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Zinc in PDB 1n4r: Protein Geranylgeranyltransferase Type-I Complexed with A Geranylgeranylated Kkksktkcvil Peptide Product

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

All present enzymatic activity of Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product, PDB code: 1n4r 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) 29.86 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 272.068, 268.801, 185.310, 90.00, 131.55, 90.00
R / Rfree (%) 20 / 21.8

Other elements in 1n4r:

The structure of Protein Geranylgeranyltransferase Type-I Complexed with A Geranylgeranylated Kkksktkcvil Peptide Product also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Protein Geranylgeranyltransferase Type-I Complexed with A Geranylgeranylated Kkksktkcvil Peptide Product (pdb code 1n4r). 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 A Geranylgeranylated Kkksktkcvil Peptide Product, PDB code: 1n4r:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1n4r

Go back to Zinc Binding Sites List in 1n4r
Zinc binding site 1 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn378

b:77.8
occ:0.93
OD2 B:ASP269 2.3 54.3 1.0
NE2 B:HIS321 2.4 49.7 1.0
SG B:CYS271 2.4 57.7 1.0
OD1 B:ASP269 2.5 55.9 1.0
CG B:ASP269 2.7 52.7 1.0
SG M:CYS108 2.7 61.8 1.0
C1 M:GER1108 3.1 62.0 1.0
CD2 B:HIS321 3.3 48.6 1.0
CE1 B:HIS321 3.3 49.2 1.0
CB B:CYS271 3.5 49.2 1.0
C2 M:GER1108 3.5 61.3 1.0
CB M:CYS108 4.0 64.8 1.0
CB B:ASP269 4.0 50.5 1.0
N B:CYS271 4.2 44.8 1.0
ND1 B:HIS321 4.3 48.2 1.0
CG B:HIS321 4.3 48.1 1.0
CB B:LYS311 4.4 62.5 1.0
CA B:CYS271 4.4 46.4 1.0
CD2 B:LEU320 4.4 44.1 1.0
C3 M:GER1108 4.8 60.9 1.0
CE B:LYS311 4.8 71.7 1.0
CE2 B:TYR272 5.0 41.7 1.0

Zinc binding site 2 out of 6 in 1n4r

Go back to Zinc Binding Sites List in 1n4r
Zinc binding site 2 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn378

b:66.2
occ:0.92
OD2 D:ASP269 2.3 50.7 1.0
SG D:CYS271 2.4 43.9 1.0
NE2 D:HIS321 2.4 47.5 1.0
OD1 D:ASP269 2.6 49.6 1.0
SG N:CYS208 2.7 58.4 1.0
CG D:ASP269 2.7 48.1 1.0
C1 N:GER1208 3.1 57.5 1.0
CD2 D:HIS321 3.2 48.3 1.0
CE1 D:HIS321 3.3 47.6 1.0
CB D:CYS271 3.4 39.4 1.0
C2 N:GER1208 3.5 56.2 1.0
CB N:CYS208 3.9 64.2 1.0
CB D:ASP269 4.0 44.4 1.0
N D:CYS271 4.2 37.6 1.0
ND1 D:HIS321 4.3 48.6 1.0
CG D:HIS321 4.3 47.4 1.0
CA D:CYS271 4.4 38.6 1.0
CD2 D:LEU320 4.4 41.6 1.0
CB D:LYS311 4.4 58.2 1.0
C3 N:GER1208 4.8 55.2 1.0
CE D:LYS311 4.9 65.2 1.0
CE2 D:TYR272 4.9 39.8 1.0

Zinc binding site 3 out of 6 in 1n4r

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Zinc binding site 3 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn378

b:78.4
occ:0.94
OD2 F:ASP269 2.2 44.5 1.0
NE2 F:HIS321 2.4 47.2 1.0
SG F:CYS271 2.5 52.6 1.0
OD1 F:ASP269 2.5 46.5 1.0
CG F:ASP269 2.6 43.9 1.0
SG O:CYS308 2.7 61.2 1.0
C1 O:GER1308 3.1 60.7 1.0
CD2 F:HIS321 3.2 46.0 1.0
CE1 F:HIS321 3.3 46.7 1.0
CB F:CYS271 3.5 43.2 1.0
C2 O:GER1308 3.5 58.6 1.0
CB F:ASP269 4.0 42.3 1.0
CB O:CYS308 4.0 64.3 1.0
N F:CYS271 4.2 41.4 1.0
ND1 F:HIS321 4.3 47.1 1.0
CG F:HIS321 4.3 47.3 1.0
CB F:LYS311 4.3 58.3 1.0
CA F:CYS271 4.4 42.5 1.0
CD2 F:LEU320 4.5 44.3 1.0
CE F:LYS311 4.8 65.6 1.0
C3 O:GER1308 4.8 58.1 1.0
O F:HOH843 4.9 49.0 1.0
CE2 F:TYR272 5.0 43.8 1.0
C F:ASP269 5.0 42.3 1.0

