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Nickel in PDB 1icj: Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg)

Enzymatic activity of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg)

All present enzymatic activity of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg):
3.5.1.31;

Protein crystallography data

The structure of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg), PDB code: 1icj was solved by A.Becker, I.Schlichting, W.Kabsch, S.Schultz, A.F.V.Wagner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 6.00 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.700, 63.400, 86.900, 90.00, 120.60, 90.00
R / Rfree (%) 19.8 / 23

Nickel Binding Sites:

The binding sites of Nickel atom in the Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg) (pdb code 1icj). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg), PDB code: 1icj:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 1icj

Go back to Nickel Binding Sites List in 1icj
Nickel binding site 1 out of 3 in the Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni2001

b:28.0
occ:1.00
O A:HOH2032 2.0 15.9 1.0
NE2 A:HIS136 2.1 17.6 1.0
NE2 A:HIS132 2.1 14.4 1.0
SG A:CYS90 2.3 17.8 1.0
CD2 A:HIS132 3.0 14.1 1.0
CD2 A:HIS136 3.0 16.1 1.0
CE1 A:HIS136 3.1 17.9 1.0
CE1 A:HIS132 3.2 15.2 1.0
CB A:CYS90 3.3 18.2 1.0
O A:HOH2029 3.6 16.6 1.0
NE2 A:GLN50 3.6 16.8 1.0
O A:HOH2027 3.7 24.6 1.0
CA A:CYS90 3.8 19.1 1.0
OE1 A:GLN50 3.8 18.4 1.0
CD A:GLN50 3.9 17.2 1.0
OE2 A:GLU133 4.1 22.4 1.0
ND1 A:HIS136 4.2 18.4 1.0
CG A:HIS132 4.2 15.1 1.0
CG A:HIS136 4.2 17.3 1.0
ND1 A:HIS132 4.2 14.6 1.0
C15 A:2PE2002 4.3 47.9 1.0
O A:GLY89 4.5 18.1 1.0
O A:HOH2030 4.5 13.8 1.0
OE1 A:GLU133 4.5 19.6 1.0
N A:LEU91 4.6 19.8 1.0
C A:CYS90 4.7 20.0 1.0
CD A:GLU133 4.7 20.4 1.0
N A:CYS90 5.0 18.9 1.0
C14 A:2PE2002 5.0 45.0 1.0

Nickel binding site 2 out of 3 in 1icj

Go back to Nickel Binding Sites List in 1icj
Nickel binding site 2 out of 3 in the Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni2001

b:22.5
occ:1.00
O B:HOH3037 2.0 12.3 1.0
NE2 B:HIS636 2.1 13.3 1.0
NE2 B:HIS632 2.2 13.1 1.0
SG B:CYS590 2.3 13.5 1.0
CE1 B:HIS636 3.0 12.1 1.0
CD2 B:HIS632 3.0 12.0 1.0
CD2 B:HIS636 3.1 12.4 1.0
CE1 B:HIS632 3.2 12.1 1.0
CB B:CYS590 3.4 13.5 1.0
O B:HOH3034 3.6 14.0 1.0
O B:HOH3032 3.6 16.2 1.0
NE2 B:GLN550 3.6 11.9 1.0
OE1 B:GLN550 3.8 13.9 1.0
CA B:CYS590 3.8 14.7 1.0
CD B:GLN550 3.9 13.8 1.0
OE2 B:GLU633 4.1 11.2 1.0
ND1 B:HIS636 4.2 12.9 1.0
CG B:HIS636 4.2 12.4 1.0
CG B:HIS632 4.2 12.7 1.0
ND1 B:HIS632 4.3 12.0 1.0
O B:HOH3035 4.5 11.2 1.0
N B:LEU591 4.5 14.4 1.0
OE1 B:GLU633 4.5 13.2 1.0
C B:CYS590 4.6 15.1 1.0
O B:GLY589 4.6 14.4 1.0
CD B:GLU633 4.7 14.4 1.0
O16 B:2PE3 4.8 43.8 1.0

Nickel binding site 3 out of 3 in 1icj

Go back to Nickel Binding Sites List in 1icj
Nickel binding site 3 out of 3 in the Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg)


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Pdf Protein Is Crystallized As NI2+ Containing Form, Cocrystallized with Inhibitor Polyethylene Glycol (Peg) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni2001

b:27.8
occ:1.00
O C:HOH2044 2.0 16.4 1.0
NE2 C:HIS1132 2.1 16.1 1.0
NE2 C:HIS1136 2.2 16.3 1.0
SG C:CYS1090 2.3 17.2 1.0
CD2 C:HIS1132 3.0 16.4 1.0
CE1 C:HIS1132 3.1 16.2 1.0
CD2 C:HIS1136 3.1 14.4 1.0
CE1 C:HIS1136 3.2 14.3 1.0
CB C:CYS1090 3.4 17.4 1.0
O C:HOH2040 3.5 21.0 1.0
O C:HOH2022 3.6 30.7 1.0
NE2 C:GLN1050 3.7 14.6 1.0
CA C:CYS1090 3.8 18.1 1.0
OE1 C:GLN1050 3.9 14.5 1.0
CD C:GLN1050 4.0 14.9 1.0
OE2 C:GLU1133 4.1 14.7 1.0
CG C:HIS1132 4.2 15.5 1.0
ND1 C:HIS1132 4.2 15.0 1.0
ND1 C:HIS1136 4.3 13.8 1.0
CG C:HIS1136 4.3 13.4 1.0
C11 C:2PE2 4.3 48.4 1.0
O C:HOH2042 4.4 16.5 1.0
OE1 C:GLU1133 4.5 14.3 1.0
O C:GLY1089 4.5 20.8 1.0
N C:LEU1091 4.6 18.0 1.0
C12 C:2PE2 4.6 46.4 1.0
C C:CYS1090 4.7 17.9 1.0
CD C:GLU1133 4.7 12.3 1.0

Reference:

A.Becker, I.Schlichting, W.Kabsch, S.Schultz, A.F.Wagner. Structure of Peptide Deformylase and Identification of the Substrate Binding Site. J.Biol.Chem. V. 273 11413 1998.
ISSN: ISSN 0021-9258
PubMed: 9565550
DOI: 10.1074/JBC.273.19.11413
Page generated: Fri Sep 25 07:54:55 2020
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