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Zinc in PDB 6e0a: Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain, PDB code: 6e0a was solved by S.J.Remington, K.Guillemin, E.Sweeney, A.Perkins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.22 / 2.43
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.779, 59.468, 77.723, 90.00, 114.09, 90.00
R / Rfree (%) 19.7 / 25.7

Other elements in 6e0a:

The structure of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain (pdb code 6e0a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain, PDB code: 6e0a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6e0a

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Zinc binding site 1 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


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 Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:31.1
occ:1.00
OE1 A:GLU167 2.0 32.4 1.0
NE2 A:HIS70 2.1 25.8 1.0
O A:HOH468 2.2 24.0 1.0
O A:HOH473 2.5 25.6 1.0
CE1 A:HIS70 3.0 30.1 1.0
CD A:GLU167 3.1 23.5 1.0
CD2 A:HIS70 3.1 25.6 1.0
OE2 A:GLU167 3.6 28.6 1.0
NZ B:LYS28 3.9 34.5 1.0
ND1 A:HIS70 4.2 26.6 1.0
CG A:HIS70 4.2 30.4 1.0
OG A:SER69 4.3 45.8 1.0
CG2 A:VAL33 4.3 37.3 1.0
CG A:GLU167 4.3 27.3 1.0
CG1 A:VAL33 4.3 29.9 1.0
CB A:VAL33 4.9 25.5 1.0

Zinc binding site 2 out of 9 in 6e0a

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Zinc binding site 2 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


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 Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.6
occ:1.00
OE2 A:GLU29 1.9 27.0 1.0
NE2 B:HIS24 2.0 29.0 1.0
O A:HOH446 2.3 13.6 1.0
CE1 B:HIS24 2.7 26.3 1.0
O B:HOH467 2.8 13.2 1.0
CD A:GLU29 2.9 30.2 1.0
OE1 A:GLU29 3.2 27.9 1.0
CD2 B:HIS24 3.3 26.6 1.0
NZ B:LYS28 3.9 34.5 1.0
ND1 B:HIS24 4.0 27.4 1.0
NZ A:LYS26 4.1 34.2 1.0
CD B:LYS28 4.2 48.5 1.0
CG A:GLU29 4.2 31.1 1.0
CG A:GLU167 4.2 27.3 1.0
CG B:HIS24 4.2 26.5 1.0
CG B:LYS28 4.3 33.2 1.0
CE B:LYS28 4.3 43.8 1.0
CB A:GLU167 4.9 33.5 1.0
CA A:GLU167 4.9 34.6 1.0
O A:HOH445 5.0 36.6 1.0

Zinc binding site 3 out of 9 in 6e0a

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Zinc binding site 3 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


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 Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:61.2
occ:1.00
ND1 A:HIS24 2.0 44.3 1.0
OE2 A:GLU239 2.2 47.2 1.0
CE1 A:HIS24 2.7 47.3 1.0
CD A:GLU239 2.8 30.6 1.0
OE1 A:GLU239 2.9 32.4 1.0
CG A:HIS24 3.0 32.6 1.0
NZ A:LYS220 3.4 64.1 1.0
CB A:HIS24 3.5 29.1 1.0
NE2 A:HIS24 3.8 34.6 1.0
O A:HOH472 3.9 39.3 1.0
O A:HOH463 3.9 44.6 1.0
CD2 A:HIS24 4.0 33.3 1.0
CG A:GLU239 4.1 33.5 1.0
CA A:HIS24 4.1 33.4 1.0
CD A:LYS220 4.2 44.6 1.0
CE A:LYS220 4.4 49.6 1.0
O A:HOH438 4.6 28.7 1.0
O A:HIS24 4.9 28.1 1.0
C A:HIS24 4.9 29.3 1.0

Zinc binding site 4 out of 9 in 6e0a

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Zinc binding site 4 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


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 Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:90.8
occ:1.00
OD2 A:ASP264 1.7 37.7 1.0
OE1 A:GLU262 1.9 44.5 1.0
CG A:ASP264 2.8 50.4 1.0
CD A:GLU262 3.1 61.7 1.0
CB A:ASP264 3.5 52.0 1.0
OD1 A:ASP264 3.8 51.2 1.0
OE2 A:GLU262 4.0 70.7 1.0
CG A:GLU262 4.1 50.0 1.0
CA A:ASP264 4.9 53.9 1.0

Zinc binding site 5 out of 9 in 6e0a

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Zinc binding site 5 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


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 Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:52.3
occ:1.00
OE2 A:GLU13 2.2 55.9 1.0
OE2 A:GLU9 2.3 37.9 1.0
OE1 A:GLU9 2.5 49.0 1.0
CD A:GLU9 2.7 43.9 1.0
O A:HOH471 2.7 49.2 1.0
CD A:GLU13 3.3 57.5 1.0
OE1 A:GLU13 3.7 74.2 1.0
CD A:LYS12 4.1 41.7 1.0
CG A:GLU9 4.2 38.0 1.0
O A:HOH403 4.4 38.3 1.0
CG A:GLU13 4.6 58.1 1.0
CB A:GLU13 4.9 48.6 1.0

Zinc binding site 6 out of 9 in 6e0a

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Zinc binding site 6 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:28.4
occ:1.00
OE1 B:GLU167 1.9 28.0 1.0
NE2 B:HIS70 2.0 28.6 1.0
C3 B:DTT305 2.6 58.1 1.0
S1 B:DTT305 2.6 34.8 1.0
S4 B:DTT305 2.7 55.6 1.0
CE1 B:HIS70 2.8 24.9 1.0
C4 B:DTT305 3.0 15.3 1.0
CD B:GLU167 3.0 32.1 1.0
CD2 B:HIS70 3.0 25.6 1.0
C2 B:DTT305 3.1 54.5 1.0
C1 B:DTT305 3.4 48.7 1.0
OE2 B:GLU167 3.5 37.0 1.0
O3 B:DTT305 3.7 66.8 1.0
ND1 B:HIS70 4.0 22.5 1.0
ND2 B:ASN166 4.0 53.5 1.0
CG B:HIS70 4.1 28.0 1.0
CG B:GLU167 4.3 33.6 1.0
O2 B:DTT305 4.4 59.3 1.0
CG2 B:VAL33 4.5 25.9 1.0
CG1 B:VAL33 4.6 24.7 1.0
OG B:SER69 4.6 41.9 1.0
CB B:ASN166 4.9 34.4 1.0
CG B:ASN166 5.0 51.6 1.0

Zinc binding site 7 out of 9 in 6e0a

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Zinc binding site 7 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:50.7
occ:1.00
OE1 B:GLU233 2.0 39.6 1.0
OE2 B:GLU233 2.5 60.6 1.0
CD B:GLU233 2.6 47.1 1.0
O B:HOH428 2.7 29.5 1.0
CG B:GLU233 4.0 39.3 1.0
NZ B:LYS263 4.2 49.2 1.0
CE B:LYS263 4.8 43.1 1.0
CB B:GLU233 4.9 38.2 1.0

Zinc binding site 8 out of 9 in 6e0a

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Zinc binding site 8 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:64.8
occ:1.00
NE2 B:HIS59 2.4 41.2 1.0
O B:HOH473 2.6 45.7 1.0
O B:HOH462 3.0 33.2 1.0
CD2 B:HIS59 3.0 29.4 1.0
CE1 B:HIS59 3.5 38.7 1.0
CD A:LYS50 3.6 43.2 1.0
CG B:HIS59 4.3 27.5 1.0
ND2 B:ASN63 4.3 27.1 1.0
ND1 B:HIS59 4.5 39.9 1.0
CG A:LYS50 4.8 38.8 1.0

Zinc binding site 9 out of 9 in 6e0a

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Zinc binding site 9 out of 9 in the Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Helicobacter Pylori Tlpa Chemoreceptor Ligand Binding Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:0.0
occ:1.00
ND1 B:HIS59 2.7 39.9 1.0
CG B:HIS59 3.6 27.5 1.0
CB B:HIS59 3.7 33.3 1.0
CE1 B:HIS59 3.7 38.7 1.0
CA B:HIS59 3.9 26.9 1.0
O B:HIS59 4.7 24.4 1.0
CD2 B:HIS59 4.8 29.4 1.0
C B:HIS59 4.8 30.2 1.0
N B:HIS59 4.8 27.2 1.0
NE2 B:HIS59 4.8 41.2 1.0
CD B:LYS62 4.9 39.5 1.0
OD1 B:ASN63 4.9 29.9 1.0

Reference:

E.G.Sweeney, A.Perkins, K.Kallio, S.James Remington, K.Guillemin. Structures of the Ligand-Binding Domain of Helicobacter Pylori Chemoreceptor Tlpa. Protein Sci. V. 27 1961 2018.
ISSN: ESSN 1469-896X
PubMed: 30171638
DOI: 10.1002/PRO.3503
Page generated: Wed Dec 16 11:41:41 2020

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