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Zinc in PDB 3amj: The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1

Protein crystallography data

The structure of The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1, PDB code: 3amj was solved by Y.Maruyama, A.Chuma, B.Mikami, W.Hashimoto, K.Murata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.76 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 67.457, 100.676, 253.770, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 30

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1 (pdb code 3amj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1, PDB code: 3amj:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3amj

Go back to Zinc Binding Sites List in 3amj
Zinc binding site 1 out of 2 in the The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:44.6
occ:1.00
NE2 C:HIS77 2.0 17.0 1.0
OE2 C:GLU157 2.0 28.3 1.0
NE2 C:HIS81 2.2 15.8 1.0
OE1 C:GLU157 2.5 28.0 1.0
CD C:GLU157 2.6 28.8 1.0
CE1 C:HIS77 2.9 17.0 1.0
CD2 C:HIS77 3.1 16.2 1.0
CD2 C:HIS81 3.1 15.8 1.0
CE1 C:HIS81 3.2 16.1 1.0
OE2 C:GLU80 4.0 21.0 1.0
ND1 C:HIS77 4.0 17.4 1.0
CG C:GLU157 4.1 29.7 1.0
CG C:HIS77 4.2 15.8 1.0
CG C:HIS81 4.3 15.7 1.0
ND1 C:HIS81 4.3 15.8 1.0
NH1 C:ARG161 4.8 48.3 1.0
CD C:GLU80 4.8 20.1 1.0

Zinc binding site 2 out of 2 in 3amj

Go back to Zinc Binding Sites List in 3amj
Zinc binding site 2 out of 2 in the The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of the Heterodimer of M16B Peptidase From Sphingomonas Sp. A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:20.0
occ:1.00
OE1 A:GLU157 2.1 15.0 1.0
NE2 A:HIS81 2.2 8.5 1.0
NE2 A:HIS77 2.4 12.7 1.0
OE2 A:GLU157 2.6 18.6 1.0
CD A:GLU157 2.7 17.3 1.0
CD2 A:HIS81 3.1 9.2 1.0
CE1 A:HIS81 3.1 7.9 1.0
CE1 A:HIS77 3.3 13.2 1.0
CD2 A:HIS77 3.4 12.3 1.0
OE2 A:GLU80 3.6 15.8 1.0
OH B:TYR310 4.1 32.4 1.0
CG A:GLU157 4.1 18.2 1.0
CE1 B:TYR310 4.2 32.7 1.0
ND1 A:HIS81 4.2 8.1 1.0
CG A:HIS81 4.3 9.1 1.0
ND1 A:HIS77 4.4 13.6 1.0
CD A:GLU80 4.4 15.1 1.0
NH1 A:ARG161 4.5 18.0 1.0
CG A:HIS77 4.5 12.7 1.0
CZ B:TYR310 4.6 32.4 1.0
OE1 A:GLU80 4.7 16.1 1.0
CB A:GLU157 4.9 19.4 1.0

Reference:

Y.Maruyama, A.Chuma, B.Mikami, W.Hashimoto, K.Murata. Heterosubunit Composition and Crystal Structures of A Novel Bacterial M16B Metallopeptidase J.Mol.Biol. V. 407 180 2011.
ISSN: ISSN 0022-2836
PubMed: 21262231
DOI: 10.1016/J.JMB.2011.01.038
Page generated: Sat Sep 26 05:30:20 2020
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