Atomistry » Zinc » PDB 3ued-3uk3 » 3uhj
Atomistry »
  Zinc »
    PDB 3ued-3uk3 »
      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 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy