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Zinc in PDB 4m6r: Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme

Enzymatic activity of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme

All present enzymatic activity of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme:
4.2.1.109;

Protein crystallography data

The structure of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme, PDB code: 4m6r was solved by W.Kang, S.H.Hong, H.M.Lee, N.Y.Kim, Y.C.Lim, L.T.M.Le, B.Lim, H.C.Kim, T.Y.Kim, H.Ashida, A.Yokota, S.S.Hah, K.H.Chun, Y.K.Jung, J.K.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 107.035, 107.735, 192.099, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme (pdb code 4m6r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme, PDB code: 4m6r:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4m6r

Go back to Zinc Binding Sites List in 4m6r
Zinc binding site 1 out of 4 in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:20.2
occ:1.00
 O D:HOH446 2.1 21.7 1.0
NE2 A:HIS115 2.1 19.0 1.0
NE2 A:HIS117 2.1 21.9 1.0
NE2 A:HIS195 2.2 19.1 1.0
O A:HOH481 2.4 29.6 1.0
O A:HOH425 2.7 29.9 1.0
CD2 A:HIS115 3.1 17.4 1.0
CE1 A:HIS117 3.1 22.3 1.0
CE1 A:HIS115 3.1 19.2 1.0
CD2 A:HIS117 3.1 21.7 1.0
CD2 A:HIS195 3.2 16.5 1.0
CE1 A:HIS195 3.2 19.0 1.0
OE2 D:GLU139 4.1 22.9 1.0
ND1 A:HIS115 4.2 18.4 1.0
ND1 A:HIS117 4.2 22.8 1.0
CG A:HIS115 4.2 19.0 1.0
CG A:HIS117 4.3 20.0 1.0
CG D:GLU139 4.3 16.9 1.0
ND1 A:HIS195 4.3 16.4 1.0
CG A:HIS195 4.4 14.9 1.0
N A:GLY46 4.5 29.9 1.0
O D:HOH486 4.6 42.3 1.0
OH A:TYR198 4.6 30.1 1.0
CD D:GLU139 4.6 20.2 1.0
O A:HOH485 4.8 53.4 1.0
CA A:GLY46 5.0 30.6 1.0

Zinc binding site 2 out of 4 in 4m6r

Go back to Zinc Binding Sites List in 4m6r
Zinc binding site 2 out of 4 in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:17.2
occ:1.00
 NE2 B:HIS117 2.1 22.3 1.0
NE2 B:HIS115 2.1 18.3 1.0
NE2 B:HIS195 2.1 18.0 1.0
O B:HOH494 2.2 34.4 1.0
O A:HOH486 2.2 21.6 1.0
O B:HOH492 2.5 42.1 1.0
CE1 B:HIS117 3.0 23.1 1.0
CE1 B:HIS115 3.1 19.0 1.0
CD2 B:HIS115 3.1 18.5 1.0
CD2 B:HIS195 3.1 16.8 1.0
CD2 B:HIS117 3.1 21.9 1.0
CE1 B:HIS195 3.2 18.6 1.0
ND1 B:HIS117 4.1 22.7 1.0
O B:HOH551 4.2 47.6 1.0
ND1 B:HIS115 4.2 17.9 1.0
OE2 A:GLU139 4.2 23.4 1.0
CG B:HIS115 4.2 19.4 1.0
CG B:HIS117 4.2 19.0 1.0
ND1 B:HIS195 4.2 17.1 1.0
CG B:HIS195 4.3 15.2 1.0
CG A:GLU139 4.3 16.6 1.0
N B:GLY46 4.4 30.0 1.0
CD A:GLU139 4.7 19.7 1.0
OH B:TYR198 4.8 30.7 1.0
SG B:CYS97 4.9 45.3 1.0
CA B:GLY46 4.9 30.3 1.0

Zinc binding site 3 out of 4 in 4m6r

Go back to Zinc Binding Sites List in 4m6r
Zinc binding site 3 out of 4 in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:18.9
occ:1.00
 O B:HOH424 2.1 20.4 1.0
NE2 C:HIS115 2.2 18.9 1.0
NE2 C:HIS117 2.2 23.3 1.0
O C:HOH443 2.2 24.9 1.0
NE2 C:HIS195 2.2 19.5 1.0
O C:HOH448 2.4 36.4 1.0
CE1 C:HIS115 3.1 19.2 1.0
CE1 C:HIS117 3.1 22.8 1.0
CD2 C:HIS115 3.2 18.9 1.0
CD2 C:HIS117 3.2 22.4 1.0
CE1 C:HIS195 3.2 18.6 1.0
CD2 C:HIS195 3.2 17.1 1.0
OE2 B:GLU139 4.1 23.4 1.0
ND1 C:HIS117 4.2 22.3 1.0
ND1 C:HIS115 4.2 18.1 1.0
ND1 C:HIS195 4.3 15.9 1.0
CG C:HIS115 4.3 19.2 1.0
CG C:HIS117 4.3 19.4 1.0
CG C:HIS195 4.3 15.7 1.0
N C:GLY46 4.4 30.2 1.0
CG B:GLU139 4.4 17.6 1.0
OH C:TYR198 4.6 30.5 1.0
CD B:GLU139 4.6 20.3 1.0
CA C:GLY46 4.9 30.8 1.0
SG C:CYS97 5.0 47.5 1.0

Zinc binding site 4 out of 4 in 4m6r

Go back to Zinc Binding Sites List in 4m6r
Zinc binding site 4 out of 4 in the Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:19.4
occ:1.00
 NE2 D:HIS117 2.1 23.2 1.0
NE2 D:HIS115 2.1 17.8 1.0
NE2 D:HIS195 2.1 18.3 1.0
O C:HOH418 2.1 24.4 1.0
O D:HOH415 2.2 31.7 1.0
O D:HOH462 2.3 38.2 1.0
CE1 D:HIS117 3.1 23.8 1.0
CE1 D:HIS115 3.1 18.8 1.0
CD2 D:HIS115 3.1 18.1 1.0
CD2 D:HIS195 3.1 17.7 1.0
CD2 D:HIS117 3.1 22.5 1.0
CE1 D:HIS195 3.1 18.2 1.0
ND1 D:HIS117 4.2 22.7 1.0
ND1 D:HIS115 4.2 19.1 1.0
ND1 D:HIS195 4.2 17.1 1.0
CG D:HIS115 4.2 18.9 1.0
OE2 C:GLU139 4.3 23.0 1.0
CG D:HIS117 4.3 19.1 1.0
CG D:HIS195 4.3 16.0 1.0
CG C:GLU139 4.3 16.6 1.0
N D:GLY46 4.4 30.1 1.0
OH D:TYR198 4.6 29.7 1.0
CD C:GLU139 4.7 20.4 1.0

Reference:

W.Kang, S.H.Hong, H.M.Lee, N.Y.Kim, Y.C.Lim, L.T.M.Le, B.Lim, H.C.Kim, T.Y.Kim, H.Ashida, A.Yokota, S.S.Hah, K.H.Chun, Y.K.Jung, J.K.Yang. Structural and Biochemical Basis For the Inhibition of Cell Death By Apip, A Methionine Salvage Enzyme. Proc.Natl.Acad.Sci.Usa V. 111 581 2014.
ISSN: ISSN 0027-8424
PubMed: 24367089
DOI: 10.1073/PNAS.1308768111
Page generated: Wed Aug 20 20:16:23 2025

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