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Zinc in PDB 6hc7: The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)

Protein crystallography data

The structure of The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution), PDB code: 6hc7 was solved by R.Alhadeff, S.Lansky, H.Feinberg, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.92 / 2.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 225.833, 225.833, 42.654, 90.00, 90.00, 120.00
R / Rfree (%) 17.8 / 25.1

Other elements in 6hc7:

The structure of The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution) also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution) (pdb code 6hc7). 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 Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution), PDB code: 6hc7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6hc7

Go back to Zinc Binding Sites List in 6hc7
Zinc binding site 1 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:41.2
occ:1.00
O A:HOH607 2.0 31.2 1.0
OD1 A:ASP262 2.1 30.3 1.0
OD2 A:ASP323 2.2 27.8 1.0
OD1 A:ASP323 2.3 27.3 1.0
NE2 A:HIS250 2.3 28.6 1.0
CG A:ASP323 2.5 30.0 1.0
CG A:ASP262 3.0 25.1 1.0
CD2 A:HIS250 3.2 25.9 1.0
CE1 A:HIS250 3.4 29.1 1.0
OD2 A:ASP262 3.5 21.7 1.0
ZN A:ZN502 3.5 43.8 1.0
CB A:ASN263 4.0 27.9 1.0
CB A:ASP323 4.1 29.9 1.0
OE2 A:GLU294 4.1 34.3 1.0
OE2 A:GLU452 4.1 37.7 1.0
CB A:ASP262 4.3 26.7 1.0
CG A:HIS250 4.4 32.8 1.0
ND1 A:HIS250 4.4 27.9 1.0
CD A:GLU294 4.5 31.1 1.0
CG A:MET324 4.5 28.8 1.0
OE1 A:GLU295 4.5 25.2 1.0
SD A:MET324 4.5 40.7 1.0
CG A:ASN263 4.6 30.3 1.0
CA A:ASP262 4.6 30.4 1.0
OE1 A:GLU294 4.6 32.1 1.0
ND2 A:ASN263 4.7 25.9 1.0
OE2 A:GLU295 4.9 31.2 1.0
CA A:ASP323 4.9 30.6 1.0
OE1 A:GLU452 4.9 33.8 1.0
CD A:GLU452 4.9 36.9 1.0
C A:ASP262 5.0 29.2 1.0
OG A:SER371 5.0 34.3 1.0

Zinc binding site 2 out of 6 in 6hc7

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Zinc binding site 2 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:43.8
occ:1.00
OD2 A:ASP262 2.0 21.7 1.0
NE2 A:HIS401 2.3 27.4 1.0
OE2 A:GLU295 2.3 31.2 1.0
OE1 A:GLU452 2.5 33.8 1.0
OE1 A:GLU295 2.6 25.2 1.0
O A:HOH607 2.6 31.2 1.0
CD A:GLU295 2.8 29.4 1.0
CG A:ASP262 3.0 25.1 1.0
OD1 A:ASP262 3.3 30.3 1.0
CD2 A:HIS401 3.3 28.5 1.0
CE1 A:HIS401 3.3 29.1 1.0
CD A:GLU452 3.3 36.9 1.0
OE2 A:GLU452 3.4 37.7 1.0
ZN A:ZN501 3.5 41.2 1.0
CE1 A:TYR400 3.9 34.7 1.0
O A:HOH617 4.2 29.9 1.0
CG A:GLU295 4.2 36.2 1.0
CB A:ASP262 4.3 26.7 1.0
ND1 A:HIS401 4.4 33.4 1.0
OE2 A:GLU294 4.4 34.3 1.0
OH A:TYR400 4.4 46.4 1.0
CG A:HIS401 4.5 34.8 1.0
CG1 A:VAL254 4.6 27.5 1.0
CZ A:TYR400 4.6 38.5 1.0
NE2 A:HIS250 4.6 28.6 1.0
CE1 A:HIS250 4.7 29.1 1.0
CD1 A:TYR400 4.7 37.7 1.0
CG A:GLU452 4.8 39.4 1.0

Zinc binding site 3 out of 6 in 6hc7

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Zinc binding site 3 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:32.8
occ:1.00
O B:HOH606 2.1 22.4 1.0
NE2 B:HIS250 2.1 23.8 1.0
OD1 B:ASP262 2.2 21.2 1.0
OD2 B:ASP323 2.3 24.4 1.0
OD1 B:ASP323 2.3 26.5 1.0
O B:HOH740 2.6 31.0 1.0
CG B:ASP323 2.6 26.4 1.0
CE1 B:HIS250 3.1 19.2 1.0
CD2 B:HIS250 3.2 19.8 1.0
CG B:ASP262 3.2 19.4 1.0
ZN B:ZN502 3.6 34.6 1.0
OD2 B:ASP262 3.6 22.3 1.0
OE2 B:GLU294 3.8 28.2 1.0
CB B:ASN263 4.1 20.1 1.0
CB B:ASP323 4.1 24.3 1.0
ND1 B:HIS250 4.2 19.2 1.0
OE2 B:GLU452 4.3 36.2 1.0
CG B:HIS250 4.3 19.5 1.0
CD B:GLU294 4.3 22.8 1.0
O B:HOH654 4.3 36.9 1.0
CG B:MET324 4.4 24.7 1.0
OE1 B:GLU295 4.4 22.8 1.0
CB B:ASP262 4.5 18.9 1.0
OE1 B:GLU452 4.5 35.5 1.0
OE1 B:GLU294 4.5 19.1 1.0
CG B:ASN263 4.5 20.7 1.0
SD B:MET324 4.6 25.1 1.0
CA B:ASP262 4.7 21.5 1.0
OG B:SER371 4.8 21.2 1.0
CD B:GLU452 4.8 34.9 1.0
ND2 B:ASN263 4.8 22.0 1.0
CA B:ASP323 4.9 22.2 1.0
C B:ASP262 5.0 21.5 1.0

Zinc binding site 4 out of 6 in 6hc7

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Zinc binding site 4 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:34.6
occ:1.00
OE1 B:GLU452 2.2 35.5 1.0
NE2 B:HIS401 2.2 20.0 1.0
OD2 B:ASP262 2.3 22.3 1.0
OE1 B:GLU295 2.5 22.8 1.0
O B:HOH606 2.6 22.4 1.0
OE2 B:GLU295 2.6 26.1 1.0
CD B:GLU295 2.8 28.2 1.0
CD B:GLU452 3.1 34.9 1.0
CG B:ASP262 3.2 19.4 1.0
CE1 B:HIS401 3.2 22.3 1.0
CD2 B:HIS401 3.3 22.2 1.0
OD1 B:ASP262 3.4 21.2 1.0
OE2 B:GLU452 3.5 36.2 1.0
ZN B:ZN501 3.6 32.8 1.0
O B:HOH740 3.6 31.0 1.0
CE1 B:TYR400 3.8 23.7 1.0
OH B:TYR400 4.0 26.6 1.0
O B:HOH646 4.0 20.9 1.0
CG B:GLU452 4.2 39.5 1.0
CZ B:TYR400 4.3 27.6 1.0
ND1 B:HIS401 4.3 24.0 1.0
OE2 B:GLU294 4.3 28.2 1.0
CG B:GLU295 4.3 26.0 1.0
CG B:HIS401 4.4 25.9 1.0
CB B:ASP262 4.5 18.9 1.0
O B:HOH618 4.6 28.8 1.0
CG1 B:VAL254 4.6 22.2 1.0
CE1 B:HIS250 4.6 19.2 1.0
NE2 B:HIS250 4.7 23.8 1.0
CD1 B:TYR400 4.8 26.4 1.0

