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Zinc in PDB 3hm7: Crystal Structure of Allantoinase From Bacillus Halodurans C-125

Enzymatic activity of Crystal Structure of Allantoinase From Bacillus Halodurans C-125

All present enzymatic activity of Crystal Structure of Allantoinase From Bacillus Halodurans C-125:
3.5.2.5;

Protein crystallography data

The structure of Crystal Structure of Allantoinase From Bacillus Halodurans C-125, PDB code: 3hm7 was solved by Y.Patskovsky, R.Romero, M.Rutter, S.Miller, S.R.Wasserman, J.M.Sauder, F.M.Raushel, S.K.Burley, S.C.Almo, New York Structural Genomix Researchconsortium (Nysgxrc), New York Sgx Research Center For Structuralgenomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.60
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 157.658, 157.658, 418.026, 90.00, 90.00, 120.00
R / Rfree (%) 24 / 26.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125 (pdb code 3hm7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125, PDB code: 3hm7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 3hm7

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Zinc binding site 1 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn447

b:43.5
occ:0.50
 OD1 A:ASP315 2.2 51.2 1.0
NE2 A:HIS65 2.2 45.1 1.0
NE2 A:HIS63 2.3 47.2 1.0
CE1 A:HIS65 3.0 36.6 1.0
O A:HOH480 3.1 46.5 1.0
CE1 A:HIS63 3.2 34.9 1.0
CG A:ASP315 3.2 43.8 1.0
CD2 A:HIS63 3.3 45.0 1.0
CD2 A:HIS65 3.3 35.0 1.0
OD2 A:ASP315 3.7 38.4 1.0
NE2 A:HIS242 3.9 58.4 1.0
ND1 A:HIS65 4.2 53.3 1.0
NZ A:LYS150 4.2 57.9 1.0
CD2 A:HIS242 4.2 38.8 1.0
ND1 A:HIS63 4.3 51.8 1.0
CG A:HIS65 4.4 45.9 1.0
CG A:HIS63 4.4 48.0 1.0
CB A:ASP315 4.4 36.6 1.0
CA A:ASP315 4.8 39.2 1.0

Zinc binding site 2 out of 6 in 3hm7

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Zinc binding site 2 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn447

b:39.3
occ:0.50
 OD1 B:ASP315 2.3 37.2 1.0
NE2 B:HIS63 2.4 40.4 1.0
NE2 B:HIS65 2.4 41.2 1.0
O B:HOH449 3.1 40.0 1.0
CE1 B:HIS65 3.1 34.0 1.0
CE1 B:HIS63 3.1 28.1 1.0
CG B:ASP315 3.2 44.7 1.0
CD2 B:HIS63 3.5 39.6 1.0
OD2 B:ASP315 3.5 37.4 1.0
CD2 B:HIS65 3.6 38.0 1.0
NE2 B:HIS242 3.8 44.4 1.0
CD2 B:HIS242 4.2 30.6 1.0
ND1 B:HIS63 4.3 40.6 1.0
ND1 B:HIS65 4.3 45.2 1.0
CG B:HIS63 4.5 44.5 1.0
CB B:ASP315 4.5 30.4 1.0
CG B:HIS65 4.6 39.4 1.0
CZ B:PHE152 4.8 40.0 1.0
NZ B:LYS150 4.8 38.1 1.0
CA B:ASP315 5.0 34.3 1.0
CE1 B:HIS242 5.0 40.6 1.0

Zinc binding site 3 out of 6 in 3hm7

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Zinc binding site 3 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn447

b:50.8
occ:0.50
 NE2 C:HIS63 2.2 51.0 1.0
NE2 C:HIS65 2.3 47.6 1.0
OD1 C:ASP315 2.3 40.2 1.0
CD2 C:HIS63 3.0 34.2 1.0
CE1 C:HIS63 3.2 60.4 1.0
CD2 C:HIS65 3.2 25.1 1.0
CE1 C:HIS65 3.3 45.4 1.0
CG C:ASP315 3.4 44.9 1.0
CE1 C:HIS242 3.5 65.7 1.0
OD2 C:ASP315 3.9 50.1 1.0
ND1 C:HIS242 3.9 38.7 1.0
CG C:HIS63 4.1 41.0 1.0
ND1 C:HIS63 4.2 54.4 1.0
ND1 C:HIS65 4.3 34.5 1.0
CG C:HIS65 4.4 29.0 1.0
CB C:ASP315 4.6 38.8 1.0
NZ C:LYS150 4.7 52.4 1.0
NE2 C:HIS242 4.7 58.9 1.0
CA C:ASP315 4.8 41.0 1.0
O C:HOH455 4.9 43.4 1.0
CB C:SER317 5.0 21.4 1.0

