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Cobalt in PDB 1jym: Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design

Enzymatic activity of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design

All present enzymatic activity of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design:
3.5.1.31;

Protein crystallography data

The structure of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design, PDB code: 1jym was solved by A.Kumar, K.T.Nguyen, S.Srivathsan, B.Ornstein, S.Turley, I.Hirsh, D.Pei, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 121.263, 121.263, 177.272, 90.00, 90.00, 90.00
R / Rfree (%) 23.1 / 29.6

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design (pdb code 1jym). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 10 binding sites of Cobalt where determined in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design, PDB code: 1jym:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 1jym

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Cobalt binding site 1 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co300

b:46.6
occ:1.00
 NE2 A:HIS196 2.0 27.4 1.0
NE2 A:HIS200 2.0 41.7 1.0
O A:HOH9319 2.1 48.7 1.0
SG A:CYS155 2.2 32.2 1.0
CD2 A:HIS196 2.6 28.4 1.0
CD2 A:HIS200 2.9 35.2 1.0
CE1 A:HIS200 3.0 34.5 1.0
OE1 A:GLN111 3.1 68.9 1.0
CE1 A:HIS196 3.2 35.2 1.0
CD A:GLN111 3.5 66.9 1.0
CB A:CYS155 3.5 34.6 1.0
NE2 A:GLN111 3.6 71.8 1.0
CG A:HIS196 3.9 28.8 1.0
CA A:CYS155 4.0 33.2 1.0
CG A:HIS200 4.1 41.3 1.0
ND1 A:HIS200 4.1 37.7 1.0
ND1 A:HIS196 4.1 34.5 1.0
N A:LEU156 4.5 38.1 1.0
CG A:GLN111 4.6 59.0 1.0
O A:GLY154 4.7 32.9 1.0
C A:CYS155 4.7 38.3 1.0
OE2 A:GLU197 4.7 66.3 1.0
OE1 A:GLU197 4.9 51.6 1.0

Cobalt binding site 2 out of 10 in 1jym

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Cobalt binding site 2 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co1300

b:39.3
occ:1.00
 NE2 B:HIS200 2.0 28.5 1.0
NE2 B:HIS196 2.0 13.6 1.0
O B:HOH9320 2.1 36.5 1.0
SG B:CYS155 2.3 33.3 1.0
CD2 B:HIS196 2.7 12.4 1.0
CB B:CYS155 2.8 32.2 1.0
CD2 B:HIS200 3.0 29.9 1.0
CE1 B:HIS200 3.0 22.5 1.0
OE1 B:GLN111 3.1 49.4 1.0
CE1 B:HIS196 3.2 17.3 1.0
CA B:CYS155 3.7 33.3 1.0
CG B:HIS196 3.9 10.8 1.0
CD B:GLN111 4.0 45.5 1.0
ND1 B:HIS200 4.1 32.9 1.0
CG B:HIS200 4.1 34.8 1.0
ND1 B:HIS196 4.1 17.1 1.0
OE1 B:GLU197 4.2 46.6 1.0
NE2 B:GLN111 4.3 44.5 1.0
C B:CYS155 4.5 34.6 1.0
N B:LEU156 4.5 37.0 1.0
OE2 B:GLU197 4.7 51.1 1.0
CD B:GLU197 4.7 46.6 1.0
O B:GLY154 4.8 27.3 1.0
N B:CYS155 4.9 27.8 1.0

Cobalt binding site 3 out of 10 in 1jym

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Cobalt binding site 3 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Co2300

b:35.4
occ:1.00
 NE2 C:HIS196 2.0 4.5 1.0
NE2 C:HIS200 2.0 26.5 1.0
O C:HOH9321 2.1 25.6 1.0
SG C:CYS155 2.3 30.4 1.0
CD2 C:HIS196 2.6 9.9 1.0
CE1 C:HIS200 2.9 13.3 1.0
CB C:CYS155 3.0 28.2 1.0
CD2 C:HIS200 3.1 23.9 1.0
CE1 C:HIS196 3.2 7.1 1.0
CA C:CYS155 3.6 26.9 1.0
OE1 C:GLN111 3.6 32.6 1.0
O C:HOH2316 3.7 38.3 1.0
CG C:HIS196 3.9 13.4 1.0
ND1 C:HIS200 4.0 22.2 1.0
N C:LEU156 4.1 32.3 1.0
ND1 C:HIS196 4.1 11.0 1.0
CG C:HIS200 4.2 23.8 1.0
OE2 C:GLU197 4.2 53.3 1.0
CD C:GLN111 4.2 22.4 1.0
NE2 C:GLN111 4.3 18.8 1.0
C C:CYS155 4.3 26.5 1.0
OE1 C:GLU197 4.7 45.2 1.0
O C:GLY154 4.7 32.0 1.0
CD C:GLU197 4.8 40.5 1.0
N C:CYS155 4.8 26.9 1.0

Cobalt binding site 4 out of 10 in 1jym

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Cobalt binding site 4 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Co3300

b:34.1
occ:1.00
 NE2 D:HIS196 2.0 16.6 1.0
NE2 D:HIS200 2.0 45.7 1.0
O D:HOH9322 2.0 29.6 1.0
SG D:CYS155 2.3 43.1 1.0
CB D:CYS155 2.7 37.1 1.0
CD2 D:HIS196 2.8 21.9 1.0
CD2 D:HIS200 2.9 44.2 1.0
CE1 D:HIS200 3.0 26.2 1.0
CE1 D:HIS196 3.2 23.9 1.0
CA D:CYS155 3.4 36.6 1.0
OE1 D:GLN111 3.4 49.8 1.0
CG D:HIS200 4.0 39.1 1.0
CG D:HIS196 4.0 20.7 1.0
ND1 D:HIS200 4.0 34.6 1.0
CD D:GLN111 4.1 49.8 1.0
NE2 D:GLN111 4.1 53.3 1.0
ND1 D:HIS196 4.1 23.3 1.0
N D:LEU156 4.2 37.3 1.0
C D:CYS155 4.2 38.5 1.0
O D:GLY154 4.6 42.3 1.0
N D:CYS155 4.7 38.8 1.0
OE1 D:GLU197 4.7 52.4 1.0
OE2 D:GLU197 4.9 51.9 1.0
O D:HOH3308 5.0 29.2 1.0

Cobalt binding site 5 out of 10 in 1jym

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Cobalt binding site 5 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Co4300

b:39.9
occ:1.00
 NE2 E:HIS196 2.0 17.9 1.0
NE2 E:HIS200 2.0 40.1 1.0
O E:HOH9323 2.1 29.8 1.0
SG E:CYS155 2.2 41.0 1.0
CD2 E:HIS196 2.7 31.0 1.0
CE1 E:HIS200 2.9 33.2 1.0
CD2 E:HIS200 3.1 33.1 1.0
CE1 E:HIS196 3.1 31.3 1.0
NE2 E:GLN111 3.3 47.8 1.0
CB E:CYS155 3.4 39.2 1.0
CD E:GLN111 3.8 46.2 1.0
OE1 E:GLN111 3.8 46.6 1.0
CG E:HIS196 4.0 33.8 1.0
CA E:CYS155 4.0 36.8 1.0
ND1 E:HIS200 4.1 37.7 1.0
ND1 E:HIS196 4.1 32.2 1.0
CG E:HIS200 4.2 33.6 1.0
OE2 E:GLU197 4.3 47.6 1.0
N E:LEU156 4.7 36.8 1.0
OE1 E:GLU197 4.7 38.8 1.0
O E:GLY154 4.8 43.5 1.0
C E:CYS155 4.8 38.1 1.0
CD E:GLU197 4.8 43.2 1.0

Cobalt binding site 6 out of 10 in 1jym

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Cobalt binding site 6 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Co5300

b:24.1
occ:1.00
 NE2 F:HIS200 2.0 13.6 1.0
NE2 F:HIS196 2.0 3.5 1.0
O F:HOH9324 2.1 32.8 1.0
SG F:CYS155 2.2 18.0 1.0
CD2 F:HIS200 2.7 11.9 1.0
CD2 F:HIS196 2.7 7.7 1.0
CE1 F:HIS200 3.1 18.8 1.0
CE1 F:HIS196 3.2 9.9 1.0
OE1 F:GLN111 3.2 33.3 1.0
OE1 F:GLU197 3.6 35.2 1.0
CB F:CYS155 3.7 22.9 1.0
O F:HOH5310 3.8 26.7 1.0
CD F:GLN111 3.9 24.6 1.0
CG F:HIS200 3.9 16.6 1.0
CG F:HIS196 3.9 7.5 1.0
NE2 F:GLN111 4.1 25.2 1.0
ND1 F:HIS200 4.1 18.2 1.0
ND1 F:HIS196 4.1 6.5 1.0
CD F:GLU197 4.2 44.5 1.0
OE2 F:GLU197 4.3 40.1 1.0
CA F:CYS155 4.3 19.9 1.0
O F:HOH5314 4.7 15.1 1.0
O F:GLY154 4.8 18.6 1.0
N F:LEU156 4.9 24.0 1.0

Cobalt binding site 7 out of 10 in 1jym

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Cobalt binding site 7 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Co6300

b:30.9
occ:1.00
 NE2 G:HIS196 2.0 17.3 1.0
NE2 G:HIS200 2.0 42.2 1.0
O G:HOH9325 2.1 22.1 1.0
SG G:CYS155 2.3 22.1 1.0
CD2 G:HIS196 2.7 29.4 1.0
CE1 G:HIS200 3.0 30.7 1.0
CD2 G:HIS200 3.0 40.2 1.0
CB G:CYS155 3.1 28.0 1.0
CE1 G:HIS196 3.2 23.8 1.0
OE1 G:GLN111 3.2 65.3 1.0
O G:HOH6309 3.3 43.5 1.0
CA G:CYS155 3.9 24.4 1.0
CG G:HIS196 4.0 28.4 1.0
ND1 G:HIS200 4.1 39.6 1.0
ND1 G:HIS196 4.1 30.2 1.0
CG G:HIS200 4.1 34.8 1.0
CD G:GLN111 4.2 60.3 1.0
OE1 G:GLU197 4.4 41.9 1.0
OE2 G:GLU197 4.5 47.4 1.0
C G:CYS155 4.6 25.4 1.0
N G:LEU156 4.7 24.2 1.0
O G:GLY154 4.7 33.5 1.0
CD G:GLU197 4.8 38.8 1.0
NE2 G:GLN111 4.8 63.0 1.0

Cobalt binding site 8 out of 10 in 1jym

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Cobalt binding site 8 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 8 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Co7300

b:34.8
occ:1.00
 NE2 H:HIS200 2.0 43.0 1.0
NE2 H:HIS196 2.0 9.0 1.0
O H:HOH9326 2.1 36.8 1.0
SG H:CYS155 2.2 26.3 1.0
OE1 H:GLN111 2.4 59.2 1.0
CD2 H:HIS196 2.6 18.5 1.0
CD2 H:HIS200 2.7 37.6 1.0
CE1 H:HIS200 3.1 27.9 1.0
CE1 H:HIS196 3.2 20.1 1.0
CD H:GLN111 3.4 54.4 1.0
CB H:CYS155 3.7 24.1 1.0
OE1 H:GLU197 3.8 48.2 1.0
CG H:HIS200 3.8 24.4 1.0
NE2 H:GLN111 3.9 55.7 1.0
CG H:HIS196 3.9 13.5 1.0
ND1 H:HIS200 4.0 35.4 1.0
ND1 H:HIS196 4.2 18.5 1.0
CA H:CYS155 4.2 18.4 1.0
CD H:GLU197 4.4 54.4 1.0
CG H:GLN111 4.5 43.1 1.0
OE2 H:GLU197 4.5 55.7 1.0
N H:LEU156 4.6 21.6 1.0
O H:HOH7302 4.8 50.4 1.0
C H:CYS155 5.0 19.6 1.0
O H:GLY154 5.0 24.0 1.0

