Atomistry » Zinc » PDB 1my2-1ndy » 1n4p
Atomistry »
  Zinc »
    PDB 1my2-1ndy »
      1n4p »

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

Go back to Zinc Binding Sites List in 1n4p
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

Go back to Zinc Binding Sites List in 1n4p
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

Go back to Zinc Binding Sites List in 1n4p
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

Go back to Zinc Binding Sites List in 1n4p
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

Go back to Zinc Binding Sites List in 1n4p
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

Go back to Zinc Binding Sites List in 1n4p
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 Oct 16 17:11:01 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy