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Zinc in PDB 1n4s: Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product

Enzymatic activity of Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product

All present enzymatic activity of Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product:
2.5.1.58; 2.5.1.59;

Protein crystallography data

The structure of Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product, PDB code: 1n4s 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) 29.98 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.121, 268.426, 184.818, 90.00, 131.58, 90.00
R / Rfree (%) 19.4 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product (pdb code 1n4s). 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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product, PDB code: 1n4s:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1n4s

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Zinc binding site 1 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:47.0
occ:1.00
OD2 B:ASP269 2.0 41.5 1.0
NE2 B:HIS321 2.2 48.0 1.0
SG B:CYS271 2.3 48.0 1.0
O B:HOH1559 2.4 40.1 1.0
CG B:ASP269 2.7 43.0 1.0
OD1 B:ASP269 2.7 46.8 1.0
CE1 B:HIS321 3.1 44.8 1.0
CD2 B:HIS321 3.2 44.4 1.0
CB B:CYS271 3.4 41.9 1.0
CB B:ASP269 4.1 41.1 1.0
ND1 B:HIS321 4.2 45.5 1.0
CG B:HIS321 4.2 44.4 1.0
N B:CYS271 4.3 38.8 1.0
CB B:LYS311 4.4 55.3 1.0
CA B:CYS271 4.4 39.6 1.0
CD2 B:LEU320 4.5 40.4 1.0
O B:HOH1580 4.6 71.0 1.0
O B:HOH1529 4.6 41.5 1.0
CE2 B:TYR272 4.8 35.8 1.0
CE B:LYS311 4.9 67.5 1.0

Zinc binding site 2 out of 6 in 1n4s

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Zinc binding site 2 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:45.5
occ:1.00
OD2 D:ASP269 2.0 38.6 1.0
NE2 D:HIS321 2.1 41.6 1.0
SG D:CYS271 2.3 38.1 1.0
O D:HOH1589 2.5 42.4 1.0
CG D:ASP269 2.7 36.6 1.0
OD1 D:ASP269 2.7 39.0 1.0
CE1 D:HIS321 3.0 41.1 1.0
CD2 D:HIS321 3.1 43.3 1.0
CB D:CYS271 3.3 34.5 1.0
ND1 D:HIS321 4.1 41.4 1.0
CB D:ASP269 4.1 35.5 1.0
CG D:HIS321 4.2 41.9 1.0
N D:CYS271 4.2 32.9 1.0
O D:HOH1623 4.3 64.5 1.0
CA D:CYS271 4.4 33.4 1.0
CB D:LYS311 4.4 53.6 1.0
CD2 D:LEU320 4.5 42.5 1.0
O D:HOH1544 4.6 39.4 1.0
CE2 D:TYR272 4.9 37.4 1.0
CE D:LYS311 4.9 64.1 1.0

Zinc binding site 3 out of 6 in 1n4s

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Zinc binding site 3 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:47.0
occ:1.00
OD2 F:ASP269 2.0 34.7 1.0
NE2 F:HIS321 2.1 41.2 1.0
SG F:CYS271 2.4 44.2 1.0
O F:HOH1586 2.4 50.4 1.0
CG F:ASP269 2.7 35.4 1.0
OD1 F:ASP269 2.7 39.2 1.0
CE1 F:HIS321 3.0 42.0 1.0
CD2 F:HIS321 3.1 39.7 1.0
CB F:CYS271 3.4 35.9 1.0
O F:HOH1603 3.8 64.9 1.0
CB F:ASP269 4.1 33.9 1.0
ND1 F:HIS321 4.1 42.7 1.0
CG F:HIS321 4.2 42.1 1.0
N F:CYS271 4.3 36.1 1.0
CB F:LYS311 4.4 54.7 1.0
CA F:CYS271 4.4 36.3 1.0
O F:HOH1589 4.4 64.6 1.0
CD2 F:LEU320 4.5 42.6 1.0
O F:HOH1543 4.6 41.8 1.0
CE F:LYS311 4.9 68.9 1.0
CE2 F:TYR272 4.9 38.3 1.0

