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Zinc in PDB 3two: The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)

Enzymatic activity of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)

All present enzymatic activity of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H):
1.1.1.195;

Protein crystallography data

The structure of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H), PDB code: 3two was solved by K.H.Seo, N.N.Zhuang, C.Cong, K.H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.31 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 85.410, 85.680, 100.491, 90.00, 90.00, 90.00
R / Rfree (%) 17.3 / 22.6

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H) (pdb code 3two). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H), PDB code: 3two:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3two

Go back to Zinc Binding Sites List in 3two
Zinc binding site 1 out of 4 in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn349

b:33.3
occ:1.00
SG A:CYS98 2.3 27.3 1.0
SG A:CYS109 2.3 28.4 1.0
SG A:CYS95 2.4 34.5 1.0
SG A:CYS101 2.4 29.4 1.0
CB A:CYS95 2.9 28.1 1.0
N A:CYS98 3.1 36.4 1.0
CB A:CYS109 3.2 24.8 1.0
CB A:CYS98 3.4 33.1 1.0
CB A:CYS101 3.4 30.1 1.0
N A:CYS95 3.5 28.2 1.0
N A:ALA97 3.6 36.3 1.0
N A:LYS96 3.7 31.6 1.0
CA A:CYS95 3.7 29.9 1.0
CA A:CYS98 3.8 33.3 1.0
CA A:CYS109 3.9 26.9 1.0
C A:CYS95 4.1 31.1 1.0
N A:CYS101 4.2 30.7 1.0
C A:ALA97 4.3 37.3 1.0
C A:LYS96 4.3 35.2 1.0
CA A:CYS101 4.4 30.8 1.0
CA A:LYS96 4.5 32.8 1.0
C A:CYS98 4.6 34.0 1.0
CA A:ALA97 4.7 36.8 1.0
C A:SER94 4.7 27.9 1.0
CB A:SER94 4.7 25.9 1.0
O A:CYS98 4.8 32.3 1.0
OG A:SER94 4.8 26.9 1.0
C A:CYS109 4.8 28.2 1.0
N A:THR110 4.9 28.7 1.0

Zinc binding site 2 out of 4 in 3two

Go back to Zinc Binding Sites List in 3two
Zinc binding site 2 out of 4 in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn350

b:82.2
occ:1.00
NE2 A:HIS64 2.1 28.6 1.0
SG A:CYS160 2.3 33.3 1.0
SG A:CYS42 2.5 30.9 1.0
CE1 A:HIS64 2.8 29.2 1.0
CD2 A:HIS64 3.0 28.8 1.0
C5N A:NDP601 3.2 21.9 1.0
CB A:CYS42 3.4 27.9 1.0
CB A:CYS160 3.4 26.0 1.0
OG A:SER44 3.6 26.2 1.0
ND1 A:HIS64 3.8 29.3 1.0
CB A:SER44 3.9 25.4 1.0
C6N A:NDP601 3.9 21.5 1.0
CG A:HIS64 3.9 28.0 1.0
C4N A:NDP601 4.0 25.8 1.0
SG A:CYS90 4.0 32.3 1.0
CA A:CYS160 4.8 27.0 1.0
OE2 A:GLU65 4.8 34.2 1.0
CA A:CYS42 4.9 27.9 1.0
NH2 A:ARG338 4.9 28.7 1.0
N A:SER44 5.0 26.5 1.0

Zinc binding site 3 out of 4 in 3two

Go back to Zinc Binding Sites List in 3two
Zinc binding site 3 out of 4 in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn349

b:67.9
occ:1.00
NE2 B:HIS64 2.1 26.3 1.0
SG B:CYS160 2.4 30.0 1.0
SG B:CYS42 2.5 29.2 1.0
CE1 B:HIS64 2.9 25.2 1.0
CD2 B:HIS64 3.1 24.1 1.0
C5N B:NDP602 3.1 22.1 1.0
CB B:CYS42 3.4 24.9 1.0
OG B:SER44 3.5 25.2 1.0
CB B:CYS160 3.5 27.0 1.0
CB B:SER44 3.8 22.2 1.0
C6N B:NDP602 3.8 20.6 1.0
C4N B:NDP602 3.9 27.1 1.0
ND1 B:HIS64 4.0 29.2 1.0
SG B:CYS90 4.1 30.2 1.0
CG B:HIS64 4.1 25.7 1.0
OE2 B:GLU65 4.8 32.7 1.0
CD1 B:ILE293 4.9 31.6 1.0
CA B:CYS42 4.9 25.1 1.0
CA B:CYS160 4.9 27.1 1.0
NH2 B:ARG338 4.9 23.6 1.0

Zinc binding site 4 out of 4 in 3two

Go back to Zinc Binding Sites List in 3two
Zinc binding site 4 out of 4 in the The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Cad From Helicobacter Pylori Complexed with Nadp(H) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn350

b:35.2
occ:1.00
SG B:CYS98 2.2 32.3 1.0
SG B:CYS109 2.3 31.8 1.0
SG B:CYS95 2.4 32.3 1.0
SG B:CYS101 2.4 31.4 1.0
CB B:CYS109 3.2 27.7 1.0
CB B:CYS98 3.4 35.3 1.0
CB B:CYS95 3.4 30.9 1.0
CB B:CYS101 3.5 33.1 1.0
N B:CYS95 3.5 29.3 1.0
N B:LYS96 3.7 32.8 1.0
N B:CYS98 3.8 36.6 1.0
CA B:CYS95 3.8 32.5 1.0
CA B:CYS109 4.0 28.1 1.0
C B:CYS95 4.1 32.8 1.0
CA B:CYS98 4.1 35.6 1.0
N B:ALA97 4.2 36.3 1.0
N B:CYS101 4.3 32.5 1.0
CA B:CYS101 4.4 33.6 1.0
CB B:SER94 4.6 30.1 1.0
C B:SER94 4.6 29.7 1.0
CA B:LYS96 4.7 34.5 1.0
OG B:SER94 4.8 30.6 1.0
C B:CYS98 4.8 35.9 1.0
C B:ALA97 4.8 37.8 1.0
C B:LYS96 4.9 35.7 1.0
C B:CYS109 4.9 29.0 1.0
N B:THR110 5.0 30.1 1.0
O B:CYS98 5.0 35.0 1.0

Reference:

K.H.Seo, N.N.Zhuang, C.Chen, J.Y.Song, H.L.Kang, K.H.Rhee, K.H.Lee. Unusual Nadph Conformation in the Crystal Structure of A Cinnamyl Alcohol Dehydrogenase From Helicobacter Pylori in Complex with Nadp(H) and Substrate Docking Analysis Febs Lett. V. 586 337 2012.
ISSN: ISSN 0014-5793
PubMed: 22269576
DOI: 10.1016/J.FEBSLET.2012.01.020
Page generated: Wed Dec 16 04:53:07 2020

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