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

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: 1rqc was solved by M.A.Robien, K.T.Nguyen, A.Kumar, I.Hirsh, S.Turley, D.Pei, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 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 (%) 22.5 / 27.7

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 1rqc). 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: 1rqc:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cobalt binding site 1 out of 10 in 1rqc

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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:Co301

b:34.6
occ:1.00
NE2 A:HIS202 2.1 29.2 1.0
NE2 A:HIS198 2.1 20.0 1.0
SG A:CYS156 2.2 27.8 1.0
O A:HOH401 2.6 37.8 1.0
CD2 A:HIS198 2.7 21.5 1.0
CD2 A:HIS202 3.0 29.3 1.0
CE1 A:HIS202 3.2 28.9 1.0
OE1 A:GLN112 3.3 41.5 1.0
CE1 A:HIS198 3.4 20.8 1.0
CB A:CYS156 3.4 29.1 1.0
NE2 A:GLN112 3.5 41.2 1.0
CD A:GLN112 3.6 40.2 1.0
CA A:CYS156 3.9 29.3 1.0
CG A:HIS198 4.0 22.1 1.0
CG A:HIS202 4.2 29.9 1.0
ND1 A:HIS202 4.2 30.0 1.0
ND1 A:HIS198 4.3 20.9 1.0
N A:LEU157 4.5 31.7 1.0
OE1 A:GLU199 4.5 38.0 1.0
O A:GLY155 4.6 29.8 1.0
C A:CYS156 4.7 30.5 1.0
OE2 A:GLU199 4.7 35.3 1.0
CG A:GLN112 4.8 37.5 1.0
CD A:GLU199 4.9 35.3 1.0

Cobalt binding site 2 out of 10 in 1rqc

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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:Co311

b:27.4
occ:1.00
NE2 B:HIS202 2.0 23.3 1.0
NE2 B:HIS198 2.1 11.9 1.0
SG B:CYS156 2.3 21.8 1.0
O B:HOH501 2.6 18.5 1.0
CD2 B:HIS198 2.9 13.1 1.0
CD2 B:HIS202 2.9 23.7 1.0
CE1 B:HIS202 3.1 23.3 1.0
CB B:CYS156 3.2 24.0 1.0
CE1 B:HIS198 3.2 12.7 1.0
OE1 B:GLN112 3.4 33.8 1.0
CA B:CYS156 3.7 23.9 1.0
NE2 B:GLN112 3.8 31.1 1.0
CD B:GLN112 3.9 32.1 1.0
OE2 B:GLU199 3.9 24.9 1.0
CG B:HIS202 4.1 24.4 1.0
CG B:HIS198 4.1 12.9 1.0
ND1 B:HIS202 4.1 24.3 1.0
ND1 B:HIS198 4.2 12.4 1.0
N B:LEU157 4.5 25.6 1.0
C B:CYS156 4.5 24.7 1.0
OE1 B:GLU199 4.5 27.0 1.0
CD B:GLU199 4.5 25.0 1.0
O B:GLY155 4.5 23.8 1.0
N B:CYS156 4.9 23.5 1.0

Cobalt binding site 3 out of 10 in 1rqc

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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:Co321

b:27.8
occ:1.00
O C:HOH601 1.9 22.7 1.0
NE2 C:HIS198 2.1 5.3 1.0
NE2 C:HIS202 2.2 18.2 1.0
SG C:CYS156 2.3 20.4 1.0
CD2 C:HIS198 2.8 8.2 1.0
CD2 C:HIS202 3.1 19.9 1.0
CE1 C:HIS202 3.1 18.2 1.0
CE1 C:HIS198 3.3 7.1 1.0
CB C:CYS156 3.3 22.0 1.0
OE1 C:GLN112 3.5 24.3 1.0
CA C:CYS156 3.7 22.0 1.0
NE2 C:GLN112 3.9 20.4 1.0
O C:HOH611 3.9 23.4 1.0
CD C:GLN112 4.0 21.3 1.0
CG C:HIS198 4.1 10.3 1.0
ND1 C:HIS202 4.2 19.4 1.0
N C:LEU157 4.2 23.0 1.0
CG C:HIS202 4.2 20.0 1.0
ND1 C:HIS198 4.2 7.4 1.0
OE2 C:GLU199 4.3 29.4 1.0
OE1 C:GLU199 4.3 31.9 1.0
C C:CYS156 4.4 22.1 1.0
O C:GLY155 4.6 22.9 1.0
CD C:GLU199 4.7 29.0 1.0
N C:CYS156 4.9 22.3 1.0

