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Zinc in PDB 3mbg: Crystal Structure of Human Augmenter of Liver Regeneration (Alr)

Enzymatic activity of Crystal Structure of Human Augmenter of Liver Regeneration (Alr)

All present enzymatic activity of Crystal Structure of Human Augmenter of Liver Regeneration (Alr):
1.8.3.2;

Protein crystallography data

The structure of Crystal Structure of Human Augmenter of Liver Regeneration (Alr), PDB code: 3mbg was solved by M.Dong, S.Schaefer, V.N.Daithankar, C.Thorpe, B.J.Bahnson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.76 / 1.85
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.719, 65.145, 63.767, 90.00, 89.97, 90.00
R / Rfree (%) 18.9 / 23.1

Other elements in 3mbg:

The structure of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr) (pdb code 3mbg). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr), PDB code: 3mbg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3mbg

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Zinc binding site 1 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


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 Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:28.3
occ:1.00
 O A:ACT206 2.0 29.2 1.0
OD2 A:ASP159 2.1 23.8 1.0
CG A:ASP159 2.7 22.0 1.0
OD1 A:ASP159 2.8 22.0 1.0
C A:ACT206 3.1 32.0 1.0
OXT A:ACT206 3.3 35.0 1.0
CB A:ARG161 4.1 28.5 1.0
CB A:ASP159 4.2 23.6 1.0
CB A:ALA165 4.2 24.0 1.0
CH3 A:ACT206 4.4 31.8 1.0
CD A:ARG161 4.5 39.2 1.0
O A:HOH7 4.8 28.9 1.0
CG A:ARG161 4.9 33.4 1.0

Zinc binding site 2 out of 10 in 3mbg

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Zinc binding site 2 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


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 Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:28.8
occ:1.00
 OE2 A:GLU100 1.8 24.3 1.0
O A:ACT207 2.0 31.3 1.0
OD2 B:ASP159 2.0 22.8 1.0
O A:HOH439 2.1 22.7 1.0
CD A:GLU100 2.7 22.0 1.0
CG B:ASP159 2.8 23.6 1.0
OD1 B:ASP159 2.8 24.3 1.0
OE1 A:GLU100 2.9 22.1 1.0
C A:ACT207 3.0 33.2 1.0
OXT A:ACT207 3.1 36.2 1.0
O4' A:FAD300 3.7 27.3 1.0
O2 A:FAD300 3.9 27.1 1.0
O A:HOH15 4.1 26.4 1.0
CB B:ARG161 4.1 28.3 1.0
CG A:GLU100 4.2 24.1 1.0
CB B:ASP159 4.2 24.1 1.0
CB B:ALA165 4.2 24.4 1.0
CH3 A:ACT207 4.4 33.3 1.0
CD B:ARG161 4.4 39.0 1.0
O B:HOH229 4.6 29.1 1.0
NE A:ARG99 4.8 39.0 1.0
CG A:ARG99 4.8 27.7 1.0
C4' A:FAD300 4.8 26.6 1.0
CG B:ARG161 4.9 33.3 1.0
C2 A:FAD300 4.9 26.8 1.0
CD1 A:LEU181 5.0 25.7 1.0

Zinc binding site 3 out of 10 in 3mbg

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Zinc binding site 3 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn208

b:50.3
occ:1.00
 OE2 A:GLU176 1.9 44.4 1.0
NE2 A:HIS172 2.2 31.4 1.0
CE1 A:HIS172 2.3 32.1 1.0
CD A:GLU176 2.9 39.9 1.0
NH1 A:ARG179 3.2 46.3 1.0
CG A:GLU176 3.5 30.8 1.0
CD2 A:HIS172 3.5 32.1 1.0
ND1 A:HIS172 3.6 33.7 1.0
OE1 A:GLU176 4.0 43.0 1.0
O A:HOH213 4.1 45.2 1.0
CG A:HIS172 4.2 29.8 1.0
CZ A:ARG179 4.3 46.5 1.0
NH2 A:ARG179 4.6 47.1 1.0
O A:HOH244 4.8 43.5 1.0
CB A:GLU176 5.0 27.4 1.0

