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Zinc in PDB 4cvc: Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site

Enzymatic activity of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site

All present enzymatic activity of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site:
1.1.2.8;

Protein crystallography data

The structure of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site, PDB code: 4cvc was solved by H.J.Rozeboom, S.Yu, R.Mikkelsen, I.Nikolaev, H.Mulder, B.W.Dijkstra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.08 / 1.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.220, 87.160, 57.000, 90.00, 90.29, 90.00
R / Rfree (%) 16.109 / 18.405

Other elements in 4cvc:

The structure of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site (pdb code 4cvc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site, PDB code: 4cvc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 4cvc

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Zinc binding site 1 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1609

b:9.5
occ:1.00
 O A:HOH2370 1.9 11.3 1.0
O A:HOH2369 2.0 10.8 1.0
O2 A:PPI1617 2.0 10.3 1.0
O1 A:PPI1617 2.0 10.3 1.0
ND1 A:HIS324 2.1 11.2 1.0
O A:HOH2374 2.1 10.8 1.0
C1 A:PPI1617 2.3 10.6 1.0
CE1 A:HIS324 2.9 11.1 1.0
CG A:HIS324 3.2 10.3 1.0
CB A:HIS324 3.6 9.9 1.0
C2 A:PPI1617 3.8 10.8 1.0
O A:LYS323 4.0 9.7 1.0
O A:HOH2417 4.1 17.3 1.0
O A:GLY390 4.1 12.0 1.0
O A:HOH2571 4.1 20.0 1.0
NE2 A:HIS324 4.1 10.7 1.0
O A:HOH2420 4.1 16.8 1.0
O A:HOH2375 4.2 11.8 1.0
CD2 A:HIS324 4.2 10.3 1.0
CA A:HIS324 4.3 9.4 1.0
O A:THR410 4.5 12.0 1.0
C3 A:PPI1617 4.7 11.3 1.0
O A:HOH2439 4.7 15.6 1.0
O A:HOH2570 4.8 33.5 1.0
C A:LYS323 4.9 9.4 1.0
CE1 A:PHE385 5.0 9.0 1.0

Zinc binding site 2 out of 7 in 4cvc

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Zinc binding site 2 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1610

b:21.0
occ:1.00
 OD2 A:ASP350 2.0 24.2 1.0
OE2 A:GLU503 2.0 23.4 1.0
O A:HOH2394 2.2 17.7 1.0
O A:HOH2499 2.8 27.7 1.0
CG A:ASP350 3.0 22.3 1.0
CD A:GLU503 3.0 20.6 1.0
CB A:ASP350 3.3 21.0 1.0
CG A:GLU503 3.4 19.2 1.0
OD1 A:ASP350 4.1 22.8 1.0
OE1 A:GLU503 4.1 20.6 1.0
O A:HOH2396 4.2 23.2 1.0
O A:HOH2391 4.3 23.3 1.0
CA A:ASP350 4.8 20.1 1.0
CB A:GLU503 4.9 17.2 1.0

Zinc binding site 3 out of 7 in 4cvc

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Zinc binding site 3 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1611

b:9.3
occ:1.00
 O A:HOH2010 1.9 8.0 1.0
OD1 A:ASP57 2.0 11.8 1.0
CL A:CL1616 2.5 12.2 1.0
CG A:ASP57 2.8 11.0 1.0
OD2 A:ASP57 3.0 11.3 1.0
O A:HOH2014 3.8 13.0 1.0
OH A:TYR112 4.0 9.7 1.0
O A:HOH2028 4.0 26.2 1.0
O A:HOH2018 4.2 6.3 1.0
CE1 A:TYR112 4.2 8.8 1.0
CB A:ASP57 4.3 10.4 1.0
CZ A:TYR112 4.6 9.2 1.0
ND2 A:ASN62 4.7 9.5 1.0
CA A:ASP57 4.8 10.2 1.0
O A:HOH2046 4.9 29.0 1.0
OG1 A:THR54 5.0 13.0 1.0

Zinc binding site 4 out of 7 in 4cvc

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Zinc binding site 4 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1612

