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Chlorine 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:

Zinc (Zn) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate, PDB code: 1n4p:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 1n4p

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Chlorine binding site 1 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl1702

b:64.0
occ:1.00
 N B:PHE286 3.3 50.9 1.0
N B:GLN287 3.4 51.2 1.0
C B:LYS284 3.5 51.6 1.0
N B:ILE285 3.7 51.1 1.0
CA B:LYS284 3.8 51.4 1.0
CG B:GLN287 3.8 49.6 1.0
CB B:GLN287 3.9 49.2 1.0
NE2 B:GLN287 3.9 47.3 1.0
CB B:PHE286 3.9 51.0 1.0
O B:LYS284 3.9 52.3 1.0
CA B:PHE286 4.0 51.5 1.0
CD B:LYS281 4.1 54.4 1.0
C B:ILE285 4.1 50.7 1.0
C B:PHE286 4.1 51.8 1.0
CA B:GLN287 4.2 51.1 1.0
CA B:ILE285 4.2 50.6 1.0
CD B:GLN287 4.2 49.8 1.0
NZ B:LYS281 4.3 60.6 1.0
O B:LYS281 4.4 51.7 1.0
CA B:LYS281 4.4 48.8 1.0
CE B:LYS281 4.5 57.6 1.0
O B:LEU280 4.7 46.7 1.0
N B:LYS284 4.7 50.5 1.0
CB B:LYS284 4.8 52.4 1.0
C B:LYS281 4.9 49.5 1.0

Chlorine binding site 2 out of 9 in 1n4p

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Chlorine binding site 2 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1705

b:56.0
occ:1.00
 NH2 C:ARG287 3.1 75.3 1.0
NH2 C:ARG291 3.4 52.4 1.0
OH C:TYR292 3.4 57.8 1.0
NE C:ARG253 3.8 66.8 1.0
NH1 C:ARG291 3.9 53.4 1.0
CZ C:ARG287 4.1 74.7 1.0
NE C:ARG287 4.1 72.6 1.0
CZ C:ARG291 4.1 52.6 1.0
NH2 C:ARG253 4.2 68.3 1.0
CZ C:TYR292 4.5 55.5 1.0
CZ C:ARG253 4.5 68.5 1.0
CG2 I:VAL64 4.6 50.5 1.0
CG C:ARG253 4.6 63.1 1.0
CE1 C:TYR292 4.7 55.8 1.0
CD C:ARG253 4.8 64.9 1.0
CD2 C:LEU256 4.8 55.9 1.0

Chlorine binding site 3 out of 9 in 1n4p

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Chlorine binding site 3 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1706

b:42.0
occ:1.00
 N D:GLN287 3.1 36.6 1.0
N D:PHE286 3.2 35.1 1.0
O D:HOH402 3.4 52.4 1.0
C D:LYS284 3.5 38.0 1.0
CG D:GLN287 3.6 42.0 1.0
N D:ILE285 3.6 35.3 1.0
CB D:GLN287 3.6 36.9 1.0
CB D:PHE286 3.8 31.5 1.0
CA D:PHE286 3.8 34.5 1.0
O D:LYS284 3.8 36.3 1.0
CA D:LYS284 3.9 40.2 1.0
C D:ILE285 3.9 34.7 1.0
C D:PHE286 3.9 36.4 1.0
CA D:GLN287 3.9 38.1 1.0
NE2 D:GLN287 4.0 45.0 1.0
CA D:ILE285 4.1 33.7 1.0
CD D:GLN287 4.2 45.3 1.0
CD D:LYS281 4.3 42.8 1.0
CA D:LYS281 4.5 38.6 1.0
O D:LYS281 4.6 38.1 1.0
O D:LEU280 4.6 38.1 1.0
N D:LYS284 4.8 41.5 1.0
O D:ILE285 4.9 34.4 1.0
CB D:LYS284 4.9 42.0 1.0
CG D:PHE286 5.0 29.9 1.0

