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Zinc in PDB 1kog: Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator

Enzymatic activity of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator

All present enzymatic activity of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator, PDB code: 1kog was solved by A.Torres-Larrios, A.C.Dock-Bregeon, P.Romby, B.Rees, R.Sankaranarayanan, J.Caillet, M.Springer, C.Ehresmann, B.Ehresmann, D.Moras, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.80 / 3.50
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 188.450, 101.740, 199.340, 90.00, 114.40, 90.00
R / Rfree (%) 25.1 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator (pdb code 1kog). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator, PDB code: 1kog:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1kog

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Zinc binding site 1 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:42.6
occ:1.00
 N A:TSB2002 1.9 35.1 1.0
NE2 A:HIS385 1.9 1.1 1.0
ND1 A:HIS511 2.0 55.3 1.0
SG A:CYS334 2.3 70.4 1.0
OG1 A:TSB2002 2.5 41.4 1.0
CA A:TSB2002 2.7 37.1 1.0
CE1 A:HIS385 2.8 17.6 1.0
CE1 A:HIS511 2.8 57.5 1.0
CD2 A:HIS385 3.0 4.7 1.0
CB A:TSB2002 3.1 43.9 1.0
CG A:HIS511 3.1 56.2 1.0
CB A:CYS334 3.4 61.0 1.0
CB A:HIS511 3.6 60.0 1.0
OH A:TYR462 3.6 53.9 1.0
OD2 A:ASP383 3.9 41.6 1.0
ND1 A:HIS385 3.9 16.5 1.0
NE2 A:HIS511 4.0 55.1 1.0
CA A:CYS334 4.1 57.6 1.0
CG A:HIS385 4.1 12.4 1.0
C A:TSB2002 4.1 34.1 1.0
CD2 A:HIS511 4.2 54.8 1.0
N A:CYS334 4.2 54.0 1.0
CG2 A:TSB2002 4.4 47.4 1.0
O A:TSB2002 4.4 35.2 1.0
CA A:HIS511 4.5 60.5 1.0
CZ A:TYR462 4.6 51.1 1.0
CE2 A:TYR462 4.6 43.1 1.0
CE A:MET332 4.6 69.1 1.0
CB A:MET332 4.8 46.5 1.0
OE1 A:GLN484 4.9 74.3 1.0

Zinc binding site 2 out of 8 in 1kog

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Zinc binding site 2 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:52.7
occ:1.00
 N B:TSB3002 1.7 43.5 1.0
ND1 B:HIS511 2.0 38.3 1.0
NE2 B:HIS385 2.1 73.5 1.0
SG B:CYS334 2.2 24.0 1.0
OG1 B:TSB3002 2.5 34.9 1.0
CA B:TSB3002 2.5 43.2 1.0
CE1 B:HIS511 2.8 37.5 1.0
CE1 B:HIS385 3.0 74.6 1.0
CB B:TSB3002 3.0 41.3 1.0
CD2 B:HIS385 3.1 71.1 1.0
CG B:HIS511 3.1 31.6 1.0
CB B:CYS334 3.5 40.8 1.0
CB B:HIS511 3.6 30.2 1.0
OH B:TYR462 3.7 39.2 1.0
C B:TSB3002 3.9 50.4 1.0
OD2 B:ASP383 4.0 31.2 1.0
NE2 B:HIS511 4.0 38.4 1.0
ND1 B:HIS385 4.1 73.2 1.0
CA B:CYS334 4.2 46.4 1.0
CD2 B:HIS511 4.2 37.5 1.0
CG B:HIS385 4.2 66.0 1.0
O B:TSB3002 4.3 55.6 1.0
CG2 B:TSB3002 4.3 44.4 1.0
N B:CYS334 4.3 54.0 1.0
CA B:HIS511 4.5 43.0 1.0
CZ B:TYR462 4.5 44.2 1.0
CE B:MET332 4.6 57.3 1.0
CB B:MET332 4.7 52.5 1.0
CE2 B:TYR462 4.8 45.0 1.0
OE1 B:GLN484 4.9 29.8 1.0

Zinc binding site 3 out of 8 in 1kog

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Zinc binding site 3 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:95.1
occ:1.00
 N C:TSB4002 1.8 88.2 1.0
ND1 C:HIS511 1.9 73.7 1.0
NE2 C:HIS385 2.1 74.7 1.0
SG C:CYS334 2.2 79.4 1.0
OG1 C:TSB4002 2.6 83.2 1.0
CA C:TSB4002 2.6 86.2 1.0
CE1 C:HIS511 2.7 77.5 1.0
CE1 C:HIS385 3.0 71.3 1.0
CG C:HIS511 3.1 73.0 1.0
CD2 C:HIS385 3.1 75.8 1.0
CB C:TSB4002 3.2 82.3 1.0
CB C:CYS334 3.4 78.7 1.0
OH C:TYR462 3.5 63.1 1.0
CB C:HIS511 3.6 74.7 1.0
NE2 C:HIS511 3.9 80.6 1.0
OD2 C:ASP383 4.0 55.0 1.0
C C:TSB4002 4.0 88.7 1.0
CD2 C:HIS511 4.1 75.9 1.0
CA C:CYS334 4.1 78.8 1.0
ND1 C:HIS385 4.2 71.5 1.0
CG C:HIS385 4.2 77.3 1.0
N C:CYS334 4.3 82.1 1.0
CZ C:TYR462 4.4 74.8 1.0
CG2 C:TSB4002 4.4 81.2 1.0
O C:TSB4002 4.4 91.1 1.0
CE2 C:TYR462 4.5 75.5 1.0
CA C:HIS511 4.5 75.4 1.0
CE C:MET332 4.6 70.8 1.0
CB C:MET332 4.7 76.4 1.0
OE1 C:GLN484 4.8 94.0 1.0

Zinc binding site 4 out of 8 in 1kog

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Zinc binding site 4 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:0.2
occ:1.00
 N D:TSB5002 1.8 0.8 1.0
ND1 D:HIS511 2.0 0.6 1.0
NE2 D:HIS385 2.0 0.6 1.0
OG1 D:TSB5002 2.5 94.1 1.0
SG D:CYS334 2.5 83.7 1.0
CA D:TSB5002 2.6 0.4 1.0
CE1 D:HIS511 2.9 0.0 1.0
CE1 D:HIS385 3.0 0.9 1.0
CB D:TSB5002 3.0 100.0 1.0
CD2 D:HIS385 3.1 0.4 1.0
CG D:HIS511 3.1 0.2 1.0
CB D:HIS511 3.5 0.5 1.0
CB D:CYS334 3.6 87.2 1.0
OH D:TYR462 3.7 0.6 1.0
OD2 D:ASP383 3.9 96.1 1.0
C D:TSB5002 4.0 0.8 1.0
NE2 D:HIS511 4.0 0.3 1.0
ND1 D:HIS385 4.1 0.9 1.0
CD2 D:HIS511 4.1 0.8 1.0
CG D:HIS385 4.2 0.8 1.0
CA D:CYS334 4.2 92.7 1.0
CG2 D:TSB5002 4.3 94.1 1.0
N D:CYS334 4.3 99.1 1.0
O D:TSB5002 4.4 1.0 1.0
CA D:HIS511 4.4 0.2 1.0
CZ D:TYR462 4.6 0.6 1.0
CE2 D:TYR462 4.6 0.4 1.0
CE D:MET332 4.7 77.9 1.0
OE1 D:GLN484 4.8 0.3 1.0
CB D:MET332 4.8 92.8 1.0
CG D:ASP383 5.0 0.9 1.0

Zinc binding site 5 out of 8 in 1kog

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Zinc binding site 5 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1

b:0.1
occ:1.00
 N E:TSB6002 1.8 0.3 1.0
ND1 E:HIS511 2.0 0.9 1.0
NE2 E:HIS385 2.0 0.6 1.0
SG E:CYS334 2.4 97.3 1.0
OG1 E:TSB6002 2.6 86.4 1.0
CA E:TSB6002 2.6 0.0 1.0
CE1 E:HIS511 2.8 0.9 1.0
CE1 E:HIS385 3.0 0.5 1.0
CD2 E:HIS385 3.0 0.7 1.0
CG E:HIS511 3.1 0.6 1.0
CB E:TSB6002 3.1 97.4 1.0
CB E:CYS334 3.4 0.0 1.0
CB E:HIS511 3.6 0.9 1.0
OH E:TYR462 3.7 0.9 1.0
NE2 E:HIS511 4.0 0.8 1.0
C E:TSB6002 4.0 0.9 1.0
OD2 E:ASP383 4.0 0.4 1.0
CA E:CYS334 4.1 1.0 1.0
ND1 E:HIS385 4.1 0.5 1.0
CD2 E:HIS511 4.1 0.7 1.0
CG E:HIS385 4.2 0.2 1.0
N E:CYS334 4.3 0.7 1.0
O E:TSB6002 4.4 0.8 1.0
CG2 E:TSB6002 4.4 87.4 1.0
CA E:HIS511 4.5 0.1 1.0
CZ E:TYR462 4.5 0.4 1.0
CE2 E:TYR462 4.6 0.1 1.0
CE E:MET332 4.6 0.9 1.0
CB E:MET332 4.8 0.2 1.0
OE1 E:GLN484 4.9 0.1 1.0

Zinc binding site 6 out of 8 in 1kog

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Zinc binding site 6 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn1

b:0.7
occ:1.00
 N F:TSB7002 1.8 95.0 1.0
ND1 F:HIS511 1.9 75.9 1.0
NE2 F:HIS385 2.1 36.5 1.0
SG F:CYS334 2.3 90.9 1.0
OG1 F:TSB7002 2.5 89.6 1.0
CA F:TSB7002 2.5 94.7 1.0
CE1 F:HIS511 2.8 76.1 1.0
CE1 F:HIS385 3.0 40.4 1.0
CG F:HIS511 3.0 79.0 1.0
CB F:TSB7002 3.0 94.6 1.0
CD2 F:HIS385 3.1 39.0 1.0
OH F:TYR462 3.5 67.6 1.0
CB F:CYS334 3.5 83.8 1.0
CB F:HIS511 3.5 78.8 1.0
C F:TSB7002 3.9 95.1 1.0
OD2 F:ASP383 3.9 66.9 1.0
NE2 F:HIS511 3.9 75.5 1.0
CD2 F:HIS511 4.1 78.0 1.0
ND1 F:HIS385 4.1 46.2 1.0
CG F:HIS385 4.2 44.8 1.0
CA F:CYS334 4.2 82.8 1.0
CG2 F:TSB7002 4.3 98.2 1.0
O F:TSB7002 4.3 96.6 1.0
CZ F:TYR462 4.4 74.2 1.0
N F:CYS334 4.4 81.0 1.0
CA F:HIS511 4.4 75.3 1.0
CE2 F:TYR462 4.5 71.9 1.0
CE F:MET332 4.6 97.9 1.0
OE1 F:GLN484 4.6 0.6 1.0
CB F:MET332 4.8 90.0 1.0
N8 F:TSB7002 5.0 96.4 1.0

