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Zinc in PDB 4igm: 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd

Enzymatic activity of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd

All present enzymatic activity of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd:
4.1.1.45;

Protein crystallography data

The structure of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd, PDB code: 4igm was solved by F.Liu, A.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.00 / 2.39
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 89.112, 101.878, 233.455, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 28.9

Zinc Binding Sites:

The binding sites of Zinc atom in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd (pdb code 4igm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd, PDB code: 4igm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4igm

Go back to Zinc Binding Sites List in 4igm
Zinc binding site 1 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:21.5
occ:1.00
 NE2 A:HIS174 2.1 12.9 1.0
NE2 A:HIS6 2.2 10.7 1.0
OD1 A:ASP291 2.3 26.1 1.0
O A:HOH577 2.3 33.2 1.0
CE1 A:HIS8 2.4 11.8 1.0
CE1 A:HIS6 3.1 11.4 1.0
CE1 A:HIS174 3.1 12.1 1.0
CD2 A:HIS174 3.1 13.2 1.0
CD2 A:HIS6 3.2 11.7 1.0
ND1 A:HIS8 3.3 11.4 1.0
CG A:ASP291 3.3 23.5 1.0
NE2 A:HIS8 3.4 12.8 1.0
OD2 A:ASP291 4.1 28.0 1.0
ND1 A:HIS174 4.2 13.3 1.0
ND1 A:HIS6 4.2 10.6 1.0
CG A:HIS174 4.3 12.8 1.0
CB A:ASP291 4.3 19.4 1.0
O A:HOH576 4.3 33.1 1.0
CG A:HIS6 4.4 11.6 1.0
CG A:HIS8 4.4 11.5 1.0
CD2 A:HIS8 4.5 11.5 1.0
CE1 A:HIS224 4.7 22.1 1.0
CA A:ASP291 4.7 16.5 1.0
NE2 A:HIS224 4.8 21.1 1.0
CG A:PRO77 4.9 15.8 1.0

Zinc binding site 2 out of 6 in 4igm

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Zinc binding site 2 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn401

b:22.0
occ:1.00
 OD1 B:ASP291 2.0 25.1 1.0
NE2 B:HIS8 2.2 15.1 1.0
NE2 B:HIS174 2.2 10.7 1.0
NE2 B:HIS6 2.3 13.2 1.0
O B:HOH597 2.8 30.2 1.0
CD2 B:HIS8 3.0 13.9 1.0
CG B:ASP291 3.1 23.9 1.0
CE1 B:HIS174 3.1 9.4 1.0
CE1 B:HIS8 3.2 14.0 1.0
CD2 B:HIS174 3.2 9.9 1.0
CD2 B:HIS6 3.3 14.0 1.0
CE1 B:HIS6 3.3 13.7 1.0
OD2 B:ASP291 3.9 27.1 1.0
CB B:ASP291 4.1 20.1 1.0
CG B:HIS8 4.2 13.3 1.0
ND1 B:HIS8 4.2 13.8 1.0
ND1 B:HIS174 4.3 9.6 1.0
CG B:HIS174 4.4 9.6 1.0
ND1 B:HIS6 4.5 13.6 1.0
CG B:HIS6 4.5 14.1 1.0
O B:HOH598 4.5 29.2 1.0
CA B:ASP291 4.6 18.2 1.0
CE1 B:HIS224 4.6 22.9 1.0
CG B:PRO77 4.7 11.9 1.0
NE2 B:HIS224 5.0 21.7 1.0

Zinc binding site 3 out of 6 in 4igm

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Zinc binding site 3 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn401

b:23.6
occ:1.00
 NE2 C:HIS174 2.1 11.9 1.0
NE2 C:HIS6 2.1 14.3 1.0
OD1 C:ASP291 2.2 28.1 1.0
NE2 C:HIS8 2.3 15.7 1.0
O C:HOH579 2.4 32.6 1.0
CE1 C:HIS174 2.9 11.1 1.0
CD2 C:HIS8 3.0 15.2 1.0
CE1 C:HIS6 3.1 15.2 1.0
CG C:ASP291 3.1 25.8 1.0
CD2 C:HIS6 3.2 15.7 1.0
CD2 C:HIS174 3.2 12.0 1.0
CE1 C:HIS8 3.4 15.1 1.0
OD2 C:ASP291 3.7 27.4 1.0
CB C:ASP291 4.1 21.8 1.0
ND1 C:HIS174 4.1 11.9 1.0
ND1 C:HIS6 4.2 15.9 1.0
O C:HOH578 4.3 33.2 1.0
CG C:HIS174 4.3 11.9 1.0
CG C:HIS8 4.3 15.8 1.0
CG C:HIS6 4.3 15.5 1.0
ND1 C:HIS8 4.5 16.0 1.0
CA C:ASP291 4.5 22.7 1.0
CE1 C:HIS224 4.6 23.4 1.0
NE2 C:HIS224 4.8 23.1 1.0
CG C:PRO77 4.8 16.1 1.0

