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Zinc in PDB 4cvb: Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes

Enzymatic activity of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes

All present enzymatic activity of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes:
1.1.2.8;

Protein crystallography data

The structure of Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes, PDB code: 4cvb 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) 27.95 / 1.72
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 127.950, 87.190, 57.100, 90.00, 90.16, 90.00
R / Rfree (%) 12.77 / 14.858

Other elements in 4cvb:

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

Zinc binding site 1 out of 4 in 4cvb

Go back to Zinc Binding Sites List in 4cvb
Zinc binding site 1 out of 4 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1609

b:10.1
occ:1.00
 O A:HOH2409 2.0 13.2 1.0
O1 A:PPI1614 2.0 12.7 1.0
ND1 A:HIS324 2.0 11.1 1.0
O2 A:PPI1614 2.0 14.3 1.0
O A:HOH2410 2.0 11.8 1.0
O A:HOH2415 2.1 14.0 1.0
C1 A:PPI1614 2.3 15.2 1.0
CE1 A:HIS324 2.9 10.9 1.0
CG A:HIS324 3.1 10.0 1.0
CB A:HIS324 3.6 9.6 1.0
C2 A:PPI1614 3.8 16.5 1.0
O A:HOH2463 4.0 17.1 1.0
O A:LYS323 4.0 9.8 1.0
O A:GLY390 4.0 11.0 1.0
O A:HOH2626 4.1 29.5 1.0
NE2 A:HIS324 4.1 10.4 1.0
O A:HOH2416 4.2 12.9 1.0
O A:HOH2467 4.2 19.3 1.0
CD2 A:HIS324 4.2 10.0 1.0
CA A:HIS324 4.3 9.4 1.0
O A:THR410 4.5 11.6 1.0
O A:HOH2487 4.6 17.1 1.0
C3 A:PPI1614 4.8 18.7 1.0
CE1 A:PHE385 4.9 8.8 1.0
C A:LYS323 4.9 9.5 1.0
O A:HOH2465 5.0 27.8 1.0

Zinc binding site 2 out of 4 in 4cvb

Go back to Zinc Binding Sites List in 4cvb
Zinc binding site 2 out of 4 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1610

b:19.3
occ:1.00
 OD2 A:ASP350 2.0 22.4 1.0
OE2 A:GLU503 2.0 22.3 1.0
O A:HOH2438 2.2 7.4 1.0
CG A:ASP350 2.9 20.4 1.0
CD A:GLU503 3.0 19.7 1.0
CB A:ASP350 3.3 19.0 1.0
CG A:GLU503 3.4 18.2 1.0
OD1 A:ASP350 4.1 21.0 1.0
OE1 A:GLU503 4.1 20.1 1.0
O A:HOH2440 4.3 28.0 1.0
CA A:ASP350 4.8 18.4 1.0
CB A:GLU503 4.9 16.1 1.0

Zinc binding site 3 out of 4 in 4cvb

Go back to Zinc Binding Sites List in 4cvb
Zinc binding site 3 out of 4 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1611

b:9.4
occ:1.00
 O A:HOH2012 2.0 6.6 1.0
OD1 A:ASP57 2.0 10.8 1.0
CL A:CL1613 2.4 12.9 1.0
CG A:ASP57 2.8 10.1 1.0
OD2 A:ASP57 3.0 10.2 1.0
O A:HOH2016 3.9 13.2 1.0
OH A:TYR112 4.0 8.7 1.0
O A:HOH2021 4.1 5.9 1.0
CE1 A:TYR112 4.2 7.9 1.0
CB A:ASP57 4.2 9.5 1.0
OE1 A:GLN51 4.4 28.3 1.0
CZ A:TYR112 4.6 8.3 1.0
ND2 A:ASN62 4.7 8.6 1.0
CA A:ASP57 4.8 9.4 1.0
O A:HOH2011 4.9 29.9 1.0
ND2 A:ASN65 5.0 7.4 1.0
ND2 A:ASN113 5.0 9.1 1.0

Zinc binding site 4 out of 4 in 4cvb

Go back to Zinc Binding Sites List in 4cvb
Zinc binding site 4 out of 4 in the Crystal Structure of Quinone-Dependent Alcohol Dehydrogenase From Pseudogluconobacter Saccharoketogenenes


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1612

b:15.3
occ:0.50
 O A:HOH2592 1.6 19.1 1.0
OE2 A:GLU545 2.0 19.1 1.0
OG A:SER548 2.2 14.4 1.0
O A:HOH2583 2.5 27.7 1.0
O A:HOH2584 2.6 20.1 1.0
CD A:GLU545 2.9 17.5 1.0
CB A:SER548 3.0 11.6 1.0
OE1 A:GLU545 3.1 18.2 1.0
OD2 A:ASP534 3.7 12.0 1.0
O A:HOH2591 3.9 27.2 1.0
O A:HOH2581 4.1 13.3 1.0
O A:HOH2590 4.1 36.5 1.0
CG A:GLU545 4.3 16.0 1.0
CA A:SER548 4.4 10.7 1.0
CG A:ASP534 4.4 10.7 1.0
O A:HOH2580 4.6 19.9 1.0
O A:HOH2565 4.6 15.8 1.0
N A:SER548 4.7 11.0 1.0

Reference:

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

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