Zinc in PDB 7l3o: Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II

Enzymatic activity of Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II

All present enzymatic activity of Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II:
6.1.1.3;

Protein crystallography data

The structure of Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II, PDB code: 7l3o was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.26 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 65.73, 67.45, 143.18, 91.59, 97.53, 120.78
R / Rfree (%) 17.8 / 21.3

Other elements in 7l3o:

The structure of Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II (pdb code 7l3o). 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 the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II, PDB code: 7l3o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7l3o

Go back to Zinc Binding Sites List in 7l3o
Zinc binding site 1 out of 4 in the Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II


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 the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn800

b:33.4
occ:1.00
 NE2 A:HIS477 2.2 36.1 1.0
SG A:CYS426 2.2 33.6 1.0
ND1 A:HIS629 2.3 29.6 1.0
O A:HOH1100 2.5 38.4 1.0
O A:HOH1019 2.6 39.8 1.0
CD2 A:HIS477 3.2 32.5 1.0
CE1 A:HIS629 3.2 30.5 1.0
CE1 A:HIS477 3.2 31.7 1.0
CG A:HIS629 3.2 29.6 1.0
CB A:CYS426 3.3 33.6 1.0
CB A:HIS629 3.5 28.8 1.0
O A:HOH905 3.9 38.9 1.0
CA A:CYS426 4.1 31.3 1.0
OH A:TYR553 4.2 39.1 1.0
NE2 A:HIS629 4.3 36.5 1.0
N A:CYS426 4.3 33.1 1.0
ND1 A:HIS477 4.3 34.5 1.0
CD2 A:HIS629 4.3 30.7 1.0
CG A:HIS477 4.3 35.1 1.0
OD1 A:ASP475 4.4 37.4 1.0
OD2 A:ASP475 4.5 34.7 1.0
O A:HOH1029 4.5 44.4 1.0
CA A:HIS629 4.6 30.2 1.0
OE1 A:GLN575 4.7 36.5 1.0
CG A:ASP475 4.9 37.2 1.0
CZ A:TYR553 4.9 36.5 1.0

Zinc binding site 2 out of 4 in 7l3o

Go back to Zinc Binding Sites List in 7l3o
Zinc binding site 2 out of 4 in the Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II


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 the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn800

b:32.5
occ:1.00
 O B:HOH920 2.0 31.5 1.0
NE2 B:HIS477 2.2 31.9 1.0
ND1 B:HIS629 2.2 25.5 1.0
SG B:CYS426 2.3 31.2 1.0
CD2 B:HIS477 3.1 28.2 1.0
CE1 B:HIS477 3.2 23.2 1.0
CE1 B:HIS629 3.2 30.2 1.0
CG B:HIS629 3.2 29.5 1.0
CB B:CYS426 3.2 25.6 1.0
O B:HOH1157 3.3 40.4 1.0
CB B:HIS629 3.5 25.1 1.0
O B:HOH904 3.9 32.9 1.0
CA B:CYS426 4.0 25.9 1.0
OD1 B:ASP475 4.1 32.0 1.0
N B:CYS426 4.2 25.5 1.0
ND1 B:HIS477 4.3 23.4 1.0
CG B:HIS477 4.3 29.4 1.0
NE2 B:HIS629 4.3 30.5 1.0
OD2 B:ASP475 4.3 32.0 1.0
CD2 B:HIS629 4.3 27.9 1.0
O B:HOH1111 4.4 37.3 1.0
CA B:HIS629 4.5 24.2 1.0
O B:HOH1035 4.6 33.1 1.0
CG B:ASP475 4.7 31.4 1.0

Zinc binding site 3 out of 4 in 7l3o

Go back to Zinc Binding Sites List in 7l3o
Zinc binding site 3 out of 4 in the Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II


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 the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn800

b:35.2
occ:1.00
 O C:HOH945 2.1 30.7 1.0
NE2 C:HIS477 2.2 30.9 1.0
ND1 C:HIS629 2.3 33.5 1.0
SG C:CYS426 2.3 34.2 1.0
CD2 C:HIS477 3.1 32.3 1.0
CE1 C:HIS477 3.2 29.4 1.0
CE1 C:HIS629 3.2 38.4 1.0
CG C:HIS629 3.2 29.6 1.0
CB C:CYS426 3.3 29.9 1.0
CB C:HIS629 3.5 27.2 1.0
CA C:CYS426 4.1 28.7 1.0
OD1 C:ASP475 4.1 29.7 1.0
O C:HOH946 4.2 34.7 1.0
CG C:HIS477 4.3 32.3 1.0
ND1 C:HIS477 4.3 32.7 1.0
N C:CYS426 4.3 26.1 1.0
NE2 C:HIS629 4.3 38.7 1.0
CD2 C:HIS629 4.4 35.8 1.0
OD2 C:ASP475 4.4 34.9 1.0
CA C:HIS629 4.5 26.4 1.0
CG C:ASP475 4.7 31.6 1.0
O C:HOH1039 5.0 41.2 1.0

Zinc binding site 4 out of 4 in 7l3o

Go back to Zinc Binding Sites List in 7l3o
Zinc binding site 4 out of 4 in the Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II


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 the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn800

b:40.8
occ:1.00
 O D:HOH970 2.2 37.2 1.0
NE2 D:HIS477 2.2 33.1 1.0
ND1 D:HIS629 2.3 34.6 1.0
SG D:CYS426 2.3 41.2 1.0
CE1 D:HIS477 3.1 32.8 1.0
CE1 D:HIS629 3.2 37.8 1.0
CD2 D:HIS477 3.2 35.3 1.0
CB D:CYS426 3.2 31.3 1.0
CG D:HIS629 3.3 36.5 1.0
CB D:HIS629 3.7 31.7 1.0
CA D:CYS426 4.1 34.6 1.0
O D:HOH939 4.1 36.3 1.0
OD1 D:ASP475 4.2 36.4 1.0
ND1 D:HIS477 4.2 36.8 1.0
N D:CYS426 4.3 33.0 1.0
CG D:HIS477 4.3 37.4 1.0
OD2 D:ASP475 4.3 35.6 1.0
NE2 D:HIS629 4.3 40.1 1.0
CD2 D:HIS629 4.4 38.0 1.0
CA D:HIS629 4.6 33.4 1.0
CG D:ASP475 4.7 36.4 1.0

Reference:

J.Abendroth, D.M.Dranow, D.D.Lorimer, P.S.Horanyi, T.E.Edwards. Crystal Structure of the Rna Binding Domain of Threonyl-Trna Synthetase From Cryptosporidium Parvum Iowa II To Be Published.
Page generated: Tue Oct 29 22:36:45 2024

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