Atomistry » Zinc » PDB 2zxc-3ad8 » 2zzg
Atomistry »
  Zinc »
    PDB 2zxc-3ad8 »
      2zzg »

Zinc in PDB 2zzg: Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain

Enzymatic activity of Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain

All present enzymatic activity of Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain:
6.1.1.7;

Protein crystallography data

The structure of Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain, PDB code: 2zzg was solved by M.Sokabe, T.Ose, K.Tokunaga, A.Nakamura, O.Nureki, M.Yao, I.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 70.874, 89.205, 94.905, 117.31, 90.40, 107.36
R / Rfree (%) 19.9 / 27.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain (pdb code 2zzg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain, PDB code: 2zzg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2zzg

Go back to Zinc Binding Sites List in 2zzg
Zinc binding site 1 out of 4 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain


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 Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn900

b:65.5
occ:1.00
 SG A:CYS23 2.3 66.4 1.0
SG A:CYS37 2.4 73.0 1.0
SG A:CYS20 2.4 71.6 1.0
SG A:CYS42 2.5 80.7 1.0
CB A:CYS37 3.0 74.7 1.0
CB A:CYS20 3.1 70.8 1.0
CB A:CYS42 3.4 81.0 1.0
CB A:CYS23 3.5 68.5 1.0
N A:CYS37 3.6 75.1 1.0
CA A:CYS37 3.9 74.7 1.0
N A:CYS23 4.0 69.0 1.0
CA A:CYS23 4.3 68.8 1.0
CA A:CYS20 4.6 70.8 1.0
CB A:VAL22 4.6 69.1 1.0
O A:ASP39 4.7 79.0 1.0
C A:THR36 4.7 75.7 1.0
CA A:CYS42 4.9 81.3 1.0
C A:CYS37 4.9 74.8 1.0
CE A:LYS188 4.9 63.3 1.0
NZ A:LYS188 4.9 64.5 1.0
C A:CYS23 5.0 69.5 1.0
CA A:THR36 5.0 76.0 1.0

Zinc binding site 2 out of 4 in 2zzg

Go back to Zinc Binding Sites List in 2zzg
Zinc binding site 2 out of 4 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain


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 Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:0.2
occ:1.00
 NE2 A:HIS617 2.2 58.0 1.0
O A:HOH902 2.4 70.8 1.0
NE2 A:HIS613 2.4 64.5 1.0
SG A:CYS717 2.5 68.8 1.0
CD2 A:HIS613 3.0 62.9 1.0
CE1 A:HIS617 3.1 58.4 1.0
CD2 A:HIS617 3.2 57.5 1.0
CB A:CYS717 3.5 67.4 1.0
CE1 A:HIS613 3.6 64.8 1.0
NE2 A:HIS721 3.7 61.9 1.0
CE1 A:HIS721 3.7 61.8 1.0
OE1 A:GLN715 4.0 66.6 1.0
ND1 A:HIS617 4.2 57.5 1.0
CG A:HIS613 4.3 60.7 1.0
CG A:HIS617 4.3 56.4 1.0
ND1 A:HIS613 4.5 62.4 1.0
CD A:GLN715 4.7 65.8 1.0
CA A:CYS717 4.8 67.0 1.0
O A:GLY553 4.9 70.4 1.0

Zinc binding site 3 out of 4 in 2zzg

Go back to Zinc Binding Sites List in 2zzg
Zinc binding site 3 out of 4 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain


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 Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn900

b:69.5
occ:1.00
 SG B:CYS20 2.4 67.1 1.0
SG B:CYS23 2.4 62.1 1.0
SG B:CYS42 2.4 79.5 1.0
SG B:CYS37 2.5 68.8 1.0
CB B:CYS37 3.2 71.4 1.0
CB B:CYS20 3.3 66.5 1.0
CB B:CYS23 3.4 64.8 1.0
CB B:CYS42 3.5 78.6 1.0
N B:CYS23 3.5 65.3 1.0
N B:CYS37 3.6 72.4 1.0
CA B:CYS37 4.0 71.5 1.0
CA B:CYS23 4.0 64.9 1.0
CB B:VAL22 4.4 65.5 1.0
C B:VAL22 4.7 65.5 1.0
O B:ASP39 4.7 76.4 1.0
C B:THR36 4.8 73.0 1.0
CA B:CYS20 4.8 66.8 1.0
CA B:VAL22 4.9 65.7 1.0
CE B:LYS188 4.9 59.6 1.0
C B:CYS23 4.9 65.5 1.0
C B:CYS37 4.9 71.8 1.0
N B:GLY24 4.9 65.3 1.0
CA B:CYS42 5.0 78.4 1.0
CA B:THR36 5.0 73.6 1.0

Zinc binding site 4 out of 4 in 2zzg

Go back to Zinc Binding Sites List in 2zzg
Zinc binding site 4 out of 4 in the Crystal Structure of Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain


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 Alanyl-Trna Synthetase in Complex with 5''-O-(N-(L-Alanyl)-Sulfamyoxyl) Adenine Without Oligomerization Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn901

b:96.1
occ:1.00
 NE2 B:HIS617 2.1 65.5 1.0
NE2 B:HIS613 2.4 77.6 1.0
CE1 B:HIS613 2.7 77.6 1.0
O B:HOH902 2.8 67.8 1.0
SG B:CYS717 2.8 73.7 1.0
CE1 B:HIS617 3.0 64.8 1.0
CB B:CYS717 3.2 72.8 1.0
CD2 B:HIS617 3.3 64.7 1.0
CD2 B:HIS613 3.3 76.7 1.0
ND1 B:HIS613 3.7 76.6 1.0
NE2 B:HIS721 3.8 72.4 1.0
CE1 B:HIS721 4.0 73.1 1.0
CG B:HIS613 4.0 75.3 1.0
OE1 B:GLN715 4.1 71.1 1.0
ND1 B:HIS617 4.1 64.8 1.0
CG B:HIS617 4.3 63.9 1.0
CA B:CYS717 4.6 72.8 1.0
CD B:GLN715 4.9 70.6 1.0
O B:GLY553 4.9 93.9 1.0
O B:HIS613 5.0 73.0 1.0

Reference:

M.Sokabe, T.Ose, A.Nakamura, K.Tokunaga, O.Nureki, M.Yao, I.Tanaka. The Structure of Alanyl-Trna Synthetase with Editing Domain. Proc.Natl.Acad.Sci.Usa V. 106 11028 2009.
ISSN: ISSN 0027-8424
PubMed: 19549823
DOI: 10.1073/PNAS.0904645106
Page generated: Thu Oct 24 11:00:31 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy