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Zinc in PDB 3cne: Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron

Protein crystallography data

The structure of Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron, PDB code: 3cne was solved by R.Zhang, L.Volkart, J.Abdullah, A.Joachimiak, Midwest Center Forstructural Genomics (Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.35 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 73.607, 68.021, 75.389, 90.00, 109.81, 90.00
R / Rfree (%) 18.6 / 23.4

Other elements in 3cne:

The structure of Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron (pdb code 3cne). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron, PDB code: 3cne:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3cne

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Zinc binding site 1 out of 4 in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron


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 the Putative Protease I From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:65.0
occ:1.00
SG A:CYS74 2.3 27.2 1.0
SG A:CYS111 2.7 35.5 1.0
O A:HOH397 3.1 33.9 1.0
CB A:CYS111 3.2 30.2 1.0
CB A:CYS74 3.4 22.7 1.0
O A:HOH307 3.6 26.2 1.0
N A:ALA112 3.6 29.8 1.0
O A:GLY75 4.0 19.6 1.0
N A:GLY75 4.0 21.4 1.0
CB A:ALA112 4.2 29.0 1.0
CA A:CYS111 4.4 30.5 1.0
C A:CYS111 4.4 30.2 1.0
C A:CYS74 4.4 22.4 1.0
CA A:CYS74 4.5 23.2 1.0
CA A:ALA112 4.5 29.0 1.0
C A:GLY75 4.5 20.1 1.0
O A:HOH323 4.6 51.9 1.0
CA A:GLY75 4.6 20.4 1.0
OE1 A:GLU160 4.8 38.3 1.0
CB A:VAL78 4.9 22.6 1.0
O A:HOH396 5.0 21.0 1.0

Zinc binding site 2 out of 4 in 3cne

Go back to Zinc Binding Sites List in 3cne
Zinc binding site 2 out of 4 in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron


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 the Putative Protease I From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:71.4
occ:1.00
SG B:CYS74 2.3 29.1 1.0
O A:HOH386 2.3 30.9 1.0
SG B:CYS111 2.6 40.4 1.0
CB B:CYS111 3.1 36.2 1.0
CB B:CYS74 3.3 25.4 1.0
O B:HOH465 3.6 35.5 1.0
N B:ALA112 3.8 36.7 1.0
N B:GLY75 3.9 22.7 1.0
O B:GLY75 4.0 21.4 1.0
CB B:ALA112 4.3 36.8 1.0
CA B:CYS111 4.3 36.4 1.0
C B:CYS74 4.4 23.9 1.0
CA B:CYS74 4.4 24.5 1.0
C B:GLY75 4.4 20.9 1.0
CA B:GLY75 4.4 21.5 1.0
C B:CYS111 4.5 36.7 1.0
CA B:ALA112 4.7 36.8 1.0
OE2 B:GLU160 4.7 38.0 1.0
O B:HOH406 4.9 27.0 1.0
CB B:VAL78 5.0 22.0 1.0

Zinc binding site 3 out of 4 in 3cne

Go back to Zinc Binding Sites List in 3cne
Zinc binding site 3 out of 4 in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron


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 the Putative Protease I From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:66.2
occ:1.00
SG C:CYS74 2.5 24.8 1.0
SG C:CYS111 2.5 34.5 1.0
O C:HOH327 3.0 32.6 1.0
CB C:CYS111 3.1 28.1 1.0
O C:HOH399 3.3 52.9 1.0
CB C:CYS74 3.3 22.8 1.0
N C:GLY75 3.8 21.1 1.0
O C:GLY75 4.0 20.8 1.0
N C:ALA112 4.1 28.8 1.0
C C:CYS74 4.3 21.6 1.0
CA C:CYS74 4.4 22.1 1.0
CA C:GLY75 4.4 20.7 1.0
CA C:CYS111 4.4 29.2 1.0
C C:GLY75 4.4 21.2 1.0
O C:HOH398 4.5 23.6 1.0
CB C:ALA112 4.6 29.0 1.0
C C:CYS111 4.7 28.9 1.0
OE2 C:GLU160 4.8 38.8 1.0
CA C:ALA112 5.0 28.1 1.0

Zinc binding site 4 out of 4 in 3cne

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Zinc binding site 4 out of 4 in the Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron


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 the Putative Protease I From Bacteroides Thetaiotaomicron within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:57.1
occ:1.00
SG D:CYS74 2.3 25.1 1.0
SG D:CYS111 2.5 35.8 1.0
CB D:CYS111 3.0 29.2 1.0
CB D:CYS74 3.2 22.4 1.0
O D:HOH367 3.4 33.7 1.0
N D:GLY75 3.8 22.8 1.0
O D:HOH366 4.0 35.1 1.0
N D:ALA112 4.0 29.2 1.0
O D:GLY75 4.1 21.2 1.0
C D:CYS74 4.2 22.4 1.0
CA D:CYS74 4.3 22.4 1.0
CA D:CYS111 4.4 30.1 1.0
CA D:GLY75 4.5 22.1 1.0
C D:GLY75 4.5 21.9 1.0
CB D:ALA112 4.6 29.4 1.0
C D:CYS111 4.6 29.5 1.0
CA D:ALA112 4.9 28.2 1.0
CB D:VAL78 4.9 23.4 1.0

Reference:

R.Zhang, L.Volkart, J.Abdullah, A.Joachimiak. The Crystal Structure of the Putative Protease I From Bacteroides Thetaiotaomicron. To Be Published.
Page generated: Wed Dec 16 04:11:02 2020

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