b:14.5
occ:1.00
 OE2 A:GLU335 2.0 13.7 1.0
OE1 A:GLN220 2.0 15.9 1.0
N6 A:PQQ1608 2.0 12.6 1.0
O5 A:PQQ1608 2.3 13.7 1.0
O7B A:PQQ1608 2.4 13.0 1.0
CD A:GLU335 2.6 12.0 1.0
OE1 A:GLU335 2.7 12.7 1.0
C6A A:PQQ1608 2.8 12.3 1.0
C5 A:PQQ1608 2.9 12.8 1.0
C7 A:PQQ1608 3.0 12.0 1.0
C7X A:PQQ1608 3.1 12.1 1.0
CD A:GLN220 3.2 14.4 1.0
O A:HOH2261 3.4 22.5 1.0
OD1 A:ASP333 3.4 11.9 1.0
O1 A:PEG1607 3.8 25.5 1.0
NE2 A:GLN220 3.8 15.2 1.0
NE1 A:TRP270 3.9 8.0 1.0
CG A:GLU335 4.0 11.1 1.0
O A:HOH2330 4.0 13.7 1.0
CG A:ASP333 4.2 11.3 1.0
OD2 A:ASP333 4.2 12.0 1.0
C9A A:PQQ1608 4.3 12.0 1.0
C8 A:PQQ1608 4.3 11.7 1.0
O7A A:PQQ1608 4.3 11.7 1.0
C4 A:PQQ1608 4.4 12.7 1.0
CG A:GLN220 4.4 13.5 1.0
NZ A:LYS378 4.5 7.7 1.0
CE2 A:TRP270 4.5 7.8 1.0
O A:HOH2343 4.6 21.5 1.0
CZ2 A:TRP270 4.6 7.9 1.0
CD1 A:TRP270 4.8 7.8 1.0
C9 A:PQQ1608 4.8 11.7 1.0
C4 A:PEG1607 4.8 32.0 1.0
O4 A:PQQ1608 4.9 12.4 1.0

Zinc binding site 5 out of 7 in 4cvc

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Zinc binding site 5 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1613

b:12.9
occ:0.50
 O A:HOH2529 1.7 16.1 1.0
OE2 A:GLU545 2.0 16.3 1.0
OG A:SER548 2.2 12.9 1.0
O A:HOH2523 2.4 22.9 1.0
O A:HOH2522 2.5 15.0 1.0
CD A:GLU545 2.9 15.3 1.0
CB A:SER548 3.1 11.0 1.0
OE1 A:GLU545 3.2 15.8 1.0
OD2 A:ASP534 3.7 10.9 1.0
O A:HOH2520 4.0 8.7 1.0
O A:HOH2528 4.0 22.2 1.0
O A:HOH2532 4.1 28.6 1.0
CG A:GLU545 4.3 14.8 1.0
CA A:SER548 4.4 10.3 1.0
CG A:ASP534 4.4 9.7 1.0
O A:HOH2504 4.6 16.3 1.0
O A:HOH2519 4.6 14.9 1.0
N A:SER548 4.7 10.7 1.0

Zinc binding site 6 out of 7 in 4cvc

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Zinc binding site 6 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1614

b:14.8
occ:0.50
 OD1 A:ASP276 2.0 14.4 1.0
OE1 A:GLU278 2.0 15.3 1.0
NZ A:LYS370 2.2 17.9 1.0
CE A:LYS370 2.8 16.4 1.0
CG A:ASP276 2.8 12.8 1.0
ZN A:ZN1615 2.9 23.7 0.5
CD A:GLU278 3.0 15.8 1.0
OD2 A:ASP276 3.0 13.3 1.0
O A:HOH2337 3.5 28.1 1.0
OE2 A:GLU278 3.7 16.5 1.0
CD A:LYS370 3.7 15.4 1.0
CG A:GLU278 3.9 15.9 1.0
CB A:GLU278 4.0 15.1 1.0
NE2 A:GLN74 4.2 8.5 1.0
CB A:ASP276 4.2 11.8 1.0
N A:GLU278 4.4 13.4 1.0
CD A:PRO277 4.4 11.6 1.0
CG1 A:VAL342 4.5 10.3 1.0
CG A:GLN74 4.6 7.8 1.0
CA A:ASP276 4.7 10.9 1.0
N A:PRO277 4.7 11.8 1.0
O A:HOH2569 4.7 28.6 1.0
CG A:LYS370 4.8 14.7 1.0
CA A:GLU278 4.8 14.2 1.0
O A:HOH2412 4.9 21.7 1.0
CD A:GLN74 4.9 8.0 1.0
C A:ASP276 5.0 11.4 1.0

Zinc binding site 7 out of 7 in 4cvc

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Zinc binding site 7 out of 7 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site


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 Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes with Zinc in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1615

b:23.7
occ:0.50
 O A:HOH2569 2.0 28.6 1.0
O A:HOH2337 2.6 28.1 1.0
ZN A:ZN1614 2.9 14.8 0.5
NE2 A:GLN74 3.8 8.5 1.0
CE A:LYS370 4.0 16.4 1.0
NZ A:LYS370 4.2 17.9 1.0
OD1 A:ASP276 4.2 14.4 1.0
OE1 A:GLU278 4.3 15.3 1.0
CG A:GLN74 4.4 7.8 1.0
O A:VAL342 4.6 10.1 1.0
CD A:GLN74 4.6 8.0 1.0
CZ2 A:TRP76 4.8 8.6 1.0
CD A:GLU278 4.8 15.8 1.0
O A:HOH2384 4.8 19.1 1.0
OE2 A:GLU278 4.9 16.5 1.0
OG A:SER344 5.0 13.7 0.5

Reference:

H.J.Rozeboom, S.Yu, R.Mikkelsen, I.Nikolaev, H.Mulder, B.W.Dijkstra. Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase Form Pseudogluconobacter Saccharoketogenenes To Be Published.
Page generated: Sat Oct 26 21:06:50 2024

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