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Zinc in PDB 1n4p: Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate

Enzymatic activity of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate

All present enzymatic activity of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate:
2.5.1.58; 2.5.1.59;

Protein crystallography data

The structure of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate, PDB code: 1n4p was solved by J.S.Taylor, T.S.Reid, 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) 29.92 / 2.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 272.338, 271.566, 185.425, 90.00, 131.56, 90.00
R / Rfree (%) 20.4 / 22.8

Other elements in 1n4p:

The structure of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate also contains other interesting chemical elements:

Chlorine (Cl) 9 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate (pdb code 1n4p). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate, PDB code: 1n4p:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1n4p

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Zinc binding site 1 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:38.2
occ:1.00
 OD2 B:ASP269 1.9 36.3 1.0
NE2 B:HIS321 2.1 40.8 1.0
O B:HOH1027 2.2 31.8 1.0
SG B:CYS271 2.2 43.1 1.0
CG B:ASP269 2.6 39.0 1.0
OD1 B:ASP269 2.7 41.4 1.0
CE1 B:HIS321 3.0 38.9 1.0
CD2 B:HIS321 3.1 39.8 1.0
CB B:CYS271 3.4 41.1 1.0
CB B:ASP269 4.0 37.5 1.0
ND1 B:HIS321 4.1 40.4 1.0
CG B:HIS321 4.2 40.4 1.0
N B:CYS271 4.3 38.1 1.0
CB B:LYS311 4.4 50.3 1.0
CA B:CYS271 4.4 39.3 1.0
O B:HOH403 4.5 37.4 1.0
CD2 B:LEU320 4.6 37.0 1.0
CE2 B:TYR272 4.8 38.5 1.0
O B:HOH1453 4.9 47.8 1.0

Zinc binding site 2 out of 6 in 1n4p

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Zinc binding site 2 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:37.4
occ:1.00
 OD2 D:ASP269 1.9 33.4 1.0
NE2 D:HIS321 2.0 39.0 1.0
SG D:CYS271 2.2 35.9 1.0
O D:HOH1035 2.2 34.1 1.0
CG D:ASP269 2.6 35.1 1.0
OD1 D:ASP269 2.7 36.0 1.0
CE1 D:HIS321 2.9 39.5 1.0
CD2 D:HIS321 3.0 41.3 1.0
CB D:CYS271 3.3 33.7 1.0
O D:HOH1604 4.0 50.1 1.0
ND1 D:HIS321 4.0 41.1 1.0
CB D:ASP269 4.1 34.1 1.0
CG D:HIS321 4.1 41.3 1.0
N D:CYS271 4.2 33.7 1.0
CA D:CYS271 4.4 33.3 1.0
CB D:LYS311 4.4 49.6 1.0
CD2 D:LEU320 4.5 34.0 1.0
O D:HOH420 4.6 37.0 1.0
CE2 D:TYR272 4.9 35.1 1.0

Zinc binding site 3 out of 6 in 1n4p

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Zinc binding site 3 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:40.8
occ:1.00
 OD2 F:ASP269 1.8 33.3 1.0
O F:HOH1051 1.9 39.5 1.0
NE2 F:HIS321 2.0 35.4 1.0
SG F:CYS271 2.2 40.7 1.0
CG F:ASP269 2.6 35.7 1.0
OD1 F:ASP269 2.7 37.9 1.0
CE1 F:HIS321 2.9 36.7 1.0
CD2 F:HIS321 3.0 36.7 1.0
CB F:CYS271 3.3 36.2 1.0
CB F:ASP269 4.0 33.9 1.0
ND1 F:HIS321 4.0 38.7 1.0
CG F:HIS321 4.1 39.4 1.0
O F:HOH1606 4.1 52.5 1.0
N F:CYS271 4.2 35.5 1.0
CB F:LYS311 4.3 50.9 1.0
CA F:CYS271 4.4 36.1 1.0
CD2 F:LEU320 4.6 35.6 1.0
O F:HOH604 4.6 34.2 1.0
CE2 F:TYR272 4.8 39.0 1.0