Zinc binding site 4 out of 6 in 1n4s

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Zinc binding site 4 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:60.8
occ:1.00
OD2 H:ASP269 2.0 42.6 1.0
NE2 H:HIS321 2.2 66.3 1.0
SG H:CYS271 2.3 57.2 1.0
CG H:ASP269 2.7 47.5 1.0
OD1 H:ASP269 2.7 53.0 1.0
O H:HOH1560 2.8 60.1 1.0
CE1 H:HIS321 3.1 65.7 1.0
CD2 H:HIS321 3.2 66.3 1.0
CB H:CYS271 3.4 52.7 1.0
CB H:ASP269 4.1 47.0 1.0
O H:HOH1559 4.1 58.4 1.0
ND1 H:HIS321 4.2 66.4 1.0
CG H:HIS321 4.2 65.3 1.0
N H:CYS271 4.2 49.3 1.0
O H:HOH1525 4.3 49.1 1.0
CA H:CYS271 4.4 50.2 1.0
CB H:LYS311 4.4 76.9 1.0
CD2 H:LEU320 4.5 60.2 1.0
CE2 H:TYR272 4.8 48.0 1.0
CE H:LYS311 4.9 83.5 1.0

Zinc binding site 5 out of 6 in 1n4s

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Zinc binding site 5 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:42.7
occ:1.00
OD2 J:ASP269 2.0 32.8 1.0
NE2 J:HIS321 2.2 41.9 1.0
SG J:CYS271 2.3 40.3 1.0
O J:HOH1581 2.4 31.2 1.0
CG J:ASP269 2.6 34.7 1.0
OD1 J:ASP269 2.7 36.3 1.0
CE1 J:HIS321 3.0 39.8 1.0
CD2 J:HIS321 3.1 41.1 1.0
CB J:CYS271 3.3 35.5 1.0
CB J:ASP269 4.1 33.3 1.0
ND1 J:HIS321 4.1 40.8 1.0
O J:HOH1589 4.2 62.7 1.0
CG J:HIS321 4.2 39.6 1.0
N J:CYS271 4.2 33.3 1.0
CA J:CYS271 4.3 34.5 1.0
CB J:LYS311 4.4 46.9 1.0
O J:HOH1545 4.4 37.4 1.0
CD2 J:LEU320 4.5 35.6 1.0
CE2 J:TYR272 4.9 31.8 1.0
CE J:LYS311 4.9 61.6 1.0

Zinc binding site 6 out of 6 in 1n4s

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Zinc binding site 6 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product


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 Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:34.4
occ:1.00
OD2 L:ASP269 1.9 30.5 1.0
NE2 L:HIS321 2.2 35.0 1.0
SG L:CYS271 2.2 31.1 1.0
O L:HOH1630 2.3 33.8 1.0
CG L:ASP269 2.6 30.9 1.0
OD1 L:ASP269 2.7 31.9 1.0
CE1 L:HIS321 3.1 34.1 1.0
CD2 L:HIS321 3.1 35.0 1.0
CB L:CYS271 3.3 25.4 1.0
O L:HOH1649 4.0 53.1 1.0
CB L:ASP269 4.0 29.0 1.0
ND1 L:HIS321 4.2 37.8 1.0
CG L:HIS321 4.2 37.0 1.0
N L:CYS271 4.2 25.9 1.0
CA L:CYS271 4.4 25.6 1.0
O L:HOH1564 4.4 27.7 1.0
CB L:LYS311 4.4 38.9 1.0
CD2 L:LEU320 4.6 32.5 1.0
CE2 L:TYR272 4.8 30.2 1.0
CE L:LYS311 4.9 59.1 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: Fri Sep 25 22:42:21 2020
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