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Cobalt in PDB 7wal: Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Co

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

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

Protein crystallography data

The structure of Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Co, PDB code: 7wal 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) 46.10 / 2.29
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.73, 46.11, 95.35, 90, 110.73, 90
R / Rfree (%) 20.9 / 25.6

Other elements in 7wal:

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

Chlorine (Cl) 3 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with Co (pdb code 7wal). 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) in Complex with Co, PDB code: 7wal:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Cobalt binding site 1 out of 8 in 7wal

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Cobalt binding site 1 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1001

b:96.7
occ:0.50
 O A:HOH1122 2.3 116.2 1.0
O A:HOH1121 2.4 106.0 1.0
OE1 A:GLN447 2.5 96.5 1.0
CD A:GLN447 3.3 93.3 1.0
NE2 A:GLN447 3.3 104.4 1.0
CG2 A:VAL474 4.4 104.5 1.0
CG A:GLN447 4.7 93.3 1.0

Cobalt binding site 2 out of 8 in 7wal

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Cobalt binding site 2 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1002

b:140.0
occ:1.00
 NE2 A:HIS712 2.3 124.0 1.0
CE1 A:HIS712 3.2 123.2 1.0
CD2 A:HIS712 3.2 124.8 1.0
ND1 A:HIS712 4.3 125.2 1.0
CG A:HIS712 4.4 125.3 1.0

Cobalt binding site 3 out of 8 in 7wal

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Cobalt binding site 3 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1003

b:118.9
occ:0.85
 NE2 A:HIS767 2.1 108.4 1.0
CE1 A:HIS767 2.6 111.2 1.0
CD2 A:HIS767 3.4 107.9 1.0
O A:ASN764 3.7 74.6 1.0
ND1 A:HIS767 3.8 108.5 1.0
ND2 A:ASN762 3.9 83.6 1.0
CG A:HIS767 4.2 97.1 1.0
CB A:ASP741 4.3 101.2 1.0
CA A:SER765 4.7 80.9 1.0
C A:ASN764 4.8 75.9 1.0
CG A:ASN762 4.9 89.8 1.0
OD1 A:ASN762 5.0 85.3 1.0

Cobalt binding site 4 out of 8 in 7wal

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Cobalt binding site 4 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1004

b:124.7
occ:1.00
 OE2 A:GLU342 2.5 100.5 1.0
CD A:GLU342 3.3 87.4 1.0
OE1 A:GLU342 3.5 92.7 1.0
CG A:GLU342 4.7 83.3 1.0
O A:GLN339 4.8 71.3 1.0

Cobalt binding site 5 out of 8 in 7wal

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Cobalt binding site 5 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1005

b:127.2
occ:0.97
 NE2 A:HIS742 2.6 86.9 1.0
CE1 A:HIS742 3.5 82.5 1.0
CD2 A:HIS742 3.6 88.0 1.0
ND1 A:HIS742 4.7 81.5 1.0
CG A:HIS742 4.7 82.3 1.0
OD2 A:ASP741 5.0 115.3 1.0

Cobalt binding site 6 out of 8 in 7wal

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Cobalt binding site 6 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1006

b:119.7
occ:0.83
 OE2 A:GLU362 2.9 98.7 1.0
OE1 A:GLU362 3.1 90.7 1.0
CD A:GLU362 3.4 90.2 1.0
CA A:LYS360 4.1 97.3 1.0
CB A:LYS360 4.6 102.5 1.0
CB A:PRO319 4.7 60.6 1.0
N A:LYS360 4.8 87.6 1.0
N A:TYR361 4.9 102.6 1.0
CG A:GLU362 4.9 76.4 1.0
CG A:PRO319 4.9 65.3 1.0

Cobalt binding site 7 out of 8 in 7wal

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Cobalt binding site 7 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1007

b:103.6
occ:0.55
 CE1 A:HIS806 2.4 98.5 1.0
OD2 A:ASP800 2.5 133.2 1.0
NE2 A:HIS806 2.5 99.3 1.0
CO A:CO1008 3.2 106.1 0.5
CG A:ASP800 3.6 127.9 1.0
ND1 A:HIS806 3.7 97.7 1.0
CD2 A:HIS806 3.9 95.2 1.0
OD1 A:ASP800 4.2 128.1 1.0
CG A:HIS806 4.4 92.7 1.0
OH A:TYR738 4.5 85.0 1.0
CB A:ASP800 4.8 119.8 1.0

Cobalt binding site 8 out of 8 in 7wal

Go back to Cobalt Binding Sites List in 7wal
Cobalt binding site 8 out of 8 in the Glutamyl-Trna Synthetase From Plasmodium Falciparum (Pfers) in Complex with 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) in Complex with Co within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co1008

b:106.1
occ:0.53
 OD2 A:ASP800 2.8 133.2 1.0
CO A:CO1007 3.2 103.6 0.6
CB A:HIS804 3.3 91.8 1.0
ND1 A:HIS804 3.5 114.4 1.0
CG A:HIS804 3.6 106.3 1.0
CG A:ASP800 3.7 127.9 1.0
NE2 A:HIS806 3.9 99.3 1.0
CB A:ASP800 4.0 119.8 1.0
CE1 A:HIS806 4.4 98.5 1.0
CE1 A:HIS804 4.5 118.1 1.0
CD2 A:HIS804 4.6 115.2 1.0
CA A:HIS804 4.7 84.5 1.0
OD1 A:ASP800 4.8 128.1 1.0
CD2 A:HIS806 5.0 95.2 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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