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Zinc in PDB 6ck7: Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin

Enzymatic activity of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin

All present enzymatic activity of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin, PDB code: 6ck7 was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 44.650, 132.060, 90.380, 90.00, 103.64, 90.00
R / Rfree (%) 18.2 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin (pdb code 6ck7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin, PDB code: 6ck7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6ck7

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Zinc binding site 1 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:18.8
occ:1.00
NE2 A:HIS133 2.0 17.4 1.0
NE2 A:HIS137 2.1 14.6 1.0
O4 A:BB2202 2.1 21.0 1.0
O2 A:BB2202 2.1 23.4 1.0
SG A:CYS91 2.3 18.3 1.0
C3 A:BB2202 2.8 23.7 1.0
N1 A:BB2202 3.0 23.5 1.0
CD2 A:HIS133 3.0 19.8 1.0
CE1 A:HIS133 3.0 20.6 1.0
CD2 A:HIS137 3.0 20.4 1.0
CE1 A:HIS137 3.1 19.9 1.0
NE2 A:GLN51 3.3 19.2 1.0
CB A:CYS91 3.4 16.1 1.0
O A:HOH376 3.6 20.8 1.0
CD A:GLN51 3.8 20.1 1.0
CA A:CYS91 3.8 18.4 1.0
OE1 A:GLN51 3.9 19.5 1.0
N A:LEU92 4.1 15.1 1.0
ND1 A:HIS133 4.1 19.0 1.0
CG A:HIS133 4.2 18.3 1.0
C5 A:BB2202 4.2 18.9 1.0
CG A:HIS137 4.2 16.5 1.0
ND1 A:HIS137 4.2 20.3 1.0
C A:CYS91 4.4 17.4 1.0
C6 A:BB2202 4.5 17.6 1.0
O A:HOH356 4.6 20.2 1.0
N A:SER93 4.8 18.1 1.0
CG A:GLN51 4.9 19.1 1.0
C7 A:BB2202 5.0 21.8 1.0

Zinc binding site 2 out of 4 in 6ck7

Go back to Zinc Binding Sites List in 6ck7
Zinc binding site 2 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:18.7
occ:1.00
NE2 B:HIS133 2.0 16.9 1.0
O4 B:BB2202 2.1 18.6 1.0
NE2 B:HIS137 2.1 16.9 1.0
O2 B:BB2202 2.3 23.3 1.0
SG B:CYS91 2.4 18.6 1.0
C3 B:BB2202 2.9 21.4 1.0
CD2 B:HIS133 3.0 17.4 1.0
CE1 B:HIS133 3.0 19.4 1.0
CD2 B:HIS137 3.0 22.4 1.0
N1 B:BB2202 3.1 23.5 1.0
CE1 B:HIS137 3.2 20.1 1.0
NE2 B:GLN51 3.3 19.8 1.0
CB B:CYS91 3.4 15.9 1.0
O B:HOH364 3.6 20.5 1.0
CD B:GLN51 3.8 21.5 1.0
CA B:CYS91 3.8 13.4 1.0
OE1 B:GLN51 3.9 20.5 1.0
N B:LEU92 4.1 14.3 1.0
ND1 B:HIS133 4.1 19.0 1.0
CG B:HIS133 4.1 16.9 1.0
CG B:HIS137 4.2 16.6 1.0
C5 B:BB2202 4.2 19.5 1.0
ND1 B:HIS137 4.3 18.7 1.0
C B:CYS91 4.4 14.7 1.0
C6 B:BB2202 4.5 18.4 1.0
O B:HOH367 4.6 17.9 1.0
N B:SER93 4.8 19.2 1.0
CG B:GLN51 4.9 17.6 1.0
C7 B:BB2202 5.0 21.3 1.0

Zinc binding site 3 out of 4 in 6ck7

Go back to Zinc Binding Sites List in 6ck7
Zinc binding site 3 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:21.1
occ:1.00
NE2 C:HIS133 2.0 19.0 1.0
O4 C:BB2202 2.1 23.1 1.0
NE2 C:HIS137 2.1 23.0 1.0
O2 C:BB2202 2.3 23.9 1.0
SG C:CYS91 2.3 18.7 1.0
C3 C:BB2202 2.8 23.2 1.0
CE1 C:HIS133 3.0 18.6 1.0
CD2 C:HIS133 3.0 22.0 1.0
CD2 C:HIS137 3.0 21.6 1.0
N1 C:BB2202 3.0 24.1 1.0
CE1 C:HIS137 3.1 24.0 1.0
NE2 C:GLN51 3.3 19.7 1.0
CB C:CYS91 3.5 17.8 1.0
O C:HOH368 3.6 23.2 1.0
CD C:GLN51 3.8 22.5 1.0
CA C:CYS91 3.9 19.0 1.0
OE1 C:GLN51 3.9 22.8 1.0
N C:LEU92 4.1 15.1 1.0
ND1 C:HIS133 4.1 22.4 1.0
CG C:HIS133 4.1 21.0 1.0
C5 C:BB2202 4.2 20.4 1.0
CG C:HIS137 4.2 21.0 1.0
ND1 C:HIS137 4.2 24.9 1.0
C C:CYS91 4.4 17.8 1.0
C6 C:BB2202 4.5 17.9 1.0
O C:HOH359 4.6 23.9 1.0
N C:SER93 4.8 18.5 1.0
C7 C:BB2202 4.9 22.9 1.0
CG C:GLN51 4.9 19.1 1.0

Zinc binding site 4 out of 4 in 6ck7

Go back to Zinc Binding Sites List in 6ck7
Zinc binding site 4 out of 4 in the Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:20.9
occ:1.00
NE2 D:HIS133 2.0 19.8 1.0
NE2 D:HIS137 2.1 21.1 1.0
O4 D:BB2202 2.1 22.1 1.0
SG D:CYS91 2.3 19.3 1.0
O2 D:BB2202 2.4 26.5 1.0
C3 D:BB2202 2.9 24.6 1.0
CE1 D:HIS133 3.0 19.7 1.0
CD2 D:HIS133 3.0 18.9 1.0
CD2 D:HIS137 3.1 22.4 1.0
CE1 D:HIS137 3.1 20.0 1.0
N1 D:BB2202 3.1 24.9 1.0
NE2 D:GLN51 3.3 21.8 1.0
CB D:CYS91 3.4 18.4 1.0
O D:HOH378 3.6 21.0 1.0
CD D:GLN51 3.8 21.0 1.0
CA D:CYS91 3.8 18.2 1.0
OE1 D:GLN51 3.9 24.6 1.0
N D:LEU92 4.0 16.8 1.0
ND1 D:HIS133 4.1 21.1 1.0
CG D:HIS133 4.2 17.9 1.0
ND1 D:HIS137 4.2 20.8 1.0
CG D:HIS137 4.2 19.9 1.0
C5 D:BB2202 4.2 22.5 1.0
C D:CYS91 4.4 16.6 1.0
C6 D:BB2202 4.5 20.0 1.0
O D:HOH369 4.6 21.1 1.0
N D:SER93 4.8 20.8 1.0
CG D:GLN51 4.9 18.0 1.0
C7 D:BB2202 4.9 21.6 1.0

Reference:

T.E.Edwards, P.S.Horanyi, D.D.Lorimer. Crystal Structure of A Peptide Deformylase From Legionella Pneumophila Bound to Actinonin To Be Published.
Page generated: Wed Dec 16 11:36:52 2020

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