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Zinc in PDB 1vhd: Crystal Structure of An Iron Containing Alcohol Dehydrogenase

Protein crystallography data

The structure of Crystal Structure of An Iron Containing Alcohol Dehydrogenase, PDB code: 1vhd was solved by Structural Genomix, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 11.99 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.903, 85.067, 72.354, 90.00, 96.57, 90.00
R / Rfree (%) 19 / 20.8

Other elements in 1vhd:

The structure of Crystal Structure of An Iron Containing Alcohol Dehydrogenase also contains other interesting chemical elements:

Arsenic (As) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of An Iron Containing Alcohol Dehydrogenase (pdb code 1vhd). 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 An Iron Containing Alcohol Dehydrogenase, PDB code: 1vhd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1vhd

Go back to Zinc Binding Sites List in 1vhd
Zinc binding site 1 out of 2 in the Crystal Structure of An Iron Containing Alcohol Dehydrogenase


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 An Iron Containing Alcohol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn371

b:18.6
occ:1.00
NE2 A:HIS256 2.1 14.3 1.0
NE2 A:HIS270 2.1 12.0 1.0
OD1 A:ASP189 2.2 10.5 1.0
O A:HOH611 2.2 21.8 1.0
NE2 A:HIS193 2.3 10.4 1.0
C5N A:NAP372 2.8 29.1 1.0
CG A:ASP189 3.1 9.5 1.0
CE1 A:HIS256 3.1 12.4 1.0
CD2 A:HIS270 3.1 11.9 1.0
CD2 A:HIS256 3.1 12.2 1.0
CE1 A:HIS193 3.1 12.3 1.0
CE1 A:HIS270 3.2 11.9 1.0
CD2 A:HIS193 3.3 9.8 1.0
OD2 A:ASP189 3.3 11.3 1.0
C6N A:NAP372 3.4 28.4 1.0
C4N A:NAP372 3.7 29.0 1.0
O A:HOH458 3.7 21.2 1.0
O A:HOH610 4.0 21.6 1.0
ND1 A:HIS256 4.2 12.6 1.0
CG A:HIS256 4.3 12.7 1.0
ND1 A:HIS193 4.3 6.7 1.0
ND1 A:HIS270 4.3 11.6 1.0
CG A:HIS270 4.3 10.8 1.0
CG A:HIS193 4.3 7.3 1.0
CB A:ASP189 4.5 7.4 1.0
OG A:SER192 4.6 7.0 0.5
N1N A:NAP372 4.6 27.2 1.0
O A:ASP189 4.7 6.3 1.0
C3N A:NAP372 4.9 29.8 1.0
CA A:ASP189 5.0 6.5 1.0

Zinc binding site 2 out of 2 in 1vhd

Go back to Zinc Binding Sites List in 1vhd
Zinc binding site 2 out of 2 in the Crystal Structure of An Iron Containing Alcohol Dehydrogenase


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 An Iron Containing Alcohol Dehydrogenase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn371

b:21.3
occ:1.00
O B:HOH517 2.1 21.2 1.0
NE2 B:HIS270 2.2 16.1 1.0
NE2 B:HIS256 2.2 17.2 1.0
NE2 B:HIS193 2.2 13.2 1.0
OD1 B:ASP189 2.3 15.0 1.0
C5N B:NAP372 3.0 35.5 1.0
CD2 B:HIS270 3.1 17.6 1.0
CE1 B:HIS256 3.1 17.1 1.0
CE1 B:HIS193 3.1 13.7 1.0
CD2 B:HIS193 3.2 11.6 1.0
CG B:ASP189 3.2 16.4 1.0
CE1 B:HIS270 3.2 18.1 1.0
CD2 B:HIS256 3.2 17.7 1.0
OD2 B:ASP189 3.4 16.3 1.0
O B:HOH481 3.5 27.9 1.0
C6N B:NAP372 3.6 35.0 1.0
C4N B:NAP372 3.9 34.1 1.0
O B:HOH423 4.1 25.7 1.0
ND1 B:HIS193 4.2 10.9 1.0
ND1 B:HIS256 4.2 18.9 1.0
CG B:HIS270 4.2 17.6 1.0
CG B:HIS193 4.3 11.3 1.0
ND1 B:HIS270 4.3 17.8 1.0
CG B:HIS256 4.3 17.3 1.0
CB B:ASP189 4.6 14.0 1.0
OG B:SER192 4.6 9.2 0.3
O B:ASP189 4.7 11.8 1.0
N1N B:NAP372 4.8 35.0 1.0

Reference:

J.Badger, J.M.Sauder, J.M.Adams, S.Antonysamy, K.Bain, M.G.Bergseid, S.G.Buchanan, M.D.Buchanan, Y.Batiyenko, J.A.Christopher, S.Emtage, A.Eroshkina, I.Feil, E.B.Furlong, K.S.Gajiwala, X.Gao, D.He, J.Hendle, A.Huber, K.Hoda, P.Kearins, C.Kissinger, B.Laubert, H.A.Lewis, J.Lin, K.Loomis, D.Lorimer, G.Louie, M.Maletic, C.D.Marsh, I.Miller, J.Molinari, H.J.Muller-Dieckmann, J.M.Newman, B.W.Noland, B.Pagarigan, F.Park, T.S.Peat, K.W.Post, S.Radojicic, A.Ramos, R.Romero, M.E.Rutter, W.E.Sanderson, K.D.Schwinn, J.Tresser, J.Winhoven, T.A.Wright, L.Wu, J.Xu, T.J.Harris. Structural Analysis of A Set of Proteins Resulting From A Bacterial Genomics Project Proteins V. 60 787 2005.
ISSN: ISSN 0887-3585
PubMed: 16021622
DOI: 10.1002/PROT.20541
Page generated: Mon Jan 25 16:15:15 2021

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