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Zinc in PDB 3mf1: Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate

Protein crystallography data

The structure of Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate, PDB code: 3mf1 was solved by I.Weygand-Durasevic, M.Mocibob, N.Ivic, S.Bilokapic, T.Maier, M.Luic, N.Ban, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.41 / 2.20
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 128.092, 101.304, 50.479, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 22.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate (pdb code 3mf1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate, PDB code: 3mf1:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3mf1

Go back to Zinc Binding Sites List in 3mf1
Zinc binding site 1 out of 2 in the Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate


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 Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1000

b:22.3
occ:1.00
OE1 A:GLU176 2.0 15.5 1.0
N A:G5A1001 2.1 13.5 1.0
SG A:CYS131 2.3 19.6 1.0
SG A:CYS279 2.4 21.3 1.0
CD A:GLU176 2.9 26.9 1.0
OE2 A:GLU176 3.1 16.0 1.0
CA A:G5A1001 3.1 13.5 1.0
CB A:CYS131 3.2 16.2 1.0
CB A:CYS279 3.2 17.3 1.0
O A:HOH458 4.2 51.5 1.0
CG A:GLU176 4.3 20.1 1.0
OH A:TYR135 4.3 20.6 1.0
N A:CYS131 4.4 16.0 1.0
CA A:CYS131 4.4 16.3 1.0
C A:G5A1001 4.4 17.3 1.0
NE2 A:HIS257 4.5 26.2 1.0
O A:HOH459 4.6 33.6 1.0
CA A:CYS279 4.7 17.6 1.0
CB A:GLU176 4.7 13.8 1.0
CE1 A:HIS257 4.7 26.1 1.0
O A:G5A1001 4.8 19.5 1.0
ND2 A:ASN255 4.8 14.4 1.0

Zinc binding site 2 out of 2 in 3mf1

Go back to Zinc Binding Sites List in 3mf1
Zinc binding site 2 out of 2 in the Crystal Structure of Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate


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 Class II Aars Homologue (BLL0957) Complexed with An Analogue of Glycyl Adenylate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1000

b:23.9
occ:1.00
N B:G5A1001 2.0 16.7 1.0
OE1 B:GLU176 2.0 20.4 1.0
SG B:CYS279 2.4 19.7 1.0
SG B:CYS131 2.4 17.4 1.0
CD B:GLU176 2.9 17.6 1.0
CA B:G5A1001 3.0 18.7 1.0
OE2 B:GLU176 3.1 14.7 1.0
CB B:CYS131 3.3 13.4 1.0
CB B:CYS279 3.3 15.7 1.0
O B:HOH455 4.0 30.4 1.0
C B:G5A1001 4.3 21.5 1.0
CG B:GLU176 4.3 14.1 1.0
OH B:TYR135 4.4 19.4 1.0
N B:CYS131 4.4 14.0 1.0
CA B:CYS131 4.4 13.7 1.0
NE2 B:HIS257 4.5 26.4 1.0
ND2 B:ASN255 4.7 31.8 1.0
O B:G5A1001 4.7 20.8 1.0
CA B:CYS279 4.7 16.1 1.0
CB B:GLU176 4.8 10.8 1.0
CE1 B:HIS257 4.9 25.8 1.0
O B:HOH456 5.0 50.9 1.0

Reference:

M.Mocibob, N.Ivic, S.Bilokapic, T.Maier, M.Luic, N.Ban, I.Weygand-Durasevic. Homologs of Aminoacyl-Trna Synthetases Acylate Carrier Proteins and Provide A Link Between Ribosomal and Nonribosomal Peptide Synthesis Proc.Natl.Acad.Sci.Usa V. 107 14585 2010.
ISSN: ISSN 0027-8424
PubMed: 20663952
DOI: 10.1073/PNAS.1007470107
Page generated: Wed Dec 16 04:34:59 2020

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