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Zinc in PDB 4q6q: Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase

Protein crystallography data

The structure of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6q was solved by H.S.Kim, J.Kim, H.N.Im, D.R.An, M.Lee, D.Hesek, S.Mobashery, J.Y.Kim, K.Cho, H.J.Yoon, B.W.Han, B.I.Lee, S.W.Suh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.314, 66.928, 144.806, 90.00, 90.00, 90.00
R / Rfree (%) 16.7 / 20.5

Other elements in 4q6q:

The structure of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase (pdb code 4q6q). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase, PDB code: 4q6q:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4q6q

Go back to Zinc Binding Sites List in 4q6q
Zinc binding site 1 out of 2 in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:82.5
occ:1.00
O A:HOH797 2.5 48.3 1.0
O A:HOH798 2.7 38.6 1.0
O A:HOH796 3.0 36.6 1.0
O A:ASN392 3.9 64.1 1.0
NH2 A:ARG380 4.3 42.4 1.0
CG A:LYS393 4.4 64.5 1.0
CD A:LYS393 4.8 69.0 1.0
C A:ASN392 5.0 64.9 1.0

Zinc binding site 2 out of 2 in 4q6q

Go back to Zinc Binding Sites List in 4q6q
Zinc binding site 2 out of 2 in the Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Analysis of the Zn-Form II of Helicobacter Pylori CSD4, A D,L-Carboxypeptidase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:53.3
occ:1.00
O A:PHE386 2.3 31.7 1.0
OD1 A:ASN382 2.4 31.0 1.0
OE2 A:GLU396 2.5 34.4 1.0
O A:VAL383 2.5 30.2 1.0
OE1 A:GLU396 2.6 32.1 1.0
O A:HOH665 2.7 34.3 1.0
O A:HOH636 2.7 31.2 1.0
CD A:GLU396 2.9 33.7 1.0
C A:VAL383 3.4 30.1 1.0
C A:PHE386 3.5 31.2 1.0
CG A:ASN382 3.6 31.3 1.0
N A:VAL383 3.7 29.6 1.0
CA A:VAL383 4.1 29.5 1.0
N A:PHE386 4.3 28.9 1.0
ND2 A:ASN382 4.3 34.5 1.0
N A:ILE384 4.3 29.9 1.0
C A:ASN382 4.3 29.5 1.0
CB A:SER387 4.3 35.4 1.0
CG A:GLU396 4.4 32.4 1.0
CA A:SER387 4.4 36.8 1.0
CA A:PHE386 4.4 30.8 1.0
N A:SER387 4.4 33.5 1.0
CG A:PRO394 4.5 42.6 1.0
CA A:ILE384 4.5 29.6 1.0
O A:HOH726 4.5 32.3 1.0
CA A:ASN382 4.6 30.4 1.0
CB A:VAL383 4.6 28.7 1.0
N A:GLY385 4.7 27.8 1.0
CB A:ASN382 4.7 30.7 1.0
CB A:PHE386 4.8 30.5 1.0
CD1 A:ILE384 4.9 29.5 1.0
CD2 A:PHE386 5.0 30.0 1.0

Reference:

H.S.Kim, J.Kim, H.N.Im, D.R.An, M.Lee, D.Hesek, S.Mobashery, J.Y.Kim, K.Cho, H.J.Yoon, B.W.Han, B.I.Lee, S.W.Suh. Structural Basis For the Recognition of Muramyltripeptide By Helicobacter Pylori CSD4, A D,L-Carboxypeptidase Controlling the Helical Cell Shape Acta Crystallogr.,Sect.D V. 70 2014.
ISSN: ESSN 1399-0047
DOI: 10.1107/S1399004714018732
Page generated: Wed Dec 16 05:42:44 2020

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