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Zinc in PDB 5nj9: E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound

Protein crystallography data

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound, PDB code: 5nj9 was solved by D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.Volkov, A.Maxwell, D.M.Lawson, K.Severinov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.77 / 1.25
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.630, 173.530, 82.860, 90.00, 90.03, 90.00
R / Rfree (%) 14.9 / 18.2

Other elements in 5nj9:

The structure of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound (pdb code 5nj9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound, PDB code: 5nj9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5nj9

Go back to Zinc Binding Sites List in 5nj9
Zinc binding site 1 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:7.1
occ:1.00
NE2 A:HIS267 2.0 7.2 1.0
NE2 A:HIS262 2.1 8.2 1.0
OXT E:TYR604 2.1 3.2 0.7
SG A:CYS454 2.3 8.2 1.0
C E:TYR604 2.7 5.8 0.7
O E:TYR604 2.7 6.0 0.7
CE1 A:HIS267 2.9 7.3 1.0
CE1 A:HIS262 3.0 7.8 1.0
CD2 A:HIS262 3.1 7.7 1.0
CD2 A:HIS267 3.1 6.5 1.0
CB A:CYS454 3.3 7.6 1.0
CA A:CYS454 3.7 6.2 1.0
N A:GLY455 3.9 6.9 1.0
ND1 A:HIS267 4.0 7.2 1.0
CA E:TYR604 4.1 6.4 0.7
ND1 A:HIS262 4.1 8.7 1.0
CG A:HIS267 4.2 7.3 1.0
CE A:MET363 4.2 7.1 1.0
CG A:HIS262 4.2 7.5 1.0
O A:GLY455 4.2 8.9 1.0
C A:CYS454 4.2 6.7 1.0
N E:TYR604 4.4 6.5 0.7
O A:HOH608 4.7 7.3 1.0
C A:GLY455 4.8 7.9 1.0
CB E:TYR604 4.9 8.2 0.7
CA A:GLY455 5.0 6.3 1.0

Zinc binding site 2 out of 2 in 5nj9

Go back to Zinc Binding Sites List in 5nj9
Zinc binding site 2 out of 2 in the E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Microcin-Processing Metalloprotease Tldd/E with Drvy Angiotensin Fragment Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:9.1
occ:1.00
OXT F:TYR604 2.0 3.9 0.7
NE2 C:HIS267 2.1 7.8 1.0
NE2 C:HIS262 2.1 8.7 1.0
SG C:CYS454 2.3 7.8 1.0
C F:TYR604 2.7 8.0 0.7
O F:TYR604 2.7 7.5 0.7
CE1 C:HIS267 2.9 6.8 1.0
CE1 C:HIS262 3.0 7.7 1.0
CD2 C:HIS262 3.1 7.1 1.0
CD2 C:HIS267 3.1 8.5 1.0
CB C:CYS454 3.3 7.9 1.0
CA C:CYS454 3.7 7.4 1.0
N C:GLY455 3.9 9.0 1.0
CA F:TYR604 4.1 7.3 0.7
ND1 C:HIS267 4.1 8.8 1.0
ND1 C:HIS262 4.2 7.5 1.0
CG C:HIS267 4.2 9.9 1.0
O C:GLY455 4.2 10.9 1.0
C C:CYS454 4.2 9.2 1.0
CG C:HIS262 4.2 6.7 1.0
CE C:MET363 4.2 8.3 1.0
N F:TYR604 4.4 7.8 0.7
O C:HOH641 4.7 8.1 1.0
C C:GLY455 4.8 9.1 1.0
CB F:TYR604 4.8 8.6 0.7
CA C:GLY455 5.0 8.6 1.0
N C:CYS454 5.0 7.5 1.0

Reference:

D.Ghilarov, M.Serebryakova, C.E.M.Stevenson, S.J.Hearnshaw, D.S.Volkov, A.Maxwell, D.M.Lawson, K.Severinov. The Origins of Specificity in the Microcin-Processing Protease Tldd/E. Structure V. 25 1549 2017.
ISSN: ISSN 1878-4186
PubMed: 28943336
DOI: 10.1016/J.STR.2017.08.006
Page generated: Wed Dec 16 06:36:06 2020

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