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Zinc in PDB 6hc6: The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis

Enzymatic activity of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis

All present enzymatic activity of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis:
3.4.11.10; 3.4.11.6;

Protein crystallography data

The structure of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis, PDB code: 6hc6 was solved by E.Rogoulenko, S.Lansky, R.Faygenboim, T.Cohen, R.Alhadeff, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.77
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 224.922, 224.922, 42.502, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 20.3

Zinc Binding Sites:

The binding sites of Zinc atom in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (pdb code 6hc6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis, PDB code: 6hc6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6hc6

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Zinc binding site 1 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:19.4
occ:1.00
 O A:HOH767 2.0 22.3 1.0
OD1 A:ASP262 2.0 15.7 1.0
O A:HOH611 2.1 18.7 1.0
OD1 A:ASP323 2.1 16.7 1.0
NE2 A:HIS250 2.2 11.6 1.0
OD2 A:ASP323 2.2 18.9 1.0
CG A:ASP323 2.5 17.7 1.0
CG A:ASP262 3.1 19.0 1.0
CD2 A:HIS250 3.1 15.7 1.0
CE1 A:HIS250 3.2 14.8 1.0
OD2 A:ASP262 3.6 15.0 1.0
ZN A:ZN502 3.8 21.5 1.0
CB A:ASP323 4.0 19.4 1.0
OE2 A:GLU294 4.0 17.1 1.0
OE2 A:GLU452 4.1 23.5 1.0
CB A:ASN263 4.1 13.3 1.0
OE2 A:GLU295 4.2 15.1 1.0
ND1 A:HIS250 4.3 14.0 1.0
CG A:HIS250 4.3 11.9 1.0
CB A:ASP262 4.3 20.0 1.0
O A:HOH739 4.4 33.3 1.0
CD A:GLU294 4.4 23.9 1.0
SD A:MET324 4.6 22.1 1.0
CG A:ASN263 4.6 15.0 1.0
CA A:ASP262 4.6 17.8 1.0
OE1 A:GLU294 4.6 21.4 1.0
CG A:MET324 4.6 19.5 1.0
OE1 A:GLU452 4.7 22.3 1.0
OG A:SER371 4.8 19.2 1.0
CA A:ASP323 4.8 16.2 1.0
CD A:GLU452 4.8 23.6 1.0
CD A:GLU295 4.9 17.2 1.0
ND2 A:ASN263 4.9 15.1 1.0
C A:ASP262 4.9 17.0 1.0

Zinc binding site 2 out of 6 in 6hc6

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Zinc binding site 2 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:21.5
occ:1.00
 OD2 A:ASP262 2.0 15.0 1.0
NE2 A:HIS401 2.1 15.2 1.0
OE2 A:GLU295 2.2 15.1 1.0
OE1 A:GLU452 2.3 22.3 1.0
O A:HOH611 2.3 18.7 1.0
OE1 A:GLU295 2.3 15.8 1.0
CD A:GLU295 2.6 17.2 1.0
CE1 A:HIS401 3.0 19.9 1.0
CG A:ASP262 3.1 19.0 1.0
CD2 A:HIS401 3.2 15.6 1.0
CD A:GLU452 3.2 23.6 1.0
OD1 A:ASP262 3.4 15.7 1.0
OE2 A:GLU452 3.4 23.5 1.0
O A:HOH767 3.7 22.3 1.0
ZN A:ZN501 3.8 19.4 1.0
CE1 A:TYR400 3.9 26.9 1.0
O A:HOH686 4.0 15.4 1.0
OH A:TYR400 4.1 28.6 1.0
CG A:GLU295 4.1 13.4 1.0
ND1 A:HIS401 4.2 17.9 1.0
CG A:HIS401 4.3 15.0 1.0
OE2 A:GLU294 4.3 17.1 1.0
CZ A:TYR400 4.3 30.1 1.0
CG1 A:VAL254 4.4 17.1 1.0
CB A:ASP262 4.4 20.0 1.0
O A:HOH710 4.5 23.1 1.0
CG A:GLU452 4.6 22.5 1.0
CE1 A:HIS250 4.7 14.8 1.0
NE2 A:HIS250 4.7 11.6 1.0
CD1 A:TYR400 4.8 22.9 1.0
CB A:GLU452 5.0 26.7 1.0

