Atomistry » Zinc » PDB 3udz-3ujp » 3uhj
Atomistry »
  Zinc »
    PDB 3udz-3ujp »
      3uhj »

Zinc in PDB 3uhj: Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021

Enzymatic activity of Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021

All present enzymatic activity of Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021:
1.1.1.6;

Protein crystallography data

The structure of Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021, PDB code: 3uhj was solved by R.Agarwal, S.Chamala, B.Evans, R.Foti, A.Gizzi, B.Hillerich, A.Kar, J.Lafleur, R.Seidel, G.Villigas, W.Zencheck, S.C.Almo, S.Swaminathan, Newyork Structural Genomics Research Consortium (Nysgrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 2.34
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 79.483, 98.996, 104.734, 76.94, 83.38, 71.47
R / Rfree (%) 19.7 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 (pdb code 3uhj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021, PDB code: 3uhj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 1 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn388

b:38.6
occ:0.40
 NE2 A:HIS278 2.3 36.1 1.0
NE2 A:HIS295 2.4 32.7 1.0
OD1 A:ASP193 2.4 40.3 1.0
OD2 A:ASP193 2.6 39.4 1.0
CG A:ASP193 2.8 33.0 1.0
OD1 A:ASP143 3.1 38.5 1.0
CD2 A:HIS278 3.1 36.0 1.0
CD2 A:HIS295 3.3 29.4 1.0
CE1 A:HIS278 3.3 35.6 1.0
CE1 A:HIS295 3.4 30.3 1.0
CG A:ASP143 4.0 37.5 1.0
CG2 A:VAL299 4.2 23.3 1.0
CB A:ASP193 4.3 28.3 1.0
O A:HOH389 4.3 42.6 1.0
CG A:HIS278 4.3 32.8 1.0
ND1 A:HIS278 4.4 36.6 1.0
OD2 A:ASP143 4.4 43.2 1.0
CG A:HIS295 4.5 30.3 1.0
ND1 A:HIS295 4.5 32.0 1.0
CE1 A:PHE269 4.5 51.1 1.0
CD1 A:PHE269 4.7 48.9 1.0
CG1 A:VAL299 5.0 26.5 1.0
N A:ASP143 5.0 31.2 1.0

Zinc binding site 2 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 2 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn388

b:47.3
occ:0.40
 NE2 B:HIS295 2.2 38.3 1.0
NE2 B:HIS278 2.4 35.0 1.0
OD1 B:ASP193 2.5 35.4 1.0
OD2 B:ASP143 2.8 46.7 1.0
OD1 B:ASP143 3.0 47.6 1.0
CD2 B:HIS295 3.1 35.0 1.0
OD2 B:ASP193 3.1 37.6 1.0
CG B:ASP193 3.2 29.3 1.0
CD2 B:HIS278 3.2 35.6 1.0
CG B:ASP143 3.2 43.7 1.0
CE1 B:HIS295 3.2 39.3 1.0
CE1 B:HIS278 3.5 32.5 1.0
CE1 B:PHE269 4.2 48.0 1.0
CG B:HIS295 4.3 34.5 1.0
ND1 B:HIS295 4.3 39.4 1.0
CG B:HIS278 4.4 29.8 1.0
CG2 B:VAL299 4.5 22.0 1.0
ND1 B:HIS278 4.5 31.1 1.0
CD1 B:PHE269 4.6 45.8 1.0
CB B:ASP193 4.6 24.6 1.0
N B:ASP143 4.7 35.2 1.0
CB B:ASP143 4.7 38.4 1.0
CB B:THR142 5.0 32.1 1.0