Zinc binding site 4 out of 6 in 1n4p

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Zinc binding site 4 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:54.1
occ:1.00
 OD2 H:ASP269 1.9 40.2 1.0
NE2 H:HIS321 2.1 66.5 1.0
SG H:CYS271 2.2 51.9 1.0
CG H:ASP269 2.6 46.2 1.0
OD1 H:ASP269 2.7 50.5 1.0
CE1 H:HIS321 3.0 65.6 1.0
CD2 H:HIS321 3.1 66.3 1.0
CB H:CYS271 3.3 51.4 1.0
CB H:ASP269 4.0 46.3 1.0
ND1 H:HIS321 4.1 66.2 1.0
CG H:HIS321 4.2 65.4 1.0
N H:CYS271 4.3 49.1 1.0
O H:HOH450 4.3 53.1 1.0
CA H:CYS271 4.4 49.4 1.0
CB H:LYS311 4.4 76.3 1.0
CD2 H:LEU320 4.6 55.6 1.0
CE2 H:TYR272 4.8 49.4 1.0

Zinc binding site 5 out of 6 in 1n4p

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Zinc binding site 5 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:35.6
occ:1.00
 OD2 J:ASP269 1.9 29.4 1.0
NE2 J:HIS321 2.0 41.3 1.0
O J:HOH1025 2.2 31.3 1.0
SG J:CYS271 2.2 37.8 1.0
CG J:ASP269 2.6 32.1 1.0
OD1 J:ASP269 2.7 33.5 1.0
CE1 J:HIS321 2.9 39.4 1.0
CD2 J:HIS321 3.0 39.9 1.0
CB J:CYS271 3.3 35.6 1.0
O J:HOH1489 3.7 57.4 1.0
ND1 J:HIS321 4.0 38.5 1.0
O J:HOH1610 4.0 49.7 1.0
CB J:ASP269 4.1 32.3 1.0
CG J:HIS321 4.1 38.5 1.0
N J:CYS271 4.2 33.5 1.0
O J:HOH527 4.4 47.9 1.0
CB J:LYS311 4.4 46.8 1.0
CA J:CYS271 4.4 35.4 1.0
CD2 J:LEU320 4.5 37.0 1.0
CE2 J:TYR272 4.9 34.0 1.0

Zinc binding site 6 out of 6 in 1n4p

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Zinc binding site 6 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:27.9
occ:1.00
 OD2 L:ASP269 1.9 27.3 1.0
NE2 L:HIS321 2.0 33.6 1.0
O L:HOH1019 2.2 34.4 1.0
SG L:CYS271 2.2 29.7 1.0
CG L:ASP269 2.6 28.9 1.0
OD1 L:ASP269 2.7 29.0 1.0
CE1 L:HIS321 2.9 33.9 1.0
CD2 L:HIS321 3.1 32.9 1.0
CB L:CYS271 3.4 26.7 1.0
O L:HOH1592 3.9 54.5 1.0
CB L:ASP269 4.0 27.2 1.0
ND1 L:HIS321 4.0 35.1 1.0
CG L:HIS321 4.1 33.7 1.0
O L:HOH1176 4.2 44.6 1.0
N L:CYS271 4.3 27.2 1.0
CB L:LYS311 4.3 38.0 1.0
O L:HOH486 4.4 26.5 1.0
CA L:CYS271 4.4 27.1 1.0
CD2 L:LEU320 4.6 30.2 1.0
CE2 L:TYR272 4.8 26.7 1.0

Reference:

J.S.Taylor, T.S.Reid, K.L.Terry, P.J.Casey, L.S.Beese. Structure of Mammalian Protein Geranylgeranyltransferase Type-I Embo J. V. 22 5963 2003.
ISSN: ISSN 0261-4189
PubMed: 14609943
DOI: 10.1093/EMBOJ/CDG571
Page generated: Wed Dec 16 02:57:59 2020

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