Zinc binding site 3 out of 6 in 6hc6

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Zinc binding site 3 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:18.4
occ:1.00
 OD1 B:ASP262 2.0 14.9 1.0
O B:HOH864 2.1 18.9 1.0
OD1 B:ASP323 2.2 13.3 1.0
O B:HOH612 2.2 14.8 1.0
NE2 B:HIS250 2.2 13.1 1.0
OD2 B:ASP323 2.2 17.2 1.0
CG B:ASP323 2.5 15.3 1.0
CG B:ASP262 3.1 17.7 1.0
CE1 B:HIS250 3.2 17.3 1.0
CD2 B:HIS250 3.2 12.1 1.0
OD2 B:ASP262 3.5 15.4 1.0
ZN B:ZN502 3.8 20.0 1.0
CB B:ASP323 4.0 17.4 1.0
OE2 B:GLU452 4.0 20.9 1.0
OE2 B:GLU294 4.1 15.3 1.0
CB B:ASN263 4.1 13.4 1.0
ND1 B:HIS250 4.3 13.3 1.0
CB B:ASP262 4.3 16.2 1.0
OE1 B:GLU295 4.3 14.3 1.0
CG B:HIS250 4.3 9.7 1.0
O B:HOH776 4.4 25.4 1.0
CD B:GLU294 4.5 17.7 1.0
CG B:MET324 4.5 12.6 1.0
SD B:MET324 4.5 17.2 1.0
OE1 B:GLU452 4.6 20.2 1.0
CA B:ASP262 4.6 14.8 1.0
OE1 B:GLU294 4.6 19.0 1.0
CG B:ASN263 4.6 15.0 1.0
CD B:GLU452 4.7 22.1 1.0
OG B:SER371 4.8 16.0 1.0
CA B:ASP323 4.8 16.1 1.0
C B:ASP262 4.9 15.6 1.0
CD B:GLU295 5.0 15.1 1.0
ND2 B:ASN263 5.0 14.7 1.0

Zinc binding site 4 out of 6 in 6hc6

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Zinc binding site 4 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:20.0
occ:1.00
 OD2 B:ASP262 2.1 15.4 1.0
NE2 B:HIS401 2.1 13.5 1.0
OE1 B:GLU295 2.2 14.3 1.0
OE1 B:GLU452 2.3 20.2 1.0
O B:HOH612 2.3 14.8 1.0
OE2 B:GLU295 2.4 15.2 1.0
CD B:GLU295 2.6 15.1 1.0
CE1 B:HIS401 3.0 13.2 1.0
CG B:ASP262 3.1 17.7 1.0
CD B:GLU452 3.2 22.1 1.0
CD2 B:HIS401 3.2 15.3 1.0
OD1 B:ASP262 3.4 14.9 1.0
OE2 B:GLU452 3.5 20.9 1.0
O B:HOH864 3.7 18.9 1.0
ZN B:ZN501 3.8 18.4 1.0
CE1 B:TYR400 3.8 13.8 1.0
OH B:TYR400 4.0 19.9 1.0
O B:HOH659 4.0 14.6 1.0
CG B:GLU295 4.1 13.2 1.0
ND1 B:HIS401 4.2 16.6 1.0
CZ B:TYR400 4.3 19.0 1.0
CG B:HIS401 4.3 12.6 1.0
OE2 B:GLU294 4.3 15.3 1.0
CG1 B:VAL254 4.4 15.5 1.0
CB B:ASP262 4.4 16.2 1.0
O B:HOH689 4.5 20.1 1.0
CG B:GLU452 4.5 21.5 1.0
CE1 B:HIS250 4.7 17.3 1.0
NE2 B:HIS250 4.7 13.1 1.0
CB B:GLU452 4.8 22.8 1.0
CD1 B:TYR400 4.8 19.0 1.0

