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
Go back to
Zinc Binding Sites List in 6j98
Zinc binding site 1 out
of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_01_stereo.jpg) 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 Sites List in 6j98
Zinc binding site 2 out
of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_02_stereo.jpg) 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
Go back to
Zinc Binding Sites List in 6j98
Zinc binding site 3 out
of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_03_stereo.jpg) 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
Go back to
Zinc Binding Sites List in 6j98
Zinc binding site 4 out
of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_04_stereo.jpg) 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
Go back to
Zinc Binding Sites List in 6j98
Zinc binding site 5 out
of 5 in the Crystal Structure of P8 From Lactobacillus Rhamnosus
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/j9/6j98-ZN-sphere_05_stereo.jpg) 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
|