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Zinc in PDB 1pl7: Human Sorbitol Dehydrogenase (Apo)

Enzymatic activity of Human Sorbitol Dehydrogenase (Apo)

All present enzymatic activity of Human Sorbitol Dehydrogenase (Apo):
1.1.1.14;

Protein crystallography data

The structure of Human Sorbitol Dehydrogenase (Apo), PDB code: 1pl7 was solved by T.A.Pauly, J.L.Ekstrom, D.A.Beebe, B.Chrunyk, D.Cunningham, M.Griffor, A.Kamath, S.E.Lee, R.Madura, D.Mcguire, T.Subashi, D.Wasilko, P.Watts, B.L.Mylari, P.J.Oates, P.D.Adams, V.L.Rath, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.17 / 2.20
Space group P 62
Cell size a, b, c (Å), α, β, γ (°) 134.946, 134.946, 224.686, 90.00, 90.00, 120.00
R / Rfree (%) 20 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Sorbitol Dehydrogenase (Apo) (pdb code 1pl7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Human Sorbitol Dehydrogenase (Apo), PDB code: 1pl7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1pl7

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Zinc binding site 1 out of 4 in the Human Sorbitol Dehydrogenase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Sorbitol Dehydrogenase (Apo) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:27.1
occ:1.00
NE2 A:HIS69 2.2 18.0 1.0
O A:HOH1952 2.3 15.5 1.0
OE2 A:GLU70 2.3 21.7 1.0
SG A:CYS44 2.4 20.5 1.0
CE1 A:HIS69 3.1 17.1 1.0
CD A:GLU70 3.1 18.4 1.0
CB A:CYS44 3.1 18.5 1.0
CD2 A:HIS69 3.2 14.3 1.0
CG A:GLU70 3.4 16.7 1.0
OE1 A:GLU155 3.5 17.7 1.0
O A:HOH1839 4.0 25.0 1.0
ND1 A:HIS69 4.2 16.7 1.0
OE1 A:GLU70 4.2 17.1 1.0
CD A:GLU155 4.2 18.4 1.0
CG A:HIS69 4.2 15.4 1.0
CA A:CYS44 4.4 19.8 1.0
OG A:SER46 4.4 31.8 1.0
OE2 A:GLU155 4.4 16.2 1.0
N A:CYS44 4.4 17.8 1.0
O A:HOH1262 4.6 22.4 1.0
O A:HOH1028 4.7 16.2 1.0
O A:HOH1833 4.7 30.0 1.0
CB A:GLU70 4.9 16.3 1.0
OD2 A:ASP47 5.0 17.3 1.0
NZ A:LYS344 5.0 17.6 1.0

Zinc binding site 2 out of 4 in 1pl7

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Zinc binding site 2 out of 4 in the Human Sorbitol Dehydrogenase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Sorbitol Dehydrogenase (Apo) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:24.4
occ:1.00
NE2 B:HIS69 2.2 14.7 1.0
O B:HOH1951 2.2 17.9 1.0
OE2 B:GLU70 2.3 16.9 1.0
SG B:CYS44 2.4 21.2 1.0
CE1 B:HIS69 2.9 15.4 1.0
CB B:CYS44 3.2 19.0 1.0
CD B:GLU70 3.2 14.1 1.0
CD2 B:HIS69 3.3 13.9 1.0
CG B:GLU70 3.5 14.1 1.0
OE1 B:GLU155 3.6 15.1 1.0
O B:HOH2058 3.7 40.2 1.0
ND1 B:HIS69 4.1 14.1 1.0
O B:HOH1034 4.2 25.5 1.0
CD B:GLU155 4.2 15.5 1.0
OG B:SER46 4.2 33.6 1.0
CG B:HIS69 4.3 13.2 1.0
OE1 B:GLU70 4.4 17.4 1.0
OE2 B:GLU155 4.4 13.0 1.0
CA B:CYS44 4.4 20.3 1.0
N B:CYS44 4.5 18.7 1.0
O B:HOH1021 4.6 14.7 1.0
O B:HOH1248 4.7 19.3 1.0
O B:HOH1838 4.9 26.2 1.0
OD2 B:ASP47 4.9 17.9 1.0
CB B:GLU70 5.0 14.1 1.0