Zinc binding site 5 out of 6 in 6hc6

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Zinc binding site 5 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:19.2
occ:1.00
 O C:HOH649 2.0 18.7 1.0
OD1 C:ASP262 2.1 16.0 1.0
OD2 C:ASP323 2.2 14.9 1.0
NE2 C:HIS250 2.2 15.2 1.0
O C:HOH851 2.2 18.2 1.0
OD1 C:ASP323 2.3 17.9 1.0
CG C:ASP323 2.5 18.5 1.0
CG C:ASP262 3.1 14.4 1.0
CE1 C:HIS250 3.1 16.9 1.0
CD2 C:HIS250 3.2 14.1 1.0
OD2 C:ASP262 3.5 17.2 1.0
ZN C:ZN502 3.8 21.5 1.0
OE2 C:GLU294 4.0 18.5 1.0
CB C:ASP323 4.1 16.8 1.0
CB C:ASN263 4.2 14.0 1.0
OE2 C:GLU452 4.2 23.7 1.0
ND1 C:HIS250 4.2 13.7 1.0
OE1 C:GLU295 4.3 16.9 1.0
CG C:HIS250 4.3 13.6 1.0
O C:HOH696 4.3 30.3 1.0
CB C:ASP262 4.3 14.9 1.0
O C:HOH818 4.3 46.2 1.0
CD C:GLU294 4.4 20.1 1.0
CG C:MET324 4.5 16.4 1.0
OE1 C:GLU294 4.6 20.1 1.0
SD C:MET324 4.6 20.3 1.0
CG C:ASN263 4.6 19.2 1.0
CA C:ASP262 4.6 13.5 1.0
OE1 C:GLU452 4.7 18.1 1.0
OG C:SER371 4.8 16.9 1.0
CD C:GLU452 4.8 23.9 1.0
CA C:ASP323 4.8 16.7 1.0
ND2 C:ASN263 4.9 11.9 1.0
C C:ASP262 4.9 16.9 1.0
CD C:GLU295 4.9 18.7 1.0

Zinc binding site 6 out of 6 in 6hc6

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Zinc binding site 6 out of 6 in the The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:21.5
occ:1.00
 NE2 C:HIS401 2.1 17.1 1.0
OD2 C:ASP262 2.1 17.2 1.0
OE1 C:GLU295 2.2 16.9 1.0
OE1 C:GLU452 2.2 18.1 1.0
O C:HOH649 2.3 18.7 1.0
OE2 C:GLU295 2.4 16.4 1.0
CD C:GLU295 2.6 18.7 1.0
CE1 C:HIS401 3.0 18.0 1.0
CG C:ASP262 3.1 14.4 1.0
CD C:GLU452 3.2 23.9 1.0
CD2 C:HIS401 3.2 17.0 1.0
OD1 C:ASP262 3.3 16.0 1.0
OE2 C:GLU452 3.5 23.7 1.0
ZN C:ZN501 3.8 19.2 1.0
O C:HOH851 3.8 18.2 1.0
CE1 C:TYR400 3.8 22.3 1.0
O C:HOH737 4.1 17.6 1.0
OH C:TYR400 4.1 25.6 1.0
ND1 C:HIS401 4.1 21.2 1.0
CG C:GLU295 4.1 15.8 1.0
CG C:HIS401 4.3 17.6 1.0
OE2 C:GLU294 4.3 18.5 1.0
CZ C:TYR400 4.3 26.4 1.0
CB C:ASP262 4.4 14.9 1.0
CG1 C:VAL254 4.5 17.6 1.0
O C:HOH709 4.5 22.1 1.0
CG C:GLU452 4.5 23.1 1.0
CE1 C:HIS250 4.6 16.9 1.0
NE2 C:HIS250 4.7 15.2 1.0
CD1 C:TYR400 4.7 22.3 1.0
CB C:GLU452 4.8 21.8 1.0

Reference:

R.Alhadeff, R.Faygenboim, S.Lansky, E.Rogoulenko, T.Cohen, Y.Fundoiano-Hershcovitz, H.Feinberg, Y.Shoham, G.Shoham. To Be Published To Be Published.
Page generated: Mon Oct 28 22:45:50 2024

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