Zinc binding site 4 out of 6 in 3hm7

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Zinc binding site 4 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn447

b:40.0
occ:0.50
 OD1 D:ASP315 2.3 37.8 1.0
NE2 D:HIS63 2.4 37.9 1.0
NE2 D:HIS65 2.5 34.8 1.0
CE1 D:HIS63 3.1 31.1 1.0
O D:HOH486 3.2 44.2 1.0
CE1 D:HIS65 3.2 40.4 1.0
CG D:ASP315 3.3 44.4 1.0
CD2 D:HIS63 3.4 46.9 1.0
OD2 D:ASP315 3.6 31.6 1.0
CD2 D:HIS65 3.6 43.2 1.0
NE2 D:HIS242 3.9 50.6 1.0
OG D:SER317 4.1 43.9 1.0
ND1 D:HIS63 4.2 41.0 1.0
CD2 D:HIS242 4.2 47.8 1.0
CG D:HIS63 4.4 38.6 1.0
ND1 D:HIS65 4.4 37.7 1.0
CB D:ASP315 4.6 33.7 1.0
CG D:HIS65 4.7 44.9 1.0
NZ D:LYS150 4.9 36.3 1.0

Zinc binding site 5 out of 6 in 3hm7

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Zinc binding site 5 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn447

b:39.7
occ:0.50
 NE2 E:HIS63 2.2 42.2 1.0
NE2 E:HIS65 2.4 44.7 1.0
OD1 E:ASP315 2.4 41.9 1.0
O E:HOH487 2.5 32.9 1.0
CE1 E:HIS65 3.1 41.7 1.0
CE1 E:HIS63 3.1 41.4 1.0
CD2 E:HIS63 3.3 45.4 1.0
CG E:ASP315 3.5 45.4 1.0
CD2 E:HIS65 3.6 35.4 1.0
NE2 E:HIS242 4.1 51.4 1.0
OD2 E:ASP315 4.2 46.8 1.0
ND1 E:HIS63 4.2 41.7 1.0
ND1 E:HIS65 4.3 44.5 1.0
CG E:HIS63 4.4 41.7 1.0
CD2 E:HIS242 4.4 43.4 1.0
O E:HOH459 4.5 49.1 1.0
CG E:HIS65 4.6 39.4 1.0
CZ E:PHE152 4.6 49.0 1.0
CB E:ASP315 4.6 36.7 1.0
NZ E:LYS150 4.7 41.7 1.0
CG E:MET95 4.7 35.5 1.0

Zinc binding site 6 out of 6 in 3hm7

Go back to Zinc Binding Sites List in 3hm7
Zinc binding site 6 out of 6 in the Crystal Structure of Allantoinase From Bacillus Halodurans C-125


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 Allantoinase From Bacillus Halodurans C-125 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn447

b:39.6
occ:0.50
 NE2 F:HIS63 2.2 37.2 1.0
NE2 F:HIS65 2.4 49.0 1.0
OD1 F:ASP315 2.4 40.9 1.0
CE1 F:HIS65 3.1 37.4 1.0
CE1 F:HIS63 3.1 38.8 1.0
CD2 F:HIS63 3.3 44.6 1.0
CG F:ASP315 3.4 44.0 1.0
O F:HOH463 3.4 33.7 1.0
CD2 F:HIS65 3.6 33.6 1.0
OD2 F:ASP315 3.8 42.8 1.0
NE2 F:HIS242 4.0 50.7 1.0
ND1 F:HIS63 4.2 37.0 1.0
ND1 F:HIS65 4.3 40.4 1.0
CD2 F:HIS242 4.3 49.5 1.0
CG F:HIS63 4.4 37.0 1.0
CG F:HIS65 4.6 41.1 1.0
CB F:ASP315 4.6 41.7 1.0

Reference:

Y.Patskovsky, R.Romero, M.Rutter, S.Miller, F.M.Raushel, S.R.Wasserman, J.M.Sauder, S.K.Burley, S.C.Almo. Crystal Structure of Allantoinase From Bacillus Halodurans To Be Published.
Page generated: Sat Oct 26 06:24:22 2024

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