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Zinc in PDB 6j98: Crystal Structure of P8 From Lactobacillus Rhamnosus

Protein crystallography data

The structure of Crystal Structure of P8 From Lactobacillus Rhamnosus, PDB code: 6j98 was solved by Y.J.Cha, H.S.Cho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.17 / 1.56
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 40.860, 40.860, 107.010, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 19.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of P8 From Lactobacillus Rhamnosus (pdb code 6j98). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of P8 From Lactobacillus Rhamnosus, PDB code: 6j98:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 6j98

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Zinc binding site 1 out of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus


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 P8 From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn101

b:14.6
occ:1.00
N A:GLY-1 2.1 14.3 1.0
O A:GLY-1 2.1 16.0 1.0
C A:GLY-1 2.8 18.9 1.0
CA A:GLY-1 2.9 19.3 1.0
N A:SER0 4.1 18.9 1.0
O A:HOH259 4.3 31.0 1.0
CA A:SER0 4.9 16.1 1.0

Zinc binding site 2 out of 5 in 6j98

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Zinc binding site 2 out of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus


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 P8 From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn102

b:23.8
occ:1.00
OE2 A:GLU7 2.0 23.2 1.0
O A:HOH262 2.0 24.6 1.0
OE1 A:GLU14 2.0 17.4 1.0
NZ A:LYS18 2.2 24.1 1.0
CD A:GLU14 2.8 17.1 1.0
CD A:GLU7 2.9 27.2 1.0
OE2 A:GLU14 2.9 17.1 1.0
CE A:LYS18 3.1 20.7 1.0
OE1 A:GLU7 3.2 27.3 1.0
CD A:LYS18 3.4 20.5 1.0
O A:HOH250 4.1 32.0 1.0
OG1 A:THR9 4.1 21.5 1.0
CG A:GLU14 4.3 14.1 1.0
CG A:GLU7 4.3 24.1 1.0
CB A:THR9 4.4 19.1 1.0
CD A:PRO15 4.5 12.5 1.0
CG2 A:THR9 4.5 17.8 1.0
CB A:GLU14 4.8 12.9 1.0
CG A:LYS18 4.9 18.0 1.0
CA A:GLU14 5.0 11.6 1.0

Zinc binding site 3 out of 5 in 6j98

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Zinc binding site 3 out of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus


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 P8 From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn103

b:14.9
occ:0.50
OD2 A:ASP5 1.9 19.4 1.0
CG A:ASP5 2.7 18.4 1.0
OD1 A:ASP5 2.9 20.6 1.0
CB A:ASP5 4.2 19.3 1.0
CG1 A:VAL4 5.0 21.7 1.0

Zinc binding site 4 out of 5 in 6j98

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Zinc binding site 4 out of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus


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 P8 From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn104

b:17.8
occ:1.00
OE2 A:GLU39 1.9 17.9 1.0
OD2 A:ASP35 2.1 19.9 1.0
O A:HOH249 2.2 27.3 1.0
OD1 A:ASP35 2.5 19.1 1.0
CG A:ASP35 2.6 13.0 1.0
CD A:GLU39 2.9 21.1 1.0
CG A:GLU39 3.2 16.8 1.0
O A:HOH260 3.9 20.7 1.0
OE1 A:GLU39 4.1 22.6 1.0
CB A:ASP35 4.1 11.3 1.0
NH2 A:ARG43 4.2 16.8 1.0
O A:ASP35 4.4 12.4 1.0
O A:HOH253 4.5 22.4 1.0
CB A:GLU39 4.7 15.5 1.0
CA A:ASP35 4.9 10.9 1.0
C A:ASP35 4.9 12.2 1.0

Zinc binding site 5 out of 5 in 6j98

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Zinc binding site 5 out of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of P8 From Lactobacillus Rhamnosus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn105

b:42.9
occ:1.00
OD2 A:ASP31 2.2 13.5 1.0
OD1 A:ASP31 2.8 15.0 1.0
CG A:ASP31 2.8 12.3 1.0
O A:HOH241 3.6 35.3 1.0
CG A:PRO28 4.2 14.1 1.0
CB A:ASP31 4.3 11.0 1.0
CD A:PRO28 4.7 11.5 1.0
CB A:PRO28 4.8 13.6 1.0
CG A:ARG30 4.9 16.1 1.0
CD A:ARG30 5.0 19.7 1.0

Reference:

Y.J.Cha, H.S.Cho. Crystal Structure of P8 From Lactobacillus Rhamnosus To Be Published.
Page generated: Wed Dec 16 12:03:50 2020

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