Zinc binding site 4 out of 10 in 3mbg

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Zinc binding site 4 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:27.5
occ:1.00
 O A:ACT600 1.9 26.9 1.0
OE2 A:GLU101 1.9 24.8 1.0
O A:ACT700 2.0 34.9 1.0
NE2 A:HIS105 2.0 22.4 1.0
C A:ACT700 2.8 36.0 1.0
OXT A:ACT700 2.8 35.5 1.0
C A:ACT600 2.8 27.1 1.0
CD2 A:HIS105 2.9 21.7 1.0
OXT A:ACT600 3.0 25.6 1.0
CD A:GLU101 3.0 24.4 1.0
CE1 A:HIS105 3.0 22.1 1.0
CG A:GLU101 3.4 23.7 1.0
CG A:HIS105 4.1 19.7 1.0
OE1 A:GLU101 4.1 26.5 1.0
ND1 A:HIS105 4.1 20.9 1.0
CH3 A:ACT700 4.2 36.3 1.0
CH3 A:ACT600 4.3 26.5 1.0
O A:HOH46 4.9 33.5 1.0
CB A:GLU101 4.9 20.2 1.0

Zinc binding site 5 out of 10 in 3mbg

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Zinc binding site 5 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:27.9
occ:1.00
 OD2 C:ASP159 2.0 24.1 1.0
O C:ACT800 2.1 31.1 1.0
CG C:ASP159 2.7 23.7 1.0
C C:ACT800 2.7 33.6 1.0
OD1 C:ASP159 2.8 23.5 1.0
CH3 C:ACT800 3.4 35.8 1.0
OXT C:ACT800 3.4 37.9 1.0
CB C:ALA165 4.2 23.9 1.0
CB C:ARG161 4.2 28.6 1.0
CB C:ASP159 4.2 23.7 1.0
CD C:ARG161 4.5 39.3 1.0
O C:HOH285 4.7 30.5 1.0
CG C:ARG161 4.9 32.5 1.0

Zinc binding site 6 out of 10 in 3mbg

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Zinc binding site 6 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:26.8
occ:1.00
 OE2 B:GLU101 1.9 24.2 1.0
O B:ACT700 1.9 34.0 1.0
NE2 B:HIS105 2.0 21.2 1.0
O C:ACT600 2.0 25.7 1.0
C B:ACT700 2.8 35.0 1.0
OXT B:ACT700 2.8 34.9 1.0
C C:ACT600 2.9 26.5 1.0
CD B:GLU101 2.9 25.7 1.0
CD2 B:HIS105 2.9 22.9 1.0
CE1 B:HIS105 3.0 21.2 1.0
CH3 C:ACT600 3.1 21.1 1.0
CG B:GLU101 3.4 24.0 1.0
O C:HOH313 4.0 29.3 1.0
OE1 B:GLU101 4.1 26.3 1.0
ND1 B:HIS105 4.1 21.2 1.0
CG B:HIS105 4.1 19.4 1.0
OXT C:ACT600 4.1 28.5 1.0
CH3 B:ACT700 4.2 35.4 1.0
CE1 C:HIS105 4.4 21.7 1.0
ND1 C:HIS105 4.5 22.6 1.0
O B:HOH211 4.8 32.3 1.0
O B:HOH283 4.9 44.4 1.0
CB B:GLU101 4.9 21.2 1.0

Zinc binding site 7 out of 10 in 3mbg

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Zinc binding site 7 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn206

b:47.4
occ:1.00
 O B:HOH468 2.1 40.4 1.0
O B:HOH469 2.2 36.9 1.0
ND1 B:HIS157 2.2 39.7 1.0
NE2 B:HIS134 2.2 35.2 1.0
O B:HOH425 2.7 48.4 1.0
CE1 B:HIS134 3.0 34.0 1.0
CE1 B:HIS157 3.1 41.4 1.0
CG B:HIS157 3.2 36.0 1.0
CD2 B:HIS134 3.2 33.9 1.0
CB B:HIS157 3.5 30.1 1.0
CD B:PRO158 3.8 26.0 1.0
ND1 B:HIS134 4.1 32.8 1.0
CG B:HIS134 4.2 30.7 1.0
NE2 B:HIS157 4.3 41.6 1.0
CD2 B:HIS157 4.3 39.6 1.0
CA B:HIS157 4.3 29.5 1.0
N B:PRO158 4.8 26.8 1.0
CG B:PRO158 4.9 26.3 1.0