Cobalt binding site 4 out of 10 in 1rqc

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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:Co331

b:28.8
occ:1.00
NE2 D:HIS198 2.1 16.1 1.0
NE2 D:HIS202 2.2 27.4 1.0
SG D:CYS156 2.2 31.6 1.0
CD2 D:HIS198 2.8 17.4 1.0
CD2 D:HIS202 3.0 27.3 1.0
OE1 D:GLN112 3.1 40.2 1.0
CE1 D:HIS202 3.2 26.5 1.0
CB D:CYS156 3.3 31.2 1.0
CE1 D:HIS198 3.3 17.2 1.0
CD D:GLN112 3.6 38.8 1.0
NE2 D:GLN112 3.7 39.1 1.0
CA D:CYS156 3.9 30.8 1.0
O D:HOH701 3.9 55.2 1.0
CG D:HIS198 4.0 18.1 1.0
CG D:HIS202 4.1 26.4 1.0
ND1 D:HIS202 4.2 27.3 1.0
ND1 D:HIS198 4.3 16.8 1.0
OE2 D:GLU199 4.3 31.5 1.0
OE1 D:GLU199 4.4 31.5 1.0
N D:LEU157 4.4 30.9 1.0
C D:CYS156 4.5 31.2 1.0
CD D:GLU199 4.6 29.4 1.0
O D:GLY155 4.9 30.8 1.0
CG D:GLN112 4.9 37.1 1.0
O D:HOH707 5.0 22.0 1.0

Cobalt binding site 5 out of 10 in 1rqc

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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:Co341

b:29.0
occ:1.00
NE2 E:HIS198 2.0 16.8 1.0
O E:HOH801 2.2 24.2 1.0
NE2 E:HIS202 2.2 27.7 1.0
SG E:CYS156 2.4 29.1 1.0
CD2 E:HIS198 2.9 18.7 1.0
CE1 E:HIS198 3.1 18.3 1.0
CE1 E:HIS202 3.2 28.4 1.0
CD2 E:HIS202 3.2 27.3 1.0
CB E:CYS156 3.3 28.6 1.0
NE2 E:GLN112 3.3 35.4 1.0
CD E:GLN112 3.9 34.7 1.0
CA E:CYS156 4.0 28.4 1.0
CG E:HIS198 4.0 19.5 1.0
OE1 E:GLN112 4.1 36.1 1.0
ND1 E:HIS198 4.1 18.7 1.0
ND1 E:HIS202 4.3 28.9 1.0
CG E:HIS202 4.3 26.7 1.0
OE1 E:GLU199 4.5 27.2 1.0
OE2 E:GLU199 4.6 26.0 1.0
N E:LEU157 4.6 28.7 1.0
C E:CYS156 4.7 28.4 1.0
O E:GLY155 4.8 29.4 1.0
CD E:GLU199 4.9 25.4 1.0

Cobalt binding site 6 out of 10 in 1rqc

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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:Co351

b:18.1
occ:1.00
NE2 F:HIS202 2.0 14.5 1.0
NE2 F:HIS198 2.1 2.0 1.0
SG F:CYS156 2.3 13.9 1.0
CD2 F:HIS202 2.8 16.1 1.0
O F:HOH901 2.9 10.4 1.0
CD2 F:HIS198 2.9 4.6 1.0
CE1 F:HIS202 3.1 15.6 1.0
OE1 F:GLN112 3.2 26.7 1.0
CE1 F:HIS198 3.3 3.5 1.0
O F:HOH910 3.5 32.5 1.0
CB F:CYS156 3.6 16.6 1.0
OE2 F:GLU199 3.8 24.6 1.0
CD F:GLN112 3.8 22.9 1.0
NE2 F:GLN112 3.9 23.0 1.0
CG F:HIS202 4.0 16.8 1.0
ND1 F:HIS202 4.1 15.9 1.0
CA F:CYS156 4.1 16.5 1.0
CG F:HIS198 4.1 5.5 1.0
ND1 F:HIS198 4.3 3.9 1.0
OE1 F:GLU199 4.3 25.0 1.0
CD F:GLU199 4.3 23.8 1.0
O F:HOH914 4.6 11.3 1.0
O F:GLY155 4.7 14.9 1.0
N F:LEU157 4.7 19.1 1.0
C F:CYS156 4.9 18.1 1.0
CG F:GLN112 5.0 21.3 1.0

Cobalt binding site 7 out of 10 in 1rqc

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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:Co361

b:26.2
occ:1.00
NE2 G:HIS198 2.0 13.2 1.0
O G:HOH1001 2.1 10.6 1.0
NE2 G:HIS202 2.1 26.6 1.0
SG G:CYS156 2.2 21.1 1.0
CD2 G:HIS198 2.7 15.7 1.0
CD2 G:HIS202 3.0 26.5 1.0
CE1 G:HIS202 3.2 25.9 1.0
CE1 G:HIS198 3.2 14.7 1.0
CB G:CYS156 3.3 23.6 1.0
O G:HOH1007 3.4 33.0 1.0
OE1 G:GLN112 3.7 35.9 1.0
NE2 G:GLN112 3.9 32.9 1.0
CA G:CYS156 3.9 23.5 1.0
CG G:HIS198 3.9 16.3 1.0
CD G:GLN112 4.0 33.6 1.0
OE1 G:GLU199 4.1 31.2 1.0
ND1 G:HIS198 4.2 14.9 1.0
CG G:HIS202 4.2 25.8 1.0
OE2 G:GLU199 4.2 27.8 1.0
ND1 G:HIS202 4.2 27.3 1.0
CD G:GLU199 4.5 28.2 1.0
O G:GLY155 4.6 24.3 1.0
C G:CYS156 4.7 23.9 1.0
N G:LEU157 4.7 23.6 1.0

