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Nickel in PDB 2ai8: E.Coli Polypeptide Deformylase Complexed with Sb-485343

Enzymatic activity of E.Coli Polypeptide Deformylase Complexed with Sb-485343

All present enzymatic activity of E.Coli Polypeptide Deformylase Complexed with Sb-485343:
3.5.1.88;

Protein crystallography data

The structure of E.Coli Polypeptide Deformylase Complexed with Sb-485343, PDB code: 2ai8 was solved by K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 139.178, 63.350, 85.672, 90.00, 121.23, 90.00
R / Rfree (%) 21.2 / 22.6

Nickel Binding Sites:

The binding sites of Nickel atom in the E.Coli Polypeptide Deformylase Complexed with Sb-485343 (pdb code 2ai8). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 3 binding sites of Nickel where determined in the E.Coli Polypeptide Deformylase Complexed with Sb-485343, PDB code: 2ai8:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 in 2ai8

Go back to Nickel Binding Sites List in 2ai8
Nickel binding site 1 out of 3 in the E.Coli Polypeptide Deformylase Complexed with Sb-485343


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of E.Coli Polypeptide Deformylase Complexed with Sb-485343 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni601

b:7.5
occ:1.00
NE2 A:HIS136 2.0 7.3 1.0
O25 A:SB7501 2.1 12.7 1.0
NE2 A:HIS132 2.1 8.7 1.0
SG A:CYS90 2.3 9.5 1.0
C24 A:SB7501 2.8 20.3 1.0
CD2 A:HIS132 3.0 8.8 1.0
CD2 A:HIS136 3.0 8.0 1.0
CE1 A:HIS136 3.0 7.5 1.0
CE1 A:HIS132 3.1 9.4 1.0
CB A:CYS90 3.3 8.8 1.0
N14 A:SB7501 3.4 21.2 1.0
NE2 A:GLN50 3.5 8.8 1.0
O22 A:SB7501 3.5 21.7 1.0
O A:HOH611 3.6 9.9 1.0
CA A:CYS90 3.9 9.1 1.0
CD A:GLN50 3.9 8.5 1.0
OE1 A:GLN50 3.9 8.8 1.0
ND1 A:HIS136 4.1 8.3 1.0
CG A:HIS136 4.1 7.4 1.0
CG A:HIS132 4.2 8.2 1.0
ND1 A:HIS132 4.2 7.8 1.0
OE2 A:GLU133 4.4 13.9 1.0
O A:HOH602 4.4 6.6 1.0
OE1 A:GLU133 4.5 10.0 1.0
N A:LEU91 4.5 8.7 1.0
O A:GLY89 4.6 10.7 1.0
C A:CYS90 4.6 8.9 1.0
C11 A:SB7501 4.7 23.0 1.0
C7 A:SB7501 4.7 25.4 1.0
CD A:GLU133 4.8 10.9 1.0
CG A:GLN50 5.0 7.8 1.0

Nickel binding site 2 out of 3 in 2ai8

Go back to Nickel Binding Sites List in 2ai8
Nickel binding site 2 out of 3 in the E.Coli Polypeptide Deformylase Complexed with Sb-485343


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of E.Coli Polypeptide Deformylase Complexed with Sb-485343 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ni603

b:11.1
occ:1.00
NE2 B:HIS136 2.1 7.4 1.0
NE2 B:HIS132 2.1 7.0 1.0
O22 B:SB7502 2.2 15.9 1.0
O25 B:SB7502 2.3 16.7 1.0
SG B:CYS90 2.4 10.4 1.0
N14 B:SB7502 2.9 16.9 1.0
C24 B:SB7502 2.9 16.4 1.0
CD2 B:HIS136 3.0 8.1 1.0
CD2 B:HIS132 3.1 7.3 1.0
CE1 B:HIS136 3.1 8.2 1.0
CE1 B:HIS132 3.1 8.3 1.0
NE2 B:GLN50 3.2 11.2 1.0
CB B:CYS90 3.5 9.2 1.0
O B:HOH614 3.8 10.1 1.0
CD B:GLN50 3.8 10.7 1.0
CA B:CYS90 3.9 9.6 1.0
OE1 B:GLN50 4.0 13.1 1.0
ND1 B:HIS136 4.2 6.9 1.0
CG B:HIS136 4.2 7.7 1.0
ND1 B:HIS132 4.2 8.0 1.0
CG B:HIS132 4.2 6.8 1.0
C11 B:SB7502 4.2 17.1 1.0
N B:LEU91 4.3 10.3 1.0
C B:CYS90 4.5 9.8 1.0
O B:HOH607 4.6 7.0 1.0
C8 B:SB7502 4.6 17.1 1.0
OE1 B:GLU133 4.6 10.4 1.0
O B:GLY89 4.7 10.4 1.0
CG B:GLN50 4.8 11.3 1.0
OE2 B:GLU133 5.0 11.8 1.0

Nickel binding site 3 out of 3 in 2ai8

Go back to Nickel Binding Sites List in 2ai8
Nickel binding site 3 out of 3 in the E.Coli Polypeptide Deformylase Complexed with Sb-485343


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of E.Coli Polypeptide Deformylase Complexed with Sb-485343 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ni602

b:11.1
occ:1.00
NE2 C:HIS136 2.0 8.5 1.0
NE2 C:HIS132 2.0 7.5 1.0
O25 C:SB7503 2.1 11.9 1.0
SG C:CYS90 2.3 11.7 1.0
C24 C:SB7503 2.7 20.2 1.0
CD2 C:HIS132 3.0 7.9 1.0
CD2 C:HIS136 3.0 8.2 1.0
CE1 C:HIS136 3.0 8.1 1.0
CE1 C:HIS132 3.1 8.8 1.0
CB C:CYS90 3.4 10.1 1.0
N14 C:SB7503 3.4 21.5 1.0
NE2 C:GLN50 3.5 8.2 1.0
O C:HOH624 3.6 9.8 1.0
O22 C:SB7503 3.6 22.9 1.0
CA C:CYS90 3.9 11.1 1.0
CD C:GLN50 3.9 7.7 1.0
OE1 C:GLN50 3.9 8.1 1.0
ND1 C:HIS136 4.1 8.0 1.0
CG C:HIS132 4.1 8.5 1.0
ND1 C:HIS132 4.2 8.7 1.0
CG C:HIS136 4.2 7.7 1.0
N C:LEU91 4.4 10.3 1.0
O C:HOH619 4.5 8.5 1.0
OE1 C:GLU133 4.5 11.0 1.0
OE2 C:GLU133 4.6 13.0 1.0
C C:CYS90 4.6 10.3 1.0
C11 C:SB7503 4.6 23.3 1.0
O C:GLY89 4.6 12.7 1.0
C8 C:SB7503 4.8 24.3 1.0
CD C:GLU133 4.9 10.5 1.0

Reference:

K.J.Smith, C.M.Petit, K.Aubart, M.Smyth, E.Mcmanus, J.Jones, A.Fosberry, C.Lewis, M.Lonetto, S.B.Christensen. Structural Variation and Inhibitor Binding in Polypeptide Deformylase From Four Different Bacterial Species. Protein Sci. V. 12 349 2003.
ISSN: ISSN 0961-8368
PubMed: 12538898
DOI: 10.1110/PS.0229303
Page generated: Wed Dec 16 01:17:18 2020

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