Cobalt binding site 9 out of 10 in 1jym

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Cobalt binding site 9 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 9 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Co8300

b:45.9
occ:1.00
 NE2 I:HIS200 2.0 38.6 1.0
NE2 I:HIS196 2.0 17.4 1.0
O I:HOH9327 2.1 51.3 1.0
SG I:CYS155 2.2 31.6 1.0
OE1 I:GLN111 2.6 49.3 1.0
CD2 I:HIS196 2.6 26.3 1.0
CD2 I:HIS200 2.9 39.2 1.0
CE1 I:HIS200 3.0 32.8 1.0
CE1 I:HIS196 3.2 24.1 1.0
CB I:CYS155 3.5 31.5 1.0
CD I:GLN111 3.6 43.4 1.0
CG I:HIS196 3.9 28.7 1.0
CA I:CYS155 4.0 26.3 1.0
CG I:HIS200 4.0 33.1 1.0
NE2 I:GLN111 4.1 48.1 1.0
ND1 I:HIS200 4.1 36.7 1.0
ND1 I:HIS196 4.1 28.3 1.0
OE1 I:GLU197 4.5 41.7 1.0
N I:LEU156 4.5 29.4 1.0
OE2 I:GLU197 4.6 52.4 1.0
C I:CYS155 4.7 27.6 1.0
CG I:GLN111 4.8 29.7 1.0
CD I:GLU197 4.8 48.9 1.0
O I:GLY154 4.9 30.5 1.0

Cobalt binding site 10 out of 10 in 1jym

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Cobalt binding site 10 out of 10 in the Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 10 of Crystals of Peptide Deformylase From Plasmodium Falciparum with Ten Subunits Per Asymmetric Unit Reveal Critical Characteristics of the Active Site For Drug Design within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Co9300

b:44.1
occ:1.00
 NE2 J:HIS196 2.0 19.0 1.0
NE2 J:HIS200 2.0 43.6 1.0
O J:HOH9328 2.1 49.8 1.0
SG J:CYS155 2.2 38.4 1.0
CD2 J:HIS196 2.7 27.1 1.0
OE1 J:GLN111 2.9 44.5 1.0
CE1 J:HIS200 2.9 33.0 1.0
CD2 J:HIS200 3.1 43.5 1.0
CE1 J:HIS196 3.2 26.9 1.0
CB J:CYS155 3.4 43.0 1.0
CD J:GLN111 3.6 45.9 1.0
NE2 J:GLN111 3.7 44.8 1.0
CG J:HIS196 3.9 26.4 1.0
OE1 J:GLU197 4.0 44.8 1.0
ND1 J:HIS200 4.1 40.3 1.0
ND1 J:HIS196 4.1 27.8 1.0
CG J:HIS200 4.2 41.3 1.0
CA J:CYS155 4.2 41.1 1.0
OE2 J:GLU197 4.3 51.4 1.0
CD J:GLU197 4.4 40.8 1.0
N J:LEU156 4.6 42.6 1.0
C J:CYS155 4.8 43.9 1.0
CG J:GLN111 4.8 43.2 1.0

Reference:

A.Kumar, K.T.Nguyen, S.Srivathsan, B.Ornstein, S.Turley, I.Hirsh, D.Pei, W.G.Hol. Crystals of Peptide Deformylase From Plasmodium Falciparum Reveal Critical Characteristics of the Active Site For Drug Design. Structure V. 10 357 2002.
ISSN: ISSN 0969-2126
PubMed: 12005434
DOI: 10.1016/S0969-2126(02)00719-0
Page generated: Tue Jul 30 14:23:38 2024

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