Cobalt binding site 8 out of 10 in 1rqc

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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:Co371

b:27.6
occ:1.00
O H:HOH1101 2.0 22.6 1.0
NE2 H:HIS202 2.1 26.9 1.0
NE2 H:HIS198 2.2 10.8 1.0
SG H:CYS156 2.3 22.4 1.0
CD2 H:HIS202 2.8 25.3 1.0
CD2 H:HIS198 2.8 13.8 1.0
OE1 H:GLN112 3.1 37.1 1.0
CE1 H:HIS202 3.2 25.8 1.0
CE1 H:HIS198 3.4 13.1 1.0
CB H:CYS156 3.5 21.8 1.0
CD H:GLN112 3.7 34.4 1.0
NE2 H:GLN112 3.8 35.6 1.0
OE2 H:GLU199 4.0 29.1 1.0
O H:HOH1102 4.0 32.5 1.0
CG H:HIS202 4.0 22.9 1.0
CA H:CYS156 4.1 21.6 1.0
CG H:HIS198 4.1 13.7 1.0
ND1 H:HIS202 4.2 26.1 1.0
ND1 H:HIS198 4.3 12.9 1.0
N H:LEU157 4.6 24.1 1.0
CD H:GLU199 4.6 29.1 1.0
OE1 H:GLU199 4.6 32.2 1.0
O H:GLY155 4.8 21.5 1.0
C H:CYS156 4.9 22.5 1.0
CG H:GLN112 4.9 31.3 1.0

Cobalt binding site 9 out of 10 in 1rqc

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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:Co381

b:37.0
occ:1.00
NE2 I:HIS202 2.1 24.9 1.0
NE2 I:HIS198 2.1 20.3 1.0
SG I:CYS156 2.3 24.4 1.0
O I:HOH1201 2.7 36.9 1.0
CD2 I:HIS198 2.8 21.0 1.0
CD2 I:HIS202 3.0 25.1 1.0
OE1 I:GLN112 3.0 36.6 1.0
CE1 I:HIS202 3.1 25.3 1.0
CE1 I:HIS198 3.3 20.3 1.0
CB I:CYS156 3.5 25.1 1.0
CD I:GLN112 3.7 34.8 1.0
NE2 I:GLN112 3.9 36.7 1.0
CG I:HIS198 4.1 20.8 1.0
CA I:CYS156 4.1 24.8 1.0
CG I:HIS202 4.1 24.6 1.0
ND1 I:HIS202 4.2 25.6 1.0
OE1 I:GLU199 4.2 29.9 1.0
ND1 I:HIS198 4.3 20.1 1.0
OE2 I:GLU199 4.4 28.1 1.0
N I:LEU157 4.5 26.8 1.0
CD I:GLU199 4.7 28.3 1.0
C I:CYS156 4.8 25.6 1.0
O I:GLY155 4.8 24.0 1.0
CG I:GLN112 4.9 32.9 1.0

Cobalt binding site 10 out of 10 in 1rqc

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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:Co391

b:34.4
occ:1.00
NE2 J:HIS198 2.0 14.1 1.0
NE2 J:HIS202 2.1 26.8 1.0
SG J:CYS156 2.3 24.8 1.0
O J:HOH1301 2.7 39.5 1.0
CD2 J:HIS198 2.8 16.3 1.0
CD2 J:HIS202 3.0 27.3 1.0
CE1 J:HIS198 3.1 15.4 1.0
CE1 J:HIS202 3.2 26.8 1.0
OE1 J:GLN112 3.4 39.1 1.0
CB J:CYS156 3.5 27.8 1.0
NE2 J:GLN112 3.5 37.9 1.0
CD J:GLN112 3.7 37.1 1.0
CA J:CYS156 4.0 27.9 1.0
CG J:HIS198 4.0 16.8 1.0
ND1 J:HIS198 4.1 15.1 1.0
CG J:HIS202 4.2 26.8 1.0
ND1 J:HIS202 4.2 27.0 1.0
OE2 J:GLU199 4.3 30.6 1.0
OE1 J:GLU199 4.4 31.9 1.0
N J:LEU157 4.6 29.9 1.0
CD J:GLU199 4.6 29.5 1.0
C J:CYS156 4.7 29.3 1.0
O J:GLY155 4.9 28.9 1.0
CG J:GLN112 4.9 35.3 1.0

Reference:

M.A.Robien, K.T.Nguyen, A.Kumar, I.Hirsh, S.Turley, D.Pei, W.G.Hol. An Improved Crystal Form of Plasmodium Falciparum Peptide Deformylase Protein Sci. V. 13 1155 2004.
ISSN: ISSN 0961-8368
PubMed: 15010544
DOI: 10.1110/PS.03456404
Page generated: Sun Dec 13 10:35:55 2020

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