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Manganese in PDB 7wao: Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn

Enzymatic activity of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn

All present enzymatic activity of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn:
6.1.1.17;

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn, PDB code: 7wao 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) 45.33 / 2.58
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 156.75, 46.88, 94.53, 90, 108.88, 90
R / Rfree (%) 18.6 / 24.6

Other elements in 7wao:

The structure of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn (pdb code 7wao). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn, PDB code: 7wao:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 7wao

Go back to Manganese Binding Sites List in 7wao
Manganese binding site 1 out of 4 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1001

b:82.9
occ:1.00
 OE2 A:GLU362 2.5 103.3 1.0
ND1 A:HIS479 2.5 85.7 1.0
OE1 A:GLU362 2.6 93.1 1.0
CD A:GLU362 2.9 84.9 1.0
CE1 A:HIS479 3.1 81.4 1.0
OE1 A:GLU357 3.2 108.1 1.0
OE2 A:GLU357 3.3 110.4 1.0
CG A:HIS479 3.7 83.6 1.0
CD A:GLU357 3.7 109.5 1.0
CB A:HIS479 4.2 80.9 1.0
CA A:LYS360 4.2 80.7 1.0
NE2 A:HIS479 4.3 76.6 1.0
CB A:LYS360 4.3 72.2 1.0
CG A:GLU362 4.4 68.8 1.0
O A:HIS479 4.4 105.0 1.0
CD2 A:HIS479 4.6 81.8 1.0
N A:TYR361 4.6 70.0 1.0
O A:PRO319 4.6 61.5 1.0
CB A:PRO319 4.8 49.7 1.0
C A:LYS360 4.9 78.3 1.0

Manganese binding site 2 out of 4 in 7wao

Go back to Manganese Binding Sites List in 7wao
Manganese binding site 2 out of 4 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1002

b:103.8
occ:1.00
 NE2 A:HIS767 2.5 87.6 1.0
CD2 A:HIS767 3.4 85.0 1.0
OD2 A:ASP741 3.4 131.0 1.0
CE1 A:HIS767 3.5 88.2 1.0
O A:ASN764 3.8 56.1 1.0
CB A:ASP741 3.9 89.3 1.0
CG A:ASP741 4.0 118.1 1.0
ND2 A:ASN762 4.1 74.2 1.0
CG A:HIS767 4.6 84.1 1.0
ND1 A:HIS767 4.6 84.7 1.0
CA A:SER765 4.7 59.9 1.0
OD1 A:ASN762 4.8 68.0 1.0
C A:ASN764 4.8 54.5 1.0
CG A:ASN762 4.9 72.5 1.0
OD1 A:ASP741 5.0 122.5 1.0

Manganese binding site 3 out of 4 in 7wao

Go back to Manganese Binding Sites List in 7wao
Manganese binding site 3 out of 4 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1003

b:143.3
occ:0.84
 NE2 A:HIS712 2.8 135.5 1.0
CE1 A:HIS712 3.6 138.4 1.0
CD2 A:HIS712 3.7 135.8 1.0
ND1 A:HIS712 4.7 137.8 1.0
CG A:HIS712 4.8 134.9 1.0
CD2 A:PHE711 4.9 82.1 1.0

Manganese binding site 4 out of 4 in 7wao

Go back to Manganese Binding Sites List in 7wao
Manganese binding site 4 out of 4 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Mn within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn1004

b:136.6
occ:1.00
 OD1 A:ASP639 3.0 120.7 1.0
OD2 A:ASP639 3.0 108.8 1.0
CG A:ASP639 3.3 107.8 1.0
N A:GLN640 4.5 74.2 1.0
CB A:ASP639 4.6 90.2 1.0
C A:ASP639 4.7 79.4 1.0
N A:ASP639 4.8 87.0 1.0
CA A:ASP639 4.9 83.5 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: Sun Oct 6 11:00:29 2024

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