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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

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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

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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

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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

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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

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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

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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

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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

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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

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