Zinc in PDB 6jf6: Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii

Enzymatic activity of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii

All present enzymatic activity of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii:
3.5.1.88;

Protein crystallography data

The structure of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf6 was solved by K.H.Jung, T.H.Ho, I.H.Lee, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.99 / 2.35
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.370, 39.347, 110.353, 90.00, 89.98, 90.00
R / Rfree (%) 21 / 29.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii (pdb code 6jf6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii, PDB code: 6jf6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6jf6

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Zinc binding site 1 out of 4 in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:68.9
occ:1.00
 SG A:CYS103 1.5 53.3 1.0
NE2 A:HIS145 2.4 50.0 1.0
NE2 A:HIS149 2.6 58.2 1.0
O A:HOH326 2.9 51.7 1.0
CD2 A:HIS145 3.1 43.2 1.0
CB A:CYS103 3.1 51.4 1.0
CD2 A:HIS149 3.2 56.8 1.0
NE2 A:GLN55 3.4 49.5 1.0
OE1 A:GLN55 3.5 43.7 1.0
CA A:CYS103 3.6 58.7 1.0
CE1 A:HIS145 3.6 47.2 1.0
OE2 A:GLU146 3.7 39.5 1.0
CD A:GLN55 3.7 42.7 1.0
CE1 A:HIS149 3.8 59.1 1.0
O A:HOH325 4.0 40.7 1.0
OE1 A:GLU146 4.1 38.5 1.0
CD A:GLU146 4.3 36.3 1.0
CG A:HIS145 4.4 41.8 1.0
N A:LEU104 4.4 60.0 1.0
CG A:HIS149 4.5 51.9 1.0
C A:CYS103 4.5 61.3 1.0
ND1 A:HIS145 4.6 45.7 1.0
O A:GLY102 4.6 68.8 1.0
N A:CYS103 4.7 60.2 1.0
ND1 A:HIS149 4.7 50.4 1.0
O A:HOH301 4.8 45.8 1.0
CG A:GLN55 4.9 38.7 1.0

Zinc binding site 2 out of 4 in 6jf6

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Zinc binding site 2 out of 4 in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:43.4
occ:1.00
 NE2 B:HIS145 2.1 53.2 1.0
NE2 B:HIS149 2.2 34.9 1.0
SG B:CYS103 2.3 43.7 1.0
O B:HOH302 2.4 25.3 1.0
CD2 B:HIS145 2.8 53.4 1.0
CD2 B:HIS149 2.9 36.6 1.0
O B:HOH324 3.1 31.2 1.0
CE1 B:HIS145 3.2 53.3 1.0
CE1 B:HIS149 3.3 33.4 1.0
CB B:CYS103 3.4 44.4 1.0
O B:HOH314 3.5 23.9 1.0
NE2 B:GLN55 3.6 34.1 1.0
OE1 B:GLN55 3.7 37.0 1.0
CD B:GLN55 3.8 38.8 1.0
CA B:CYS103 4.0 43.1 1.0
CG B:HIS145 4.0 47.3 1.0
O B:HOH312 4.1 34.4 1.0
OE1 B:GLU146 4.2 34.1 1.0
CG B:HIS149 4.2 34.9 1.0
ND1 B:HIS145 4.2 43.2 1.0
ND1 B:HIS149 4.3 36.0 1.0
OE2 B:GLU146 4.5 37.3 1.0
CD B:GLU146 4.7 38.1 1.0
O B:GLY102 4.8 39.6 1.0
CG B:GLN55 4.9 35.7 1.0
C B:CYS103 4.9 45.0 1.0
N B:LEU104 5.0 40.3 1.0

Zinc binding site 3 out of 4 in 6jf6

Go back to Zinc Binding Sites List in 6jf6
Zinc binding site 3 out of 4 in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:43.7
occ:1.00
 NE2 C:HIS145 2.1 58.2 1.0
NE2 C:HIS149 2.2 43.4 1.0
O E:HOH101 2.2 37.6 1.0
SG C:CYS103 2.2 40.4 1.0
CD2 C:HIS145 2.9 55.0 1.0
O C:HOH315 3.0 36.0 1.0
CE1 C:HIS149 3.1 46.8 1.0
CD2 C:HIS149 3.1 42.7 1.0
CB C:CYS103 3.2 45.0 1.0
CE1 C:HIS145 3.3 56.3 1.0
NE2 C:GLN55 3.7 34.1 1.0
O C:HOH311 3.8 28.4 1.0
N E:MET1 3.9 71.1 1.0
CD C:GLN55 3.9 39.1 1.0
OE1 C:GLN55 3.9 40.0 1.0
CA C:CYS103 4.0 42.5 1.0
CG C:HIS145 4.1 50.0 1.0
ND1 C:HIS149 4.2 48.5 1.0
CG C:HIS149 4.3 45.9 1.0
ND1 C:HIS145 4.3 50.3 1.0
O C:HOH302 4.3 46.1 1.0
OE1 C:GLU146 4.3 39.0 1.0
OE2 C:GLU146 4.5 38.2 1.0
CA E:MET1 4.7 64.4 1.0
N C:LEU104 4.8 44.9 1.0
CD C:GLU146 4.8 40.0 1.0
CG C:GLN55 4.8 37.8 1.0
C C:CYS103 4.8 44.1 1.0
O C:GLY102 4.8 38.6 1.0

Zinc binding site 4 out of 4 in 6jf6

Go back to Zinc Binding Sites List in 6jf6
Zinc binding site 4 out of 4 in the Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:50.4
occ:1.00
 NE2 D:HIS145 2.2 49.1 1.0
SG D:CYS103 2.2 56.0 1.0
NE2 D:HIS149 2.2 36.0 1.0
O D:HOH304 2.3 35.7 1.0
CD2 D:HIS145 3.1 42.5 1.0
CE1 D:HIS145 3.2 45.7 1.0
CD2 D:HIS149 3.2 34.6 1.0
CB D:CYS103 3.2 56.8 1.0
CE1 D:HIS149 3.2 41.2 1.0
O D:HOH318 3.3 44.2 1.0
O D:HOH319 3.4 45.6 1.0
OE1 D:GLN55 3.7 48.0 1.0
CA D:CYS103 3.8 56.9 1.0
NE2 D:GLN55 3.8 44.0 1.0
CD D:GLN55 4.0 42.6 1.0
CG D:HIS145 4.2 43.2 1.0
ND1 D:HIS145 4.3 48.1 1.0
N D:LEU104 4.3 64.1 1.0
OE2 D:GLU146 4.3 36.0 1.0
ND1 D:HIS149 4.3 40.4 1.0
CG D:HIS149 4.4 36.9 1.0
C D:CYS103 4.5 61.7 1.0
OE1 D:GLU146 4.6 37.8 1.0
O D:HOH314 4.7 50.1 1.0
O D:GLY102 4.8 58.0 1.0
CD D:GLU146 4.8 39.2 1.0
N D:SER105 5.0 55.7 1.0

Reference:

K.H.Jung, T.H.Ho, I.H.Lee, L.W.Kang. Met-Ala-Ser Bound Crystal Structure of Class I Type B Peptide Deformylase From Acinetobacter Baumannii To Be Published.
Page generated: Wed Dec 16 12:04:30 2020

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