Zinc binding site 8 out of 10 in 3mbg

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Zinc binding site 8 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:50.7
occ:1.00
 OE2 B:GLU176 2.0 42.4 0.5
NE2 B:HIS172 2.1 31.2 1.0
OE1 A:GLU147 2.4 36.9 1.0
OE2 A:GLU147 2.5 41.3 1.0
CE1 B:HIS172 2.5 32.7 1.0
CD A:GLU147 2.7 36.2 1.0
CD B:GLU176 2.9 39.5 0.5
OE2 B:GLU176 3.0 47.1 0.5
CG B:GLU176 3.4 31.4 0.5
CD2 B:HIS172 3.4 32.4 1.0
NH1 B:ARG179 3.4 46.8 1.0
CG B:GLU176 3.6 31.7 0.5
CD B:GLU176 3.7 40.3 0.5
ND1 B:HIS172 3.8 33.5 1.0
OE1 B:GLU176 3.9 43.0 0.5
O B:HOH208 3.9 44.7 1.0
CG A:GLU147 4.2 29.8 1.0
CG B:HIS172 4.2 29.8 1.0
CA A:GLU144 4.4 27.9 1.0
N A:GLU144 4.6 27.6 1.0
CZ B:ARG179 4.7 45.9 1.0
C A:GLU143 4.8 28.0 1.0
O A:GLU143 4.8 26.4 1.0
CB A:GLU147 4.8 28.5 1.0
CB A:GLU144 4.9 29.0 1.0
OE1 B:GLU176 4.9 43.1 0.5
CB B:GLU176 4.9 27.7 0.5

Zinc binding site 9 out of 10 in 3mbg

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Zinc binding site 9 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:27.2
occ:1.00
 O C:ACT700 1.8 32.7 1.0
OE2 C:GLU101 1.9 25.3 1.0
NE2 C:HIS105 2.0 23.0 1.0
O B:ACT600 2.0 25.9 1.0
C C:ACT700 2.7 33.5 1.0
OXT C:ACT700 2.9 33.2 1.0
C B:ACT600 2.9 26.6 1.0
CD2 C:HIS105 3.0 23.2 1.0
CD C:GLU101 3.0 26.8 1.0
CE1 C:HIS105 3.0 21.7 1.0
CH3 B:ACT600 3.0 22.2 1.0
CG C:GLU101 3.4 24.1 1.0
O B:HOH271 4.0 29.7 1.0
OXT B:ACT600 4.1 28.7 1.0
ND1 C:HIS105 4.1 22.6 1.0
CH3 C:ACT700 4.1 34.0 1.0
CG C:HIS105 4.1 19.9 1.0
OE1 C:GLU101 4.1 26.8 1.0
CE1 B:HIS105 4.4 21.2 1.0
ND1 B:HIS105 4.5 21.2 1.0
O C:HOH331 4.9 33.1 1.0
CB C:GLU101 4.9 21.2 1.0
O C:HOH387 4.9 45.6 1.0

Zinc binding site 10 out of 10 in 3mbg

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Zinc binding site 10 out of 10 in the Crystal Structure of Human Augmenter of Liver Regeneration (Alr)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Human Augmenter of Liver Regeneration (Alr) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn4

b:49.7
occ:1.00
 OE2 C:GLU176 2.1 41.9 0.5
NE2 C:HIS172 2.1 31.8 1.0
CE1 C:HIS172 2.4 32.8 1.0
OE2 C:GLU176 2.8 46.7 0.5
CD C:GLU176 2.8 38.8 0.5
CG C:GLU176 3.3 30.2 0.5
CD2 C:HIS172 3.5 32.6 1.0
CG C:GLU176 3.5 30.9 0.5
NH1 C:ARG179 3.5 47.4 1.0
CD C:GLU176 3.6 40.3 0.5
ND1 C:HIS172 3.7 34.8 1.0
OE1 C:GLU176 3.8 42.3 0.5
O C:HOH341 3.9 44.2 1.0
CG C:HIS172 4.2 30.3 1.0
CZ C:ARG179 4.7 46.6 1.0
OE1 C:GLU176 4.8 42.7 0.5
CB C:GLU176 4.9 27.3 0.5
CB C:GLU176 5.0 27.7 0.5

Reference:

V.N.Daithankar, S.A.Schaefer, M.Dong, B.J.Bahnson, C.Thorpe. Structure of the Human Sulfhydryl Oxidase Augmenter of Liver Regeneration and Characterization of A Human Mutation Causing An Autosomal Recessive Myopathy . Biochemistry V. 49 6737 2010.
ISSN: ISSN 0006-2960
PubMed: 20593814
DOI: 10.1021/BI100912M
Page generated: Sat Oct 26 09:22:05 2024

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