Zinc binding site 3 out of 4 in 1pl7

Go back to Zinc Binding Sites List in 1pl7
Zinc binding site 3 out of 4 in the Human Sorbitol Dehydrogenase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Sorbitol Dehydrogenase (Apo) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn402

b:25.9
occ:1.00
O C:HOH1950 2.2 15.8 1.0
NE2 C:HIS69 2.2 14.3 1.0
OE2 C:GLU70 2.3 17.4 1.0
SG C:CYS44 2.4 20.9 1.0
CE1 C:HIS69 3.0 15.6 1.0
CB C:CYS44 3.2 18.6 1.0
CD C:GLU70 3.2 13.4 1.0
CD2 C:HIS69 3.3 14.5 1.0
CG C:GLU70 3.4 14.3 1.0
O C:HOH1817 3.5 34.4 1.0
OE1 C:GLU155 3.5 15.0 1.0
O C:HOH1831 4.0 24.6 1.0
ND1 C:HIS69 4.1 14.3 1.0
CD C:GLU155 4.2 16.8 1.0
O C:HOH2078 4.2 33.8 1.0
OG C:SER46 4.3 33.6 1.0
OE2 C:GLU155 4.3 15.3 1.0
CG C:HIS69 4.3 14.3 1.0
OE1 C:GLU70 4.4 13.2 1.0
CA C:CYS44 4.4 19.4 1.0
N C:CYS44 4.5 16.8 1.0
O C:HOH1011 4.7 18.3 1.0
O C:HOH1301 4.7 22.6 1.0
O C:HOH1054 4.8 22.2 1.0
OD2 C:ASP47 4.9 15.1 1.0
CB C:GLU70 5.0 14.3 1.0

Zinc binding site 4 out of 4 in 1pl7

Go back to Zinc Binding Sites List in 1pl7
Zinc binding site 4 out of 4 in the Human Sorbitol Dehydrogenase (Apo)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Sorbitol Dehydrogenase (Apo) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn402

b:26.2
occ:1.00
NE2 D:HIS69 2.2 19.4 1.0
OE2 D:GLU70 2.2 15.2 1.0
O D:HOH1949 2.3 21.9 1.0
SG D:CYS44 2.4 22.5 1.0
CE1 D:HIS69 2.9 19.8 1.0
CD D:GLU70 3.2 15.5 1.0
CB D:CYS44 3.2 17.6 1.0
CD2 D:HIS69 3.3 17.1 1.0
CG D:GLU70 3.5 13.7 1.0
OE1 D:GLU155 3.5 17.3 1.0
O D:HOH1842 3.9 27.4 1.0
ND1 D:HIS69 4.1 17.8 1.0
CD D:GLU155 4.2 18.9 1.0
CG D:HIS69 4.3 15.8 1.0
OE1 D:GLU70 4.3 16.3 1.0
OG D:SER46 4.4 32.3 1.0
O D:HOH1279 4.4 23.5 1.0
OE2 D:GLU155 4.4 14.9 1.0
CA D:CYS44 4.4 18.8 1.0
N D:CYS44 4.5 17.0 1.0
O D:HOH1020 4.6 13.9 1.0
O D:HOH1955 4.8 26.9 1.0
OD2 D:ASP47 4.9 18.2 1.0
CB D:GLU70 5.0 15.9 1.0

Reference:

T.A.Pauly, J.L.Ekstrom, D.A.Beebe, B.Chrunyk, D.Cunningham, M.Griffor, A.Kamath, S.E.Lee, R.Madura, D.Mcguire, T.Subashi, D.Wasilko, P.Watts, B.L.Mylari, P.J.Oates, P.D.Adams, V.L.Rath. X-Ray Crystallographic and Kinetic Studies of Human Sorbitol Dehydrogenase. Structure V. 11 1071 2003.
ISSN: ISSN 0969-2126
PubMed: 12962626
DOI: 10.1016/S0969-2126(03)00167-9
Page generated: Mon Jan 25 16:11:33 2021

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