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Gold in PDB 1a79: Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii

Protein crystallography data

The structure of Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii, PDB code: 1a79 was solved by H.Li, C.R.Trotta, J.N.Abelson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.28
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.950, 80.040, 193.590, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 26.7

Gold Binding Sites:

The binding sites of Gold atom in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii (pdb code 1a79). This binding sites where shown within 5.0 Angstroms radius around Gold atom.
In total 4 binding sites of Gold where determined in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii, PDB code: 1a79:
Jump to Gold binding site number: 1; 2; 3; 4;

Gold binding site 1 out of 4 in 1a79

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Gold binding site 1 out of 4 in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 1 of Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Au4

b:45.3
occ:0.20
SG A:CYS86 3.0 70.7 1.0
OH A:TYR75 3.1 55.8 1.0
CE2 A:TYR75 3.5 54.4 1.0
CZ A:TYR75 3.7 56.1 1.0
CA A:CYS86 3.8 44.9 1.0
CD2 A:LEU90 3.8 29.5 1.0
O A:CYS86 3.8 43.8 1.0
CB A:CYS86 4.0 54.9 1.0
CD1 A:LEU90 4.1 23.3 1.0
C A:CYS86 4.2 43.0 1.0
CD2 A:TYR89 4.2 36.5 1.0
CG A:LEU90 4.5 30.0 1.0
CD2 A:TYR75 4.7 51.2 1.0
NH2 A:ARG79 4.8 99.8 1.0
CE2 A:TYR89 4.9 36.4 1.0
CE1 A:TYR75 5.0 56.7 1.0

Gold binding site 2 out of 4 in 1a79

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Gold binding site 2 out of 4 in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 2 of Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Au2

b:73.4
occ:1.00
CB B:CYS86 3.1 44.1 1.0
SG B:CYS86 3.1 68.4 1.0
O C:HOH186 3.5 25.2 1.0
N B:LEU87 3.5 39.9 1.0
C B:CYS86 3.6 39.0 1.0
CD C:ARG18 3.8 23.3 1.0
CA B:CYS86 3.9 40.9 1.0
CD1 B:LEU87 3.9 33.1 1.0
CB C:ARG18 4.0 18.2 1.0
CA B:LEU87 4.0 36.0 1.0
O B:CYS86 4.0 32.8 1.0
CG C:ARG18 4.1 17.8 1.0
O C:ASP15 4.3 45.7 1.0
N C:ARG18 4.4 27.5 1.0
CB B:LEU87 4.5 36.5 1.0
OD1 C:ASP15 4.6 59.5 1.0
CD1 B:LEU90 4.7 23.5 1.0
N B:CYS86 4.7 38.5 1.0
CA C:ARG18 4.8 29.1 1.0
CG B:LEU87 4.9 37.2 1.0
N C:ASP17 4.9 38.8 1.0

Gold binding site 3 out of 4 in 1a79

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Gold binding site 3 out of 4 in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 3 of Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Au3

b:89.8
occ:0.50
SG C:CYS86 3.0 62.7 1.0
OH C:TYR75 3.1 54.8 1.0
CE2 C:TYR75 3.4 43.5 1.0
CZ C:TYR75 3.6 50.0 1.0
CD2 C:LEU90 3.8 23.6 1.0
CA C:CYS86 3.8 44.7 1.0
O C:CYS86 3.9 35.0 1.0
CB C:CYS86 3.9 50.1 1.0
CD1 C:LEU90 4.0 11.1 1.0
C C:CYS86 4.3 41.2 1.0
CD2 C:TYR89 4.4 32.1 1.0
CG C:LEU90 4.5 26.0 1.0
CD2 C:TYR75 4.5 44.6 1.0
NH2 C:ARG79 4.9 95.5 1.0
CE1 C:TYR75 4.9 45.6 1.0

Gold binding site 4 out of 4 in 1a79

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Gold binding site 4 out of 4 in the Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii


Mono view


Stereo pair view

A full contact list of Gold with other atoms in the Au binding site number 4 of Crystal Structure of the Trna Splicing Endonuclease From Methanococcus Jannaschii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Au1

b:69.4
occ:1.00
SG D:CYS86 3.0 75.8 1.0
CB D:CYS86 3.0 48.2 1.0
O A:HOH181 3.4 24.1 1.0
N D:LEU87 3.5 35.7 1.0
C D:CYS86 3.6 37.1 1.0
CD A:ARG18 3.8 35.8 1.0
CA D:CYS86 3.9 44.7 1.0
CA D:LEU87 4.0 32.5 1.0
CD1 D:LEU87 4.0 32.4 1.0
CB A:ARG18 4.0 27.7 1.0
CG A:ARG18 4.0 34.9 1.0
O D:CYS86 4.1 31.6 1.0
CD1 D:LEU90 4.3 31.2 1.0
O A:ASP15 4.4 44.0 1.0
CB D:LEU87 4.5 28.7 1.0
N A:ARG18 4.6 30.6 1.0
N D:CYS86 4.8 45.0 1.0
CG D:LEU87 4.9 33.9 1.0
CA A:ARG18 4.9 32.3 1.0
N A:ASP17 5.0 35.6 1.0

Reference:

H.Li, C.R.Trotta, J.Abelson. Crystal Structure and Evolution of A Transfer Rna Splicing Enzyme. Science V. 280 279 1998.
ISSN: ISSN 0036-8075
PubMed: 9535656
DOI: 10.1126/SCIENCE.280.5361.279
Page generated: Sat Dec 12 01:52:55 2020

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