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Cobalt in PDB 7waj: Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co

Enzymatic activity of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co

All present enzymatic activity of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co:
6.1.1.17;

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co, PDB code: 7waj was solved by V.Sharma, Y.Manickam, P.Babbar, A.Sharma, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.04 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.19, 46.34, 95.32, 90, 110.72, 90
R / Rfree (%) 19.9 / 24.7

Other elements in 7waj:

The structure of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co (pdb code 7waj). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co, PDB code: 7waj:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 7waj

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Cobalt binding site 1 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co903

b:98.5
occ:0.63
 OE1 A:GLU444 2.4 110.1 1.0
OE1 A:GLN447 2.5 94.7 1.0
OE2 A:GLU444 2.8 100.4 1.0
CD A:GLU444 3.0 105.4 1.0
CD A:GLN447 3.5 90.9 1.0
NE2 A:GLN447 3.9 94.6 1.0
CG A:GLU444 4.5 91.3 1.0
CG A:GLN447 4.8 80.6 1.0
CB A:GLN447 4.9 79.6 1.0

Cobalt binding site 2 out of 8 in 7waj

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Cobalt binding site 2 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co904

b:118.9
occ:0.93
 NE2 A:HIS767 2.0 109.4 1.0
CE1 A:HIS767 2.8 107.9 1.0
CD2 A:HIS767 3.1 105.1 1.0
O A:ASN764 3.8 75.5 1.0
ND1 A:HIS767 3.9 105.9 1.0
CG A:HIS767 4.1 94.5 1.0
ND2 A:ASN762 4.1 93.8 1.0
CB A:ASP741 4.3 93.3 1.0
OD2 A:ASP741 4.3 119.4 1.0
CA A:SER765 4.8 71.6 1.0
CG A:ASP741 4.8 111.8 1.0
C A:ASN764 5.0 71.3 1.0

Cobalt binding site 3 out of 8 in 7waj

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Cobalt binding site 3 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co905

b:136.5
occ:1.00
 NE2 A:HIS742 3.0 83.4 1.0
CD2 A:HIS742 3.6 86.1 1.0
CE1 A:HIS742 4.1 80.7 1.0
OD2 A:ASP604 4.5 99.8 1.0
CG A:HIS742 4.9 80.8 1.0

Cobalt binding site 4 out of 8 in 7waj

Go back to Cobalt Binding Sites List in 7waj
Cobalt binding site 4 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co906

b:115.8
occ:0.76
 OD2 A:ASP800 2.3 122.5 1.0
CE1 A:HIS806 2.7 97.3 1.0
NE2 A:HIS806 2.7 96.2 1.0
CE1 A:HIS804 2.9 113.6 1.0
ND1 A:HIS804 3.4 114.5 1.0
CG A:ASP800 3.5 114.0 1.0
NE2 A:HIS804 3.9 112.5 1.0
OD1 A:ASP800 4.0 112.1 1.0
ND1 A:HIS806 4.0 93.2 1.0
CD2 A:HIS806 4.0 93.2 1.0
CG A:HIS804 4.5 111.0 1.0
CB A:ASP800 4.7 106.7 1.0
CG A:HIS806 4.7 87.0 1.0
CD2 A:HIS804 4.7 112.7 1.0
OH A:TYR738 4.9 77.2 1.0

Cobalt binding site 5 out of 8 in 7waj

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Cobalt binding site 5 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co907

b:115.9
occ:0.87
 OD1 A:ASP639 2.2 110.1 1.0
OD2 A:ASP639 2.8 99.2 1.0
CG A:ASP639 2.9 95.7 1.0
CB A:ASP639 4.3 77.8 1.0
N A:ASP639 4.8 70.9 1.0
CA A:ASP639 5.0 75.5 1.0

Cobalt binding site 6 out of 8 in 7waj

Go back to Cobalt Binding Sites List in 7waj
Cobalt binding site 6 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co908

b:144.4
occ:1.00
 CG A:GLU342 3.7 76.4 1.0
OE1 A:GLU342 3.9 103.3 1.0
CD A:GLU342 4.0 95.2 1.0
O A:GLN339 4.7 64.6 1.0
OE2 A:GLU342 4.9 100.8 1.0

Cobalt binding site 7 out of 8 in 7waj

Go back to Cobalt Binding Sites List in 7waj
Cobalt binding site 7 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co909

b:141.2
occ:1.00
 NE2 A:HIS712 3.1 125.2 1.0
CE1 A:HIS712 3.3 122.3 1.0
CD2 A:HIS712 4.2 125.2 1.0
ND1 A:HIS712 4.5 122.6 1.0
CG A:HIS712 4.9 123.5 1.0

Cobalt binding site 8 out of 8 in 7waj

Go back to Cobalt Binding Sites List in 7waj
Cobalt binding site 8 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) Complexed with Atp and Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co910

b:127.8
occ:1.00
 OE1 A:GLU362 3.0 93.4 1.0
OE2 A:GLU362 3.1 77.6 1.0
CD A:GLU362 3.4 83.1 1.0
CA A:LYS360 4.5 95.2 1.0
CB A:LYS360 4.7 94.5 1.0
CB A:PRO319 4.8 53.9 1.0
O A:PRO319 4.8 69.6 1.0
CG A:PRO319 4.8 57.8 1.0
CG A:GLU362 4.9 75.2 1.0

Reference:

V.K.Sharma, J.Chhibber-Goel, M.Yogavel, A.Sharma. Structural Characterization of Glutamyl-Trna Synthetase (Glurs) From Plasmodium Falciparum. Mol.Biochem.Parasitol. V. 253 11530 2022.
ISSN: ISSN 0166-6851
PubMed: 36370911
DOI: 10.1016/J.MOLBIOPARA.2022.111530
Page generated: Tue Jul 30 19:33:21 2024

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