Zinc in PDB 4j3b: A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization

The structure of A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization, PDB code: 4j3b was solved by S.Dalal, D.R.T.Ragheb, F.D.Schubot, M.Klemba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.950, 109.460, 112.910, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 20.1

The structure of A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization (pdb code 4j3b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization, PDB code: 4j3b:

Zinc binding site 1 out of 1 in the A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Naturally Variable Residue in the S1 Subsite of M1-Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:12.6 occ:1.00 OE1 A:GLU519 2.0 9.4 1.0 NE2 A:HIS496 2.0 11.2 1.0 NE2 A:HIS500 2.1 10.0 1.0 O A:ARG1101 2.4 31.8 1.0 OXT A:ARG1101 2.6 35.5 1.0 C A:ARG1101 2.6 32.3 1.0 CD A:GLU519 2.7 11.7 1.0 OE2 A:GLU519 2.8 9.5 1.0 CD2 A:HIS496 3.0 9.5 1.0 CE1 A:HIS496 3.0 9.4 1.0 CD2 A:HIS500 3.0 9.6 1.0 CE1 A:HIS500 3.1 14.1 1.0 CA A:ARG1101 3.8 33.1 1.0 N A:ARG1101 3.9 30.5 1.0 ND1 A:HIS496 4.1 11.6 1.0 CG A:HIS496 4.1 12.1 1.0 CE2 A:TYR580 4.1 15.2 1.0 ND1 A:HIS500 4.2 12.4 1.0 CG A:HIS500 4.2 9.8 1.0 CG A:GLU519 4.2 10.2 1.0 OH A:TYR580 4.2 15.0 1.0 OE1 A:GLU463 4.4 13.6 1.0 CZ A:TYR580 4.6 12.9 1.0 CG2 A:THR522 4.6 7.6 1.0 CA A:GLU519 4.6 9.9 1.0 OE2 A:GLU497 4.7 16.7 1.0 OE1 A:GLU497 4.7 14.6 1.0 CB A:GLU519 4.8 8.5 1.0 CB A:THR522 4.8 9.5 1.0 CD A:GLU463 4.9 13.4 1.0 NZ A:LYS518 4.9 12.2 1.0 CB A:ARG1101 4.9 32.4 1.0 OE2 A:GLU463 4.9 12.3 1.0

S.Dalal, D.R.Ragheb, F.D.Schubot, M.Klemba. A Naturally Variable Residue in the S1 Subsite of M1 Family Aminopeptidases Modulates Catalytic Properties and Promotes Functional Specialization. J.Biol.Chem. V. 288 26004 2013.
ISSN: ISSN 0021-9258
PubMed: 23897806
DOI: 10.1074/JBC.M113.465625