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Zinc in PDB 1n4q: Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide

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

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

Protein crystallography data

The structure of Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide, PDB code: 1n4q 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) 29.99 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 271.055, 268.033, 184.971, 90.00, 131.73, 90.00
R / Rfree (%) 21.4 / 23.4

Other elements in 1n4q:

The structure of Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide 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 Ggpp Analog and A Kkksktkcvil Peptide (pdb code 1n4q). 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 Ggpp Analog and A Kkksktkcvil Peptide, PDB code: 1n4q:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 1n4q

Go back to Zinc Binding Sites List in 1n4q
Zinc binding site 1 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide


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

b:47.8
occ:1.00
OD2 B:ASP269 2.0 48.3 1.0
NE2 B:HIS321 2.1 50.4 1.0
SG B:CYS271 2.2 50.8 1.0
SG M:CYS108 2.4 56.6 1.0
OD1 B:ASP269 2.6 52.6 1.0
CG B:ASP269 2.6 47.3 1.0
CD2 B:HIS321 3.1 47.2 1.0
CE1 B:HIS321 3.1 47.3 1.0
CB B:CYS271 3.4 46.4 1.0
CB M:CYS108 3.6 58.7 1.0
CB B:ASP269 4.1 46.0 1.0
N B:CYS271 4.2 43.4 1.0
ND1 B:HIS321 4.2 48.8 1.0
CB B:LYS311 4.2 60.5 1.0
CG B:HIS321 4.2 49.7 1.0
CA B:CYS271 4.4 45.6 1.0
O B:HOH1452 4.4 69.2 1.0
CD2 B:LEU320 4.5 42.7 1.0
CE B:LYS311 4.6 68.9 1.0
O B:HOH1443 4.7 60.1 1.0
CE2 B:TYR272 4.7 53.3 1.0
CA M:CYS108 4.9 60.9 1.0
CA B:LYS311 5.0 58.4 1.0

Zinc binding site 2 out of 6 in 1n4q

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


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

b:39.5
occ:1.00
OD2 D:ASP269 2.1 44.0 1.0
NE2 D:HIS321 2.1 40.5 1.0
SG D:CYS271 2.2 41.8 1.0
SG N:CYS208 2.4 55.6 1.0
OD1 D:ASP269 2.6 44.3 1.0
CG D:ASP269 2.7 40.9 1.0
CD2 D:HIS321 3.0 41.1 1.0
CE1 D:HIS321 3.1 41.0 1.0
CB D:CYS271 3.3 39.1 1.0
CB N:CYS208 3.6 59.0 1.0
N D:CYS271 4.1 39.0 1.0
CB D:ASP269 4.1 39.9 1.0
ND1 D:HIS321 4.1 42.0 1.0
CG D:HIS321 4.1 43.3 1.0
CB D:LYS311 4.2 54.5 1.0
CA D:CYS271 4.3 39.5 1.0
O D:HOH1477 4.4 58.4 1.0
CD2 D:LEU320 4.4 43.7 1.0
O D:HOH1461 4.6 53.2 1.0
CE D:LYS311 4.7 61.1 1.0
CE2 D:TYR272 4.8 49.4 1.0
CA N:CYS208 4.9 61.6 1.0
CA D:LYS311 5.0 52.2 1.0

Zinc binding site 3 out of 6 in 1n4q

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


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

b:45.4
occ:1.00
OD2 F:ASP269 2.0 42.0 1.0
NE2 F:HIS321 2.1 41.1 1.0
SG F:CYS271 2.3 47.4 1.0
SG O:CYS308 2.4 56.2 1.0
OD1 F:ASP269 2.6 47.4 1.0
CG F:ASP269 2.6 42.4 1.0
CD2 F:HIS321 3.0 39.2 1.0
CE1 F:HIS321 3.0 40.9 1.0
CB F:CYS271 3.3 39.0 1.0
CB O:CYS308 3.5 59.1 1.0
ND1 F:HIS321 4.1 42.3 1.0
CB F:ASP269 4.1 41.6 1.0
CG F:HIS321 4.1 43.1 1.0
CB F:LYS311 4.2 54.2 1.0
N F:CYS271 4.2 40.2 1.0
CA F:CYS271 4.4 40.5 1.0
O F:HOH1472 4.4 58.0 1.0
CD2 F:LEU320 4.5 43.3 1.0
CE F:LYS311 4.6 59.6 1.0
CE2 F:TYR272 4.8 48.5 1.0
CA O:CYS308 4.9 60.5 1.0
CA F:LYS311 4.9 50.6 1.0

Zinc binding site 4 out of 6 in 1n4q

Go back to Zinc Binding Sites List in 1n4q
Zinc binding site 4 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide


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

b:60.5
occ:1.00
OD2 H:ASP269 2.0 48.6 1.0
NE2 H:HIS321 2.1 67.0 1.0
SG H:CYS271 2.2 66.0 1.0
SG P:CYS408 2.6 68.3 1.0
OD1 H:ASP269 2.6 61.2 1.0
CG H:ASP269 2.6 55.9 1.0
CD2 H:HIS321 3.0 66.0 1.0
CE1 H:HIS321 3.1 65.5 1.0
CB H:CYS271 3.3 60.9 1.0
CB P:CYS408 3.7 72.7 1.0
CB H:ASP269 4.0 54.9 1.0
N H:CYS271 4.1 57.8 1.0
ND1 H:HIS321 4.2 65.8 1.0
CG H:HIS321 4.2 65.8 1.0
CB H:LYS311 4.2 75.4 1.0
CA H:CYS271 4.3 58.9 1.0
O H:HOH1447 4.4 60.0 1.0
CD2 H:LEU320 4.5 62.0 1.0
CE H:LYS311 4.6 77.9 1.0
O H:HOH1435 4.7 59.2 1.0
CE2 H:TYR272 4.8 57.9 1.0
CA H:LYS311 5.0 74.8 1.0

Zinc binding site 5 out of 6 in 1n4q

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


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

b:42.8
occ:1.00
OD2 J:ASP269 2.0 40.1 1.0
NE2 J:HIS321 2.2 45.4 1.0
SG J:CYS271 2.2 39.3 1.0
SG Q:CYS508 2.4 61.1 1.0
OD1 J:ASP269 2.5 41.5 1.0
CG J:ASP269 2.6 41.0 1.0
CD2 J:HIS321 3.1 44.0 1.0
CE1 J:HIS321 3.2 43.4 1.0
CB J:CYS271 3.2 39.3 1.0
CB Q:CYS508 3.6 66.8 1.0
CB J:ASP269 4.0 38.7 1.0
N J:CYS271 4.0 37.0 1.0
CG J:HIS321 4.2 44.0 1.0
ND1 J:HIS321 4.2 45.0 1.0
CA J:CYS271 4.2 37.3 1.0
O J:HOH1469 4.2 57.2 1.0
CB J:LYS311 4.2 51.4 1.0
O J:HOH1462 4.4 67.3 1.0
CD2 J:LEU320 4.5 40.4 1.0
CE2 J:TYR272 4.7 41.8 1.0
CE J:LYS311 4.8 65.3 1.0
CA Q:CYS508 5.0 68.9 1.0
C J:ASP269 5.0 38.2 1.0

Zinc binding site 6 out of 6 in 1n4q

Go back to Zinc Binding Sites List in 1n4q
Zinc binding site 6 out of 6 in the Protein Geranylgeranyltransferase Type-I Complexed with A Ggpp Analog and A Kkksktkcvil Peptide


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

b:36.7
occ:1.00
OD2 L:ASP269 2.0 38.2 1.0
NE2 L:HIS321 2.2 39.9 1.0
SG L:CYS271 2.2 37.1 1.0
O L:HOH1410 2.3 34.1 1.0
CG L:ASP269 2.6 36.5 1.0
OD1 L:ASP269 2.6 36.4 1.0
CD2 L:HIS321 3.1 38.5 1.0
CE1 L:HIS321 3.1 41.9 1.0
CB L:CYS271 3.3 31.9 1.0
CB L:ASP269 4.1 33.8 1.0
N L:CYS271 4.2 32.8 1.0
ND1 L:HIS321 4.2 42.8 1.0
CG L:HIS321 4.2 41.6 1.0
CB L:LYS311 4.3 42.3 1.0
CA L:CYS271 4.3 31.2 1.0
CD2 L:LEU320 4.5 35.2 1.0
O L:HOH1499 4.5 52.6 1.0
O L:HOH1484 4.6 43.0 1.0
CE2 L:TYR272 4.7 40.4 1.0
CE L:LYS311 4.7 56.9 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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