Zinc binding site 5 out of 6 in 6hc7

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Zinc binding site 5 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:37.3
occ:1.00
OD1 C:ASP262 2.0 22.2 1.0
O C:HOH609 2.2 29.7 1.0
OD1 C:ASP323 2.3 23.3 1.0
NE2 C:HIS250 2.3 25.7 1.0
OD2 C:ASP323 2.4 27.0 1.0
CG C:ASP323 2.6 23.7 1.0
CG C:ASP262 3.0 24.2 1.0
CE1 C:HIS250 3.1 27.5 1.0
CD2 C:HIS250 3.4 25.7 1.0
OD2 C:ASP262 3.5 32.9 1.0
ZN C:ZN502 3.7 45.5 1.0
OE2 C:GLU294 4.0 35.8 1.0
CB C:ASN263 4.0 21.1 1.0
CB C:ASP323 4.1 23.2 1.0
OE2 C:GLU452 4.2 38.0 1.0
OE2 C:GLU295 4.2 32.4 1.0
CB C:ASP262 4.3 29.1 1.0
ND1 C:HIS250 4.3 26.6 1.0
CD C:GLU294 4.4 34.6 1.0
CG C:MET324 4.4 26.4 1.0
CG C:HIS250 4.5 26.2 1.0
OE1 C:GLU294 4.5 33.2 1.0
CG C:ASN263 4.6 27.4 1.0
OE1 C:GLU452 4.6 36.6 1.0
CA C:ASP262 4.7 29.1 1.0
OG C:SER371 4.7 32.0 1.0
SD C:MET324 4.8 32.5 1.0
CD C:GLU452 4.9 39.1 1.0
CA C:ASP323 4.9 24.5 1.0
C C:ASP262 4.9 28.4 1.0
CD C:GLU295 5.0 34.2 1.0
ND2 C:ASN263 5.0 25.8 1.0

Zinc binding site 6 out of 6 in 6hc7

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Zinc binding site 6 out of 6 in the The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution)


Mono view


Stereo pair view

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

b:45.5
occ:1.00
NE2 C:HIS401 2.1 29.5 1.0
OD2 C:ASP262 2.2 32.9 1.0
O C:HOH609 2.2 29.7 1.0
OE1 C:GLU452 2.3 36.6 1.0
OE2 C:GLU295 2.4 32.4 1.0
OE1 C:GLU295 2.7 36.9 1.0
CD C:GLU295 2.9 34.2 1.0
CE1 C:HIS401 3.0 27.1 1.0
CD2 C:HIS401 3.2 29.1 1.0
CG C:ASP262 3.2 24.2 1.0
CD C:GLU452 3.2 39.1 1.0
OE2 C:GLU452 3.5 38.0 1.0
OD1 C:ASP262 3.6 22.2 1.0
ZN C:ZN501 3.7 37.3 1.0
CE1 C:TYR400 3.7 32.9 1.0
OH C:TYR400 3.9 40.6 1.0
CZ C:TYR400 4.1 35.3 1.0
ND1 C:HIS401 4.2 32.8 1.0
CG C:HIS401 4.3 34.5 1.0
O C:HOH619 4.3 26.3 1.0
OE2 C:GLU294 4.4 35.8 1.0
CG C:GLU295 4.5 31.6 1.0
CB C:ASP262 4.5 29.1 1.0
CG C:GLU452 4.6 43.5 1.0
CD1 C:TYR400 4.6 32.8 1.0
CG1 C:VAL254 4.7 29.0 1.0
CE1 C:HIS250 4.9 27.5 1.0
CB C:GLU452 4.9 43.5 1.0

Reference:

R.Alhadeff, R.Faygenboim, S.Lansky, E.Rogoulenko, T.Cohen, Y.Fundoiano-Hershcovitz, H.Feinberg, Y.Shoham, G.Shoham. The Crystal Structure of Bsap, A Zinc Aminopeptidase From Bacillus Subtilis (Medium Resolution) To Be Published.
Page generated: Wed Dec 16 11:56:26 2020

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