Zinc binding site 3 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 3 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn388

b:41.7
occ:0.40
 NE2 C:HIS295 2.2 38.9 1.0
OD1 C:ASP193 2.3 40.6 1.0
NE2 C:HIS278 2.4 36.8 1.0
OD1 C:ASP143 2.8 49.4 1.0
OD2 C:ASP193 2.8 41.6 1.0
CG C:ASP193 2.9 34.6 1.0
CD2 C:HIS295 3.2 37.9 1.0
CD2 C:HIS278 3.2 35.1 1.0
CE1 C:HIS295 3.3 38.2 1.0
CE1 C:HIS278 3.5 35.0 1.0
CG C:ASP143 3.9 47.0 1.0
CG2 C:VAL299 4.2 28.8 1.0
CG C:HIS295 4.3 37.8 1.0
ND1 C:HIS295 4.3 41.0 1.0
CB C:ASP193 4.4 30.9 1.0
CG C:HIS278 4.4 35.8 1.0
OD2 C:ASP143 4.6 53.9 1.0
ND1 C:HIS278 4.6 34.0 1.0
CE1 C:PHE269 4.6 49.3 1.0
CD1 C:PHE269 4.9 46.8 1.0
CG1 C:VAL299 4.9 30.5 1.0
N C:ASP143 4.9 38.3 1.0
CB C:THR142 5.0 36.7 1.0
CB C:ASP143 5.0 41.9 1.0

Zinc binding site 4 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 4 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn388

b:42.1
occ:0.40
 OD2 D:ASP143 2.3 42.6 1.0
NE2 D:HIS278 2.6 31.0 1.0
NE2 D:HIS295 2.7 33.7 1.0
OD1 D:ASP193 2.7 46.3 1.0
OD2 D:ASP193 2.8 46.9 1.0
CG D:ASP143 2.9 41.7 1.0
OD1 D:ASP143 3.0 44.4 1.0
CG D:ASP193 3.1 37.5 1.0
CD2 D:HIS278 3.3 32.8 1.0
CD2 D:HIS295 3.6 33.6 1.0
CE1 D:HIS278 3.7 31.1 1.0
CE1 D:HIS295 3.7 34.6 1.0
CB D:ASP143 4.4 37.9 1.0
N D:ASP143 4.5 37.0 1.0
CG D:HIS278 4.6 31.4 1.0
CB D:ASP193 4.6 31.1 1.0
ND1 D:HIS278 4.7 29.6 1.0
CG D:HIS295 4.8 32.3 1.0
CG2 D:VAL299 4.8 26.1 1.0
ND1 D:HIS295 4.8 35.1 1.0

Zinc binding site 5 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 5 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn389

b:39.8
occ:0.30
 NE2 E:HIS278 2.1 33.7 1.0
NE2 E:HIS295 2.2 33.5 1.0
OD1 E:ASP193 2.7 42.4 1.0
OD2 E:ASP193 2.8 45.7 1.0
CD2 E:HIS278 3.0 33.8 1.0
CE1 E:HIS295 3.0 29.8 1.0
CG E:ASP193 3.1 37.2 1.0
CE1 E:HIS278 3.2 33.2 1.0
CD2 E:HIS295 3.4 30.8 1.0
OD2 E:ASP143 3.4 48.5 1.0
OD1 E:ASP143 3.4 41.6 1.0
CG E:ASP143 3.8 40.1 1.0
CE1 E:PHE269 3.9 52.7 1.0
CG2 E:VAL299 4.1 24.8 1.0
CG E:HIS278 4.2 32.9 1.0
ND1 E:HIS278 4.2 32.8 1.0
ND1 E:HIS295 4.2 32.3 1.0
CD1 E:PHE269 4.4 48.3 1.0
CG E:HIS295 4.4 31.9 1.0
CB E:ASP193 4.7 31.0 1.0
CZ E:PHE269 5.0 51.1 1.0

Zinc binding site 6 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 6 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn388

b:37.9
occ:0.30
 NE2 F:HIS295 2.4 38.5 1.0
NE2 F:HIS278 2.4 34.3 1.0
OD2 F:ASP193 2.6 43.6 1.0
OD1 F:ASP193 2.9 45.6 1.0
OD1 F:ASP143 3.0 44.7 1.0
CG F:ASP193 3.1 37.2 1.0
OD2 F:ASP143 3.1 48.0 1.0
CD2 F:HIS278 3.1 34.3 1.0
CD2 F:HIS295 3.2 40.0 1.0
CG F:ASP143 3.4 44.0 1.0
CE1 F:HIS295 3.5 37.1 1.0
CE1 F:HIS278 3.5 32.1 1.0
CE1 F:PHE269 4.0 48.6 1.0
CG2 F:VAL299 4.4 28.4 1.0
CG F:HIS278 4.4 34.7 1.0
CG F:HIS295 4.4 38.6 1.0
ND1 F:HIS278 4.5 32.8 1.0
CD1 F:PHE269 4.5 47.9 1.0
ND1 F:HIS295 4.5 39.4 1.0
CB F:ASP193 4.6 32.4 1.0
CB F:ASP143 4.9 41.1 1.0
N F:ASP143 4.9 39.7 1.0

Zinc binding site 7 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 7 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


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 A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn388

b:36.4
occ:0.30
 OD1 G:ASP193 2.3 42.7 1.0
NE2 G:HIS278 2.3 38.7 1.0
NE2 G:HIS295 2.5 39.8 1.0
OD2 G:ASP193 2.7 43.6 1.0
CG G:ASP193 2.9 36.2 1.0
OD1 G:ASP143 3.0 52.1 1.0
CD2 G:HIS278 3.1 35.5 1.0
CD2 G:HIS295 3.4 36.4 1.0
CE1 G:HIS278 3.4 34.5 1.0
CE1 G:HIS295 3.5 38.4 1.0
OD2 G:ASP143 3.6 53.4 1.0
CG G:ASP143 3.6 47.1 1.0
CG G:HIS278 4.3 29.9 1.0
CG2 G:VAL299 4.4 25.9 1.0
CB G:ASP193 4.4 32.0 1.0
ND1 G:HIS278 4.5 31.7 1.0
CG G:HIS295 4.5 35.7 1.0
ND1 G:HIS295 4.6 38.0 1.0
CE1 G:PHE269 4.7 50.4 1.0
CD1 G:PHE269 4.8 48.6 1.0
N G:ASP143 4.9 37.4 1.0
CB G:ASP143 5.0 41.1 1.0

Zinc binding site 8 out of 8 in 3uhj

Go back to Zinc Binding Sites List in 3uhj
Zinc binding site 8 out of 8 in the Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn389

b:44.1
occ:0.40
 NE2 H:HIS278 2.3 42.4 1.0
OD1 H:ASP193 2.5 42.6 1.0
NE2 H:HIS295 2.7 44.6 1.0
OD2 H:ASP193 2.8 40.4 1.0
OD1 H:ASP143 2.9 47.8 1.0
CG H:ASP193 3.0 33.6 1.0
OD2 H:ASP143 3.0 52.0 1.0
CD2 H:HIS278 3.2 39.2 1.0
CG H:ASP143 3.2 45.9 1.0
CE1 H:HIS278 3.3 40.1 1.0
CD2 H:HIS295 3.5 42.7 1.0
CE1 H:HIS295 3.8 42.7 1.0
CE1 H:PHE269 4.4 50.0 1.0
CG H:HIS278 4.4 37.1 1.0
ND1 H:HIS278 4.4 38.0 1.0
CG2 H:VAL299 4.4 29.1 1.0
CD1 H:PHE269 4.5 50.4 1.0
CB H:ASP193 4.5 30.0 1.0
CB H:ASP143 4.6 42.8 1.0
N H:ASP143 4.7 38.3 1.0
CG H:HIS295 4.7 39.5 1.0
ND1 H:HIS295 4.9 43.3 1.0

Reference:

R.Agarwal, S.C.Almo, S.Swaminathan. Crystal Structure of A Probable Glycerol Dehydrogenase From Sinorhizobium Meliloti 1021 To Be Published.
Page generated: Sat Oct 26 17:20:38 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy