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Zinc in PDB 2z2y: Crystal Structure of Autoprocessed Form of Tk-Subtilisin

Enzymatic activity of Crystal Structure of Autoprocessed Form of Tk-Subtilisin

All present enzymatic activity of Crystal Structure of Autoprocessed Form of Tk-Subtilisin:
3.4.21.62;

Protein crystallography data

The structure of Crystal Structure of Autoprocessed Form of Tk-Subtilisin, PDB code: 2z2y was solved by S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.88 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.908, 65.365, 70.385, 87.59, 67.44, 69.76
R / Rfree (%) 16.3 / 19.8

Other elements in 2z2y:

The structure of Crystal Structure of Autoprocessed Form of Tk-Subtilisin also contains other interesting chemical elements:

Calcium (Ca) 14 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin (pdb code 2z2y). 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 Autoprocessed Form of Tk-Subtilisin, PDB code: 2z2y:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 1 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:22.7
occ:1.00
 OXT B:LEU69 2.1 26.0 1.0
O B:HOH2027 2.1 24.1 1.0
NE2 A:HIS153 2.1 14.6 1.0
SG A:CYS324 2.2 18.3 1.0
O B:LEU69 2.8 26.3 1.0
C B:LEU69 2.8 26.8 1.0
CD2 A:HIS153 3.0 13.2 1.0
CB A:CYS324 3.1 15.4 1.0
CE1 A:HIS153 3.2 16.5 1.0
O A:HOH2254 3.6 36.6 1.0
CG A:HIS153 4.2 15.1 1.0
ND1 A:HIS153 4.3 16.6 1.0
CA B:LEU69 4.3 26.8 1.0
ND2 A:ASN264 4.4 14.8 1.0
CE A:MET325 4.5 16.7 1.0
O A:HOH2074 4.5 44.7 1.0
CA A:CYS324 4.5 14.8 1.0
CD2 B:LEU69 4.7 27.9 1.0
CG B:LEU68 4.8 26.5 1.0
N A:CYS324 4.9 14.0 1.0
SD A:MET325 4.9 21.9 1.0
CD1 B:LEU68 5.0 27.6 1.0
N B:LEU69 5.0 27.2 1.0

Zinc binding site 2 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 2 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2002

b:25.0
occ:1.00
 NE2 B:HIS64 2.1 24.1 1.0
OE1 B:GLU61 2.2 29.9 1.0
O B:HOH2037 2.4 23.3 1.0
CE1 B:HIS64 3.0 27.4 1.0
CD B:GLU61 3.0 31.7 1.0
CD2 B:HIS64 3.1 25.6 1.0
OE2 B:GLU61 3.2 30.9 1.0
O B:PHE62 4.1 29.0 1.0
N B:PHE62 4.1 30.3 1.0
ND1 B:HIS64 4.2 28.3 1.0
O B:HOH2010 4.2 26.7 1.0
CG B:HIS64 4.2 27.0 1.0
O B:HOH2028 4.2 30.9 1.0
CG B:GLU61 4.4 31.3 1.0
CA B:GLU61 4.6 31.2 1.0
CB B:GLU61 4.7 31.5 1.0
CB B:PHE62 4.8 31.3 1.0
CA B:PHE62 4.8 30.3 1.0
O A:HOH2121 4.8 41.9 1.0
C B:GLU61 4.8 31.0 1.0
C B:PHE62 4.8 29.6 1.0

Zinc binding site 3 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 3 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2006

b:53.9
occ:1.00
 NE2 B:HIS28 1.9 44.3 1.0
OD2 B:ASP42 2.2 37.0 1.0
CE1 B:HIS28 2.3 44.6 1.0
O A:HOH2257 2.8 47.8 1.0
CG B:ASP42 3.1 36.0 1.0
CD2 B:HIS28 3.2 43.5 1.0
CB B:ASP42 3.3 33.8 1.0
O B:HOH2042 3.4 57.3 1.0
ND1 B:HIS28 3.5 45.3 1.0
CG B:HIS28 4.0 42.2 1.0
NH2 B:ARG7 4.2 24.1 1.0
OD1 B:ASP42 4.2 36.3 1.0
CG2 B:VAL30 4.3 28.9 1.0
CA B:ASP42 4.8 33.8 1.0
O B:HOH2015 4.8 55.5 1.0

