aTYR PHARMA INC 10-Q

Item 5. Other Information None. 59 Index to Exhibits Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 3.1 Restated Certificate of Incorporation of the Registrant S-1/A 333-203272 3.2 May 1, 2015 3.2 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 8-K 001-37378 3.1 June 28, 2019 3.3 Certificate of Amendment to Restated Certificate of Incorporation of the Registrant 10-Q 001-37378 3.3 May 12, 2020 3.4 Amended and Restated Bylaws of the Registrant S-1/A 333-203272 3.4 April 27, 2015 3.5 Certificate of Designation of Preferences, Rights and Limitations of Class X Convertible Preferred Stock 8-K 001-37378 3.1 August 31, 2017 4.1 Specimen Common Stock Certificate S-1/A 333-203272 4.1 April 27, 2015 4.2 Warrant to Purchase Stock issued to Comerica Bank on March 18, 2011 S-1 333-203272 4.3 April 6, 2015 4.3 Warrant to Purchase Stock issued to Silicon Valley Bank on July 24, 2013 S-1 333-203272 4.4 April 6, 2015 4.4 Warrant to Purchase Stock issued to Silicon Valley Bank on November 18, 2016 10-K 001-37378 4.5 March 16, 2017 4.5 Warrant to Purchase Stock issued to Solar Capital Ltd on November 18, 2016 10-K 001-37378 4.6 March 16, 2017 4.6 Warrant to Purchase Stock issued to Silicon Valley Bank on June 30, 2017 10-Q 001-37378 4.7 August 14, 2017 4.7 Warrant to Purchase Stock issued to Solar Capital Ltd on June 30, 2017 10-Q 001-37378 4.8 August 14, 2017 4.8 Warrant to Purchase Stock issued to Silicon Valley Bank on December 22, 2017 10-K 001-37378 4.8 March 20, 2018 4.9 Warrant to Purchase Stock issued to Solar Capital Ltd on December 22, 2017 10-K 001-37378 4.9 March 20, 2018 4.10 Registration Right Agreement dated September 11, 2020 by and between aTyr Pharma, Inc. and Aspire Capital Fund, LLC. 8-K 001-37378 4.1 September 14, 2020 5.1 Opinion of Cooley LLP — — — Filed herewith 10.1 Amendment No. 2 to Common Stock Sales Agreement, dated November 13, 2020, between the Registrant and H.C. Wainwright & Co., LLC — — — Filed herewith 31.1 Certification of Principal Executive Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 31.2 Certification of Principal Financial Officer required by Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 60 Incorporated by Reference Exhibit Number Exhibit Title Form File No. Exhibit Filing Date 32.1# Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes- Oxley Act of 2002 — — — Filed herewith 32.2# Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 — — — Filed herewith 101.INS XBRL Instance Document — — — Filed herewith 101.SCH XBRL Taxonomy Extension Schema Document — — — Filed herewith 101.CAL XBRL Taxonomy Extension Calculation Linkbase Document — — — Filed herewith 101.DEF XBRL Taxonomy Extension Definition Linkbase Document — — — Filed herewith 101.LAB XBRL Taxonomy Extension Label Linkbase Document — — — Filed herewith 101.PRE XBRL Taxonomy Extension Presentation Linkbase Document — — — Filed herewith # The information in Exhibits 32.1 and 32.2 shall not be deemed “filed” for purposes of Section 18 of the Exchange Act, or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act or the Exchange Act (including this Quarterly Report on Form 10-Q), unless the Registrant specifically incorporates the foregoing information into those documents by reference. 61 SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. aTyr Pharma, Inc. Date: November 13, 2020 By: /s/ Sanjay S. Shukla Sanjay S. Shukla, M.D., M.S. President and Chief Executive Officer (Principal Executive Officer) By: /s/ Jill M. Broadfoot Jill M. Broadfoot Chief Financial Officer (Principal Financial and Accounting Officer) 62