 2.6 73.0 1.0
CE1 H:HIS321 3.0 81.0 1.0
CD2 H:HIS321 3.2 81.5 1.0
CB P:CYS3 3.4 90.6 1.0
CB H:CYS271 3.5 75.4 1.0
CB H:ASP269 4.1 73.8 1.0
CB H:LYS311 4.1 90.0 1.0
ND1 H:HIS321 4.1 82.9 1.0
N H:CYS271 4.2 74.3 1.0
CG H:HIS321 4.3 82.0 1.0
CD2 H:LEU320 4.4 73.0 1.0
CA H:CYS271 4.4 74.0 1.0
CE2 H:TYR272 4.6 72.7 1.0
CE H:LYS311 4.6 89.9 1.0
CA P:CYS3 4.8 91.3 1.0
NZ H:LYS311 4.9 87.4 1.0
CD2 H:TYR272 4.9 72.9 1.0
CA H:LYS311 5.0 89.9 1.0

Zinc binding site 5 out of 6 in 1tnz

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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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:67.5
occ:1.00
NE2 J:HIS321 2.2 65.2 1.0
OD2 J:ASP269 2.3 57.3 1.0
SG J:CYS271 2.3 61.9 1.0
SG Q:CYS3 2.4 73.0 1.0
OD1 J:ASP269 2.5 62.6 1.0
CG J:ASP269 2.7 60.9 1.0
CE1 J:HIS321 3.0 64.2 1.0
CD2 J:HIS321 3.1 63.7 1.0
CB J:CYS271 3.2 61.3 1.0
CB Q:CYS3 3.5 74.5 1.0
N J:CYS271 4.1 62.0 1.0
ND1 J:HIS321 4.1 64.8 1.0
O J:HOH397 4.1 61.4 1.0
CG J:HIS321 4.1 63.9 1.0
CD2 J:LEU320 4.2 53.5 1.0
CB J:ASP269 4.2 59.6 1.0
CA J:CYS271 4.2 62.1 1.0
CB J:LYS311 4.2 72.3 1.0
CE2 J:TYR272 4.6 63.5 1.0
CA Q:CYS3 4.9 75.4 1.0
CE J:LYS311 4.9 81.7 1.0
CD2 J:TYR272 5.0 61.9 1.0

Zinc binding site 6 out of 6 in 1tnz

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Zinc binding site 6 out of 6 in the Rat Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Rrcvll Peptide Derived From CDC42 Splice Isoform-2


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 Rrcvll Peptide Derived From CDC42 Splice Isoform-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:65.7
occ:1.00
NE2 L:HIS321 2.1 58.0 1.0
OD2 L:ASP269 2.2 61.8 1.0
SG L:CYS271 2.3 55.7 1.0
SG R:CYS3 2.3 71.5 1.0
OD1 L:ASP269 2.5 59.8 1.0
CG L:ASP269 2.6 59.7 1.0
CE1 L:HIS321 3.0 60.0 1.0
CD2 L:HIS321 3.1 58.8 1.0
CB L:CYS271 3.3 53.6 1.0
CB R:CYS3 3.5 73.4 1.0
ND1 L:HIS321 4.1 62.0 1.0
N L:CYS271 4.1 54.4 1.0
CB L:ASP269 4.1 57.2 1.0
CB L:LYS311 4.2 62.8 1.0
CG L:HIS321 4.2 61.4 1.0
O L:HOH413 4.2 56.1 1.0
CD2 L:LEU320 4.3 55.4 1.0
CA L:CYS271 4.3 54.0 1.0
CE2 L:TYR272 4.6 56.4 1.0
CE L:LYS311 4.8 74.5 1.0
CA R:CYS3 4.8 74.0 1.0
CD2 L:TYR272 5.0 57.3 1.0
CA L:LYS311 5.0 60.3 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 03:05:18 2020

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