Zinc binding site 4 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 4 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2003

b:24.0
occ:1.00
 O D:HOH2034 2.0 19.2 1.0
NE2 C:HIS153 2.0 15.9 1.0
OXT D:LEU69 2.2 24.0 1.0
SG C:CYS324 2.2 19.2 1.0
O D:LEU69 2.7 24.9 1.0
C D:LEU69 2.8 25.4 1.0
CD2 C:HIS153 3.0 16.7 1.0
CE1 C:HIS153 3.0 15.6 1.0
CB C:CYS324 3.0 15.6 1.0
O C:HOH2195 3.7 39.5 1.0
ND1 C:HIS153 4.1 15.8 1.0
CG C:HIS153 4.2 15.9 1.0
CA D:LEU69 4.3 25.5 1.0
ND2 C:ASN264 4.4 16.6 1.0
CA C:CYS324 4.5 14.9 1.0
CE C:MET325 4.7 18.7 1.0
O C:HOH2064 4.7 44.2 1.0
CG D:LEU68 4.8 25.4 1.0
CD1 D:LEU69 4.9 28.0 1.0
CD1 D:LEU68 4.9 26.7 1.0
N C:CYS324 4.9 13.9 1.0
N D:LEU69 5.0 26.2 1.0
SD C:MET325 5.0 22.7 1.0

Zinc binding site 5 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 5 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2004

b:25.8
occ:1.00
 OE2 A:GLU318 2.0 26.3 1.0
NE2 D:HIS64 2.1 29.5 1.0
OE1 D:GLU61 2.1 33.4 1.0
O A:HOH2005 2.5 28.1 1.0
CD A:GLU318 2.8 21.4 1.0
CE1 D:HIS64 2.9 30.2 1.0
CD D:GLU61 3.0 34.1 1.0
OE1 A:GLU318 3.0 23.0 1.0
CD2 D:HIS64 3.2 29.9 1.0
OE2 D:GLU61 3.2 34.8 1.0
O D:PHE62 4.0 30.3 1.0
N D:PHE62 4.1 31.3 1.0
ND1 D:HIS64 4.1 29.6 1.0
O D:HOH2009 4.2 29.8 1.0
CG A:GLU318 4.2 18.0 1.0
CG D:HIS64 4.2 28.3 1.0
O A:HOH2205 4.3 35.7 1.0
CG D:GLU61 4.3 33.2 1.0
O C:HOH2077 4.5 29.1 1.0
N A:THR319 4.5 15.8 1.0
CA A:GLU318 4.5 15.8 1.0
CB D:PHE62 4.7 32.6 1.0
CA D:GLU61 4.7 32.6 1.0
CA D:PHE62 4.7 31.5 1.0
O C:HOH2020 4.7 34.9 1.0
CB D:GLU61 4.7 33.0 1.0
C D:PHE62 4.8 30.6 1.0
CB A:GLU318 4.8 15.2 1.0
O A:TYR317 4.8 19.2 1.0
C D:GLU61 4.8 32.2 1.0

Zinc binding site 6 out of 6 in 2z2y

Go back to Zinc Binding Sites List in 2z2y
Zinc binding site 6 out of 6 in the Crystal Structure of Autoprocessed Form of Tk-Subtilisin


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 Autoprocessed Form of Tk-Subtilisin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2005

b:51.2
occ:1.00
 OD2 D:ASP42 2.2 33.2 1.0
CE1 D:HIS28 2.3 42.7 1.0
O C:HOH2184 2.4 43.1 1.0
NE2 D:HIS28 2.6 43.9 1.0
CG D:ASP42 3.2 34.3 1.0
CB D:ASP42 3.5 33.9 1.0
ND1 D:HIS28 3.6 42.3 1.0
CD2 D:HIS28 3.9 42.4 1.0
O D:HOH2041 4.1 46.7 1.0
NH2 D:ARG7 4.2 25.1 1.0
OD1 D:ASP42 4.3 32.8 1.0
CG D:HIS28 4.4 40.4 1.0
CG2 D:VAL30 4.5 27.3 1.0
CA D:ASP42 4.9 34.8 1.0

Reference:

S.Tanaka, H.Matsumura, Y.Koga, K.Takano, S.Kanaya. Four New Crystal Structures of Tk-Subtilisin in Unautoprocessed, Autoprocessed and Mature Forms: Insight Into Structural Changes During Maturation J.Mol.Biol. V. 372 1055 2007.
ISSN: ISSN 0022-2836
PubMed: 17706669
DOI: 10.1016/J.JMB.2007.07.027
Page generated: Thu Oct 24 10:36:06 2024

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