Zinc binding site 7 out of 8 in 1kog

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Zinc binding site 7 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1

b:27.2
occ:1.00
 ND1 G:HIS511 1.7 6.4 1.0
N G:TSB8002 2.0 30.5 1.0
NE2 G:HIS385 2.1 22.7 1.0
SG G:CYS334 2.3 35.5 1.0
CA G:TSB8002 2.6 41.1 1.0
OG1 G:TSB8002 2.6 46.7 1.0
CE1 G:HIS511 2.7 4.3 1.0
CG G:HIS511 2.8 17.0 1.0
CD2 G:HIS385 3.1 16.1 1.0
CB G:TSB8002 3.1 47.9 1.0
CE1 G:HIS385 3.1 14.1 1.0
CB G:HIS511 3.3 19.3 1.0
CB G:CYS334 3.4 33.1 1.0
OH G:TYR462 3.6 7.5 1.0
NE2 G:HIS511 3.8 9.7 1.0
CD2 G:HIS511 3.9 13.0 1.0
C G:TSB8002 4.0 39.6 1.0
OD2 G:ASP383 4.1 0.4 1.0
ND1 G:HIS385 4.2 9.9 1.0
CG G:HIS385 4.2 12.1 1.0
CA G:CYS334 4.3 28.2 1.0
CG2 G:TSB8002 4.3 50.4 1.0
CA G:HIS511 4.3 23.2 1.0
CZ G:TYR462 4.4 1.0 1.0
O G:TSB8002 4.4 41.5 1.0
CE2 G:TYR462 4.4 0.0 1.0
N G:CYS334 4.6 20.9 1.0
OE1 G:GLN484 4.6 34.4 1.0
CE G:MET332 4.6 56.9 1.0
CB G:MET332 5.0 47.9 1.0
N8 G:TSB8002 5.0 41.7 1.0

Zinc binding site 8 out of 8 in 1kog

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Zinc binding site 8 out of 8 in the Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of E. Coli Threonyl-Trna Synthetase Interacting with the Essential Domain of Its Mrna Operator within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn1

b:54.7
occ:1.00
 ND1 H:HIS511 1.6 28.3 1.0
NE2 H:HIS385 2.0 47.9 1.0
N H:TSB9002 2.1 69.2 1.0
SG H:CYS334 2.3 46.6 1.0
CE1 H:HIS511 2.5 26.7 1.0
OG1 H:TSB9002 2.7 72.4 1.0
CA H:TSB9002 2.8 70.3 1.0
CG H:HIS511 2.8 34.9 1.0
CD2 H:HIS385 2.9 35.7 1.0
CE1 H:HIS385 3.1 40.4 1.0
CB H:TSB9002 3.3 71.0 1.0
CB H:HIS511 3.3 43.6 1.0
CB H:CYS334 3.3 62.3 1.0
OH H:TYR462 3.6 49.6 1.0
NE2 H:HIS511 3.7 33.0 1.0
CD2 H:HIS511 3.8 30.4 1.0
CG H:HIS385 4.1 37.0 1.0
ND1 H:HIS385 4.1 34.4 1.0
C H:TSB9002 4.2 71.6 1.0
CA H:CYS334 4.2 62.4 1.0
OD2 H:ASP383 4.2 15.1 1.0
CA H:HIS511 4.3 45.6 1.0
CZ H:TYR462 4.4 49.9 1.0
CE2 H:TYR462 4.4 50.1 1.0
N H:CYS334 4.4 62.5 1.0
CG2 H:TSB9002 4.4 72.7 1.0
O H:TSB9002 4.6 71.3 1.0
OE1 H:GLN484 4.6 55.5 1.0
CE H:MET332 4.8 68.7 1.0

Reference:

A.Torres-Larios, A.C.Dock-Bregeon, P.Romby, B.Rees, R.Sankaranarayanan, J.Caillet, M.Springer, C.Ehresmann, B.Ehresmann, D.Moras. Structural Basis of Translational Control By Escherichia Coli Threonyl Trna Synthetase. Nat.Struct.Biol. V. 9 343 2002.
ISSN: ISSN 1072-8368
PubMed: 11953757
Page generated: Sun Oct 13 04:35:02 2024

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