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Zinc in PDB 3tj9: Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+

Protein crystallography data

The structure of Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+, PDB code: 3tj9 was solved by K.Banaszak, M.Bellucci, B.Zambelli, W.R.Rypniewski, S.Ciurli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.52
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 109.343, 109.343, 280.343, 90.00, 90.00, 120.00
R / Rfree (%) 20.3 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+ (pdb code 3tj9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+, PDB code: 3tj9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3tj9

Go back to Zinc Binding Sites List in 3tj9
Zinc binding site 1 out of 2 in the Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+


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 Uree Bound to ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn171

b:37.5
occ:1.00
NE2 B:HIS152 1.8 55.2 1.0
OE2 A:GLU154 1.9 47.8 0.1
NE2 A:HIS102 2.0 19.7 1.0
NE2 D:HIS152 2.1 41.7 0.9
NE2 B:HIS102 2.1 27.7 1.0
OE1 A:GLU154 2.4 47.5 0.1
CD A:GLU154 2.4 48.3 0.1
CE1 B:HIS152 2.7 58.4 1.0
CE1 D:HIS152 2.7 46.7 0.9
CD2 B:HIS152 2.9 58.9 1.0
CE1 A:HIS102 3.0 17.4 1.0
CE1 B:HIS102 3.1 26.1 1.0
CD2 A:HIS102 3.1 17.4 1.0
CD2 B:HIS102 3.2 27.0 1.0
CD2 D:HIS152 3.3 47.0 0.9
ND1 B:HIS152 3.8 65.8 1.0
CG A:GLU154 3.8 49.7 0.1
ND1 D:HIS152 3.9 53.7 0.9
CG B:HIS152 3.9 69.1 1.0
ND1 A:HIS102 4.1 19.3 1.0
CG A:HIS102 4.2 18.8 1.0
ND1 B:HIS102 4.2 24.5 1.0
CG D:HIS152 4.2 57.1 0.9
CG B:HIS102 4.3 25.1 1.0
ND1 D:HIS102 4.4 18.4 1.0
CE1 D:HIS102 4.5 18.9 1.0
O B:ASN100 4.5 24.2 1.0
CB A:GLU154 4.6 50.5 0.1
CG D:HIS102 4.7 20.0 1.0
O A:ASN100 4.7 21.4 1.0
NE2 D:HIS102 4.8 24.3 1.0
O B:HIS152 4.9 74.0 1.0
CD2 D:HIS102 4.9 18.0 1.0
O B:SER153 5.0 79.3 1.0

Zinc binding site 2 out of 2 in 3tj9

Go back to Zinc Binding Sites List in 3tj9
Zinc binding site 2 out of 2 in the Crystal Structure of Helicobacter Pylori Uree Bound to ZN2+


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 Uree Bound to ZN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn171

b:33.4
occ:1.00
NE2 D:HIS102 2.1 24.3 1.0
NE2 C:HIS102 2.1 24.1 1.0
ND1 C:HIS152 2.2 64.7 1.0
OE1 D:GLU154 2.3 32.0 0.9
NE2 A:HIS152 2.3 48.2 0.1
CE1 C:HIS152 2.7 65.7 1.0
OE2 D:GLU154 2.8 43.1 0.9
CE1 A:HIS152 2.8 48.0 0.1
CD D:GLU154 2.9 42.8 0.9
CE1 D:HIS102 3.0 18.9 1.0
CE1 C:HIS102 3.1 18.3 1.0
CD2 D:HIS102 3.1 18.0 1.0
CD2 C:HIS102 3.2 19.4 1.0
CG C:HIS152 3.3 69.5 1.0
CD2 A:HIS152 3.5 48.4 0.1
NE2 C:HIS152 3.8 68.9 1.0
CB C:HIS152 4.0 70.6 1.0
ND1 A:HIS152 4.1 48.3 0.1
ND1 D:HIS102 4.1 18.4 1.0
CD2 C:HIS152 4.2 69.2 1.0
CG D:HIS102 4.2 20.0 1.0
ND1 C:HIS102 4.2 20.1 1.0
CG C:HIS102 4.3 20.9 1.0
CG D:GLU154 4.4 55.4 0.9
CG A:HIS152 4.4 48.5 0.1
O D:ASN100 4.5 18.9 1.0
ND1 A:HIS102 4.6 19.3 1.0
O C:ASN100 4.6 18.4 1.0
CE1 D:HIS152 4.7 46.7 0.9
CE1 A:HIS102 4.7 17.4 1.0
OE2 A:GLU154 5.0 47.8 0.1

Reference:

K.Banaszak, V.Martin-Diaconescu, M.Bellucci, B.Zambelli, W.Rypniewski, M.J.Maroney, S.Ciurli. Crystallographic and X-Ray Absorption Spectroscopic Characterization of Helicobacter Pylori Uree Bound to NI2+ and ZN2+ Reveals A Role For the Disordered C-Terminal Arm in Metal Trafficking. Biochem.J. V. 441 1017 2012.
ISSN: ISSN 0264-6021
PubMed: 22010876
DOI: 10.1042/BJ20111659
Page generated: Wed Dec 16 04:52:23 2020

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