Zinc binding site 4 out of 6 in 1n4r

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Zinc binding site 4 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn378

b:87.3
occ:0.93
OD2 H:ASP269 2.3 59.1 1.0
NE2 H:HIS321 2.4 68.7 1.0
SG H:CYS271 2.4 65.4 1.0
OD1 H:ASP269 2.5 60.2 1.0
CG H:ASP269 2.7 58.0 1.0
SG P:CYS408 2.8 75.6 1.0
C1 P:GER1408 3.2 73.3 1.0
CD2 H:HIS321 3.2 67.8 1.0
CE1 H:HIS321 3.3 69.0 1.0
CB H:CYS271 3.4 59.0 1.0
C2 P:GER1408 3.5 70.0 1.0
CB P:CYS408 4.0 76.5 1.0
CB H:ASP269 4.0 56.6 1.0
N H:CYS271 4.2 56.3 1.0
ND1 H:HIS321 4.3 68.3 1.0
CG H:HIS321 4.3 67.0 1.0
CB H:LYS311 4.4 84.2 1.0
CA H:CYS271 4.4 56.9 1.0
CD2 H:LEU320 4.4 57.0 1.0
C3 P:GER1408 4.8 68.3 1.0
CE H:LYS311 4.8 86.9 1.0
CE2 H:TYR272 5.0 49.1 1.0

Zinc binding site 5 out of 6 in 1n4r

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Zinc binding site 5 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn378

b:68.1
occ:1.00
OD2 J:ASP269 2.3 44.2 1.0
SG J:CYS271 2.4 44.9 1.0
NE2 J:HIS321 2.5 46.3 1.0
OD1 J:ASP269 2.5 42.9 1.0
CG J:ASP269 2.6 42.7 1.0
SG Q:CYS508 2.7 56.8 1.0
C1 Q:GER1508 3.1 56.9 1.0
CD2 J:HIS321 3.3 45.7 1.0
CE1 J:HIS321 3.3 46.1 1.0
CB J:CYS271 3.4 40.0 1.0
C2 Q:GER1508 3.4 55.1 1.0
CB Q:CYS508 4.0 60.3 1.0
CB J:ASP269 4.0 40.2 1.0
N J:CYS271 4.2 37.0 1.0
ND1 J:HIS321 4.3 47.5 1.0
CG J:HIS321 4.3 44.5 1.0
CA J:CYS271 4.3 38.9 1.0
CB J:LYS311 4.4 51.9 1.0
CD2 J:LEU320 4.4 34.3 1.0
C3 Q:GER1508 4.8 54.1 1.0
CE J:LYS311 4.9 66.9 1.0
CE2 J:TYR272 4.9 33.2 1.0

Zinc binding site 6 out of 6 in 1n4r

Go back to Zinc Binding Sites List in 1n4r
Zinc binding site 6 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with 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 A Geranylgeranylated Kkksktkcvil Peptide Product within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn378

b:58.3
occ:0.94
OD2 L:ASP269 2.3 39.7 1.0
SG L:CYS271 2.4 40.0 1.0
NE2 L:HIS321 2.5 40.0 1.0
OD1 L:ASP269 2.5 36.5 1.0
CG L:ASP269 2.6 37.1 1.0
SG R:CYS608 2.7 55.3 1.0
C1 R:GER1608 3.0 54.2 1.0
CD2 L:HIS321 3.3 38.7 1.0
CE1 L:HIS321 3.4 41.7 1.0
C2 R:GER1608 3.4 53.9 1.0
CB L:CYS271 3.4 33.1 1.0
CB R:CYS608 4.0 58.8 1.0
CB L:ASP269 4.0 34.4 1.0
N L:CYS271 4.2 30.8 1.0
ND1 L:HIS321 4.4 42.4 1.0
CA L:CYS271 4.4 31.5 1.0
CG L:HIS321 4.4 40.4 1.0
CB L:LYS311 4.4 41.5 1.0
CD2 L:LEU320 4.5 32.2 1.0
C3 R:GER1608 4.7 53.3 1.0
O L:HOH855 4.7 39.1 1.0
CE2 L:TYR272 4.9 32.1 1.0
CE L:LYS311 4.9 56.8 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: Mon Jan 25 16:10:22 2021

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