Zinc binding site 4 out of 6 in 4igm

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Zinc binding site 4 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn401

b:27.4
occ:1.00
 NE2 D:HIS6 2.1 13.0 1.0
NE2 D:HIS174 2.2 11.2 1.0
OD1 D:ASP291 2.2 26.8 1.0
CE1 D:HIS8 2.3 13.0 1.0
O D:HOH591 2.4 36.0 1.0
CE1 D:HIS6 3.0 13.8 1.0
CD2 D:HIS174 3.1 11.2 1.0
NE2 D:HIS8 3.1 13.5 1.0
CD2 D:HIS6 3.1 13.9 1.0
CE1 D:HIS174 3.2 10.3 1.0
CG D:ASP291 3.3 26.2 1.0
ND1 D:HIS8 3.3 13.1 1.0
O D:HOH592 3.7 29.8 1.0
OD2 D:ASP291 3.9 32.1 1.0
ND1 D:HIS6 4.2 15.0 1.0
CB D:ASP291 4.3 22.4 1.0
CG D:HIS6 4.3 14.4 1.0
CG D:HIS174 4.3 11.1 1.0
ND1 D:HIS174 4.3 11.1 1.0
CD2 D:HIS8 4.3 13.0 1.0
CG D:HIS8 4.4 13.5 1.0
CE1 D:HIS224 4.7 21.3 1.0
CA D:ASP291 4.7 20.7 1.0
CG D:PRO77 4.8 13.9 1.0

Zinc binding site 5 out of 6 in 4igm

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Zinc binding site 5 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn401

b:27.0
occ:1.00
 NE2 E:HIS174 2.2 16.7 1.0
NE2 E:HIS6 2.2 19.8 1.0
OD1 E:ASP291 2.4 34.4 1.0
NE2 E:HIS8 2.4 18.5 1.0
CE1 E:HIS174 3.0 15.4 1.0
CD2 E:HIS8 3.2 18.6 1.0
CE1 E:HIS6 3.2 21.1 1.0
CD2 E:HIS6 3.3 19.8 1.0
CG E:ASP291 3.3 31.0 1.0
CD2 E:HIS174 3.3 16.3 1.0
CE1 E:HIS8 3.4 19.2 1.0
OD2 E:ASP291 3.8 32.4 1.0
O E:HOH573 3.8 30.7 1.0
ND1 E:HIS174 4.2 17.5 1.0
CG E:HIS174 4.3 16.7 1.0
CB E:ASP291 4.3 27.5 1.0
ND1 E:HIS6 4.4 18.9 1.0
CG E:HIS8 4.4 18.7 1.0
CG E:HIS6 4.4 19.3 1.0
ND1 E:HIS8 4.5 20.8 1.0
CE1 E:HIS224 4.5 25.1 1.0
CA E:ASP291 4.6 24.0 1.0
CG E:PRO77 4.8 18.5 1.0

Zinc binding site 6 out of 6 in 4igm

Go back to Zinc Binding Sites List in 4igm
Zinc binding site 6 out of 6 in the 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn401

b:30.9
occ:1.00
 OD1 F:ASP291 2.0 30.5 1.0
NE2 F:HIS6 2.1 18.8 1.0
NE2 F:HIS174 2.2 16.4 1.0
NE2 F:HIS8 2.2 21.4 1.0
O F:HOH554 2.9 35.5 1.0
CE1 F:HIS174 3.0 14.6 1.0
CD2 F:HIS8 3.0 20.7 1.0
CG F:ASP291 3.1 29.8 1.0
CE1 F:HIS6 3.1 19.3 1.0
CD2 F:HIS6 3.1 19.9 1.0
CD2 F:HIS174 3.2 15.9 1.0
CE1 F:HIS8 3.2 22.5 1.0
OD2 F:ASP291 3.6 33.5 1.0
O F:HOH553 3.7 34.6 1.0
ND1 F:HIS174 4.1 15.6 1.0
ND1 F:HIS6 4.2 18.9 1.0
CG F:HIS8 4.2 20.9 1.0
CB F:ASP291 4.3 26.6 1.0
CG F:HIS174 4.3 16.0 1.0
CG F:HIS6 4.3 19.6 1.0
ND1 F:HIS8 4.3 21.7 1.0
CG F:PRO77 4.7 30.4 1.0
CA F:ASP291 4.7 27.2 1.0
CE1 F:PHE294 4.7 36.3 1.0
CD1 F:PHE294 4.8 35.8 1.0
NE2 F:HIS224 4.9 28.2 1.0
CE1 F:HIS224 5.0 27.1 1.0

Reference:

F.Liu, A.Liu. 2.39 Angstrom X-Ray Crystal Structure of Human Acmsd To Be Published.
Page generated: Sun Oct 27 00:44:20 2024

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