Chlorine binding site 4 out of 9 in 1n4p

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Chlorine binding site 4 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1709

b:46.3
occ:1.00
 N F:PHE286 3.4 40.9 1.0
N F:GLN287 3.4 40.5 1.0
C F:LYS284 3.6 38.2 1.0
N F:ILE285 3.7 38.3 1.0
CA F:LYS284 3.8 38.8 1.0
CG F:GLN287 3.8 40.9 1.0
CB F:GLN287 3.9 40.0 1.0
O F:LYS284 3.9 37.2 1.0
CD F:LYS281 3.9 48.2 1.0
NE2 F:GLN287 4.0 39.3 1.0
CB F:PHE286 4.0 39.6 1.0
CA F:PHE286 4.1 40.4 1.0
C F:ILE285 4.2 40.6 1.0
C F:PHE286 4.2 40.4 1.0
CA F:GLN287 4.2 40.7 1.0
CA F:ILE285 4.3 38.9 1.0
CD F:GLN287 4.3 41.6 1.0
O F:LYS281 4.4 40.1 1.0
CE F:LYS281 4.5 51.2 1.0
CA F:LYS281 4.5 40.0 1.0
O F:LEU280 4.7 39.6 1.0
CB F:LYS284 4.7 39.3 1.0
N F:LYS284 4.8 39.6 1.0
NZ F:LYS281 4.8 54.3 1.0
CG F:LYS281 5.0 43.5 1.0
C F:LYS281 5.0 40.1 1.0

Chlorine binding site 5 out of 9 in 1n4p

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Chlorine binding site 5 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1711

b:55.4
occ:1.00
 O G:HOH383 2.3 48.3 1.0
OH G:TYR292 3.3 49.7 1.0
NH2 G:ARG287 3.5 69.9 1.0
NE G:ARG253 3.8 58.1 1.0
NH2 G:ARG291 3.9 44.8 1.0
CG G:ARG253 4.1 54.5 1.0
CD2 G:LEU256 4.3 45.4 1.0
NE G:ARG287 4.3 65.1 1.0
CZ G:ARG287 4.3 67.9 1.0
CZ G:TYR292 4.4 49.8 1.0
NH1 G:ARG291 4.4 45.2 1.0
NH2 G:ARG253 4.5 58.0 1.0
CD G:ARG253 4.6 55.5 1.0
CE1 G:TYR292 4.6 49.9 1.0
CZ G:ARG291 4.6 45.6 1.0
CZ G:ARG253 4.7 58.8 1.0
O G:HOH540 4.8 53.6 1.0

Chlorine binding site 6 out of 9 in 1n4p

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Chlorine binding site 6 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1712

b:58.6
occ:1.00
 N H:PHE286 3.2 51.2 1.0
N H:GLN287 3.3 52.4 1.0
C H:LYS284 3.5 51.7 1.0
N H:ILE285 3.6 51.1 1.0
CA H:LYS284 3.8 52.5 1.0
CB H:PHE286 3.8 51.8 1.0
O H:LYS284 3.8 52.3 1.0
CB H:GLN287 3.9 52.8 1.0
CA H:PHE286 3.9 52.3 1.0
CG H:GLN287 4.0 56.0 1.0
C H:ILE285 4.0 50.4 1.0
NE2 H:GLN287 4.0 57.2 1.0
C H:PHE286 4.1 51.7 1.0
CA H:ILE285 4.1 50.5 1.0
CD H:LYS281 4.2 60.3 1.0
CA H:GLN287 4.2 52.9 1.0
CA H:LYS281 4.3 52.0 1.0
CD H:GLN287 4.3 57.5 1.0
O H:LYS281 4.4 52.3 1.0
O H:LEU280 4.5 50.6 1.0
CE H:LYS281 4.7 65.1 1.0
N H:LYS284 4.7 53.4 1.0
CB H:LYS284 4.8 51.6 1.0
NZ H:LYS281 4.8 66.1 1.0
C H:LYS281 4.8 51.8 1.0

Chlorine binding site 7 out of 9 in 1n4p

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Chlorine binding site 7 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl1715

b:58.1
occ:1.00
 N J:PHE286 3.1 47.8 1.0
N J:GLN287 3.2 50.6 1.0
C J:LYS284 3.5 47.6 1.0
N J:ILE285 3.6 45.4 1.0
NZ J:LYS281 3.6 60.2 1.0
CB J:PHE286 3.7 49.5 1.0
CA J:LYS284 3.8 48.2 1.0
CA J:PHE286 3.8 49.3 1.0
CB J:GLN287 3.8 51.8 1.0
O J:LYS284 3.8 48.2 1.0
CG J:GLN287 3.9 58.0 1.0
C J:ILE285 3.9 47.0 1.0
C J:PHE286 4.0 49.8 1.0
CA J:ILE285 4.1 45.4 1.0
CA J:GLN287 4.1 51.2 1.0
CD J:LYS281 4.1 53.6 1.0
NE2 J:GLN287 4.1 59.8 1.0
CE J:LYS281 4.1 57.1 1.0
CA J:LYS281 4.4 47.3 1.0
CD J:GLN287 4.4 60.4 1.0
O J:LYS281 4.4 48.3 1.0
O J:LEU280 4.5 47.7 1.0
N J:LYS284 4.7 49.0 1.0
CB J:LYS284 4.8 49.6 1.0
C J:LYS281 4.9 46.6 1.0
O J:ILE285 4.9 48.7 1.0
CG J:PHE286 5.0 49.5 1.0

Chlorine binding site 8 out of 9 in 1n4p

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Chlorine binding site 8 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Cl1717

b:55.7
occ:1.00
 O K:HOH391 2.4 44.4 1.0
O K:HOH444 2.9 52.6 1.0
O A:HOH409 3.0 37.3 1.0
OH K:TYR292 3.2 50.3 1.0
NH2 K:ARG287 3.3 65.4 1.0
NE K:ARG253 3.8 58.1 1.0
NH2 K:ARG291 3.9 45.0 1.0
NE K:ARG287 4.1 62.3 1.0
CZ K:ARG287 4.2 65.4 1.0
CZ K:TYR292 4.2 47.4 1.0
NH1 K:ARG291 4.2 44.9 1.0
CD2 K:LEU256 4.4 36.1 1.0
CG K:ARG253 4.4 50.9 1.0
CE1 K:TYR292 4.4 47.5 1.0
CG2 A:VAL64 4.4 40.5 1.0
CD K:ARG253 4.6 55.0 1.0
CZ K:ARG291 4.6 46.1 1.0
NH2 K:ARG253 4.6 57.5 1.0
CZ K:ARG253 4.7 58.9 1.0

Chlorine binding site 9 out of 9 in 1n4p

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Chlorine binding site 9 out of 9 in the Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Protein Geranylgeranyltransferase Type-I Complexed with Geranylgeranyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Cl1718

b:43.2
occ:1.00
 O L:HOH878 3.1 48.9 1.0
N L:PHE286 3.2 34.0 1.0
N L:GLN287 3.3 35.0 1.0
C L:LYS284 3.4 36.5 1.0
N L:ILE285 3.5 34.2 1.0
CA L:LYS284 3.7 38.1 1.0
O L:LYS284 3.7 37.4 1.0
CB L:PHE286 3.8 32.1 1.0
CG L:GLN287 3.8 39.3 1.0
CA L:PHE286 3.9 34.2 1.0
CB L:GLN287 3.9 34.8 1.0
NE2 L:GLN287 3.9 38.7 1.0
C L:ILE285 3.9 34.2 1.0
CA L:ILE285 4.0 34.0 1.0
C L:PHE286 4.0 34.5 1.0
CD L:GLN287 4.2 39.6 1.0
CA L:GLN287 4.2 36.1 1.0
CD L:LYS281 4.2 41.9 1.0
CA L:LYS281 4.3 34.0 1.0
O L:LYS281 4.3 35.8 1.0
O L:LEU280 4.5 33.9 1.0
CE L:LYS281 4.6 49.0 1.0
N L:LYS284 4.6 38.0 1.0
CB L:LYS284 4.8 39.8 1.0
C L:LYS281 4.8 33.8 1.0
NZ L:LYS281 4.8 50.9 1.0
O L:ILE285 4.9 35.3 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: Sat Jul 20 00:17:43 2024

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