Atomistry » Zinc » PDB 1kjz-1kys » 1kog
Atomistry »
  Zinc »
    PDB 1kjz-1kys »
      1kog »

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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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

Go back to Zinc Binding Sites List in 1kog
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: Wed Dec 16 02:55:25 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy