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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

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