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
|
Other elements in 1n4s:
The structure of Protein Geranylgeranyltransferase Type-I Complexed with Ggpp and A Geranylgeranylated Kkksktkcvil Peptide Product also contains other interesting chemical elements:
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
Go back to
Zinc Binding Sites List in 1n4s
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 Sites List in 1n4s
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 Sites List in 1n4s
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 Sites List in 1n4s
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
Go back to
Zinc Binding Sites List in 1n4s
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
Go back to
Zinc Binding Sites List in 1n4s
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: Wed Oct 16 17:11:21 2024
|