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Zinc in PDB 1jiz: Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12

Enzymatic activity of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12

All present enzymatic activity of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12, PDB code: 1jiz was solved by H.Nar, K.Werle, M.M.T.Bauer, H.Dollinger, B.Jung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.83 / 2.60
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 67.400, 87.200, 169.200, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1jiz:

The structure of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 (pdb code 1jiz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12, PDB code: 1jiz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 1jiz

Go back to Zinc Binding Sites List in 1jiz
Zinc binding site 1 out of 4 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn257

b:20.5
occ:1.00
O47 A:CGS998 2.1 31.2 1.0
NE2 A:HIS129 2.1 19.8 1.0
NE2 A:HIS123 2.2 20.7 1.0
NE2 A:HIS119 2.2 20.3 1.0
O48 A:CGS998 2.4 30.2 1.0
C34 A:CGS998 2.9 31.6 1.0
N35 A:CGS998 3.0 30.7 1.0
CD2 A:HIS123 3.1 20.7 1.0
CE1 A:HIS129 3.1 20.3 1.0
CD2 A:HIS119 3.1 19.7 1.0
CD2 A:HIS129 3.2 20.3 1.0
CE1 A:HIS123 3.2 20.7 1.0
CE1 A:HIS119 3.2 19.7 1.0
O A:HOH603 4.1 13.7 1.0
OE2 A:GLU120 4.2 20.7 1.0
ND1 A:HIS129 4.2 20.8 1.0
CG A:HIS119 4.3 20.0 1.0
CG A:HIS123 4.3 20.6 1.0
ND1 A:HIS119 4.3 19.9 1.0
CG A:HIS129 4.3 20.9 1.0
ND1 A:HIS123 4.3 20.7 1.0
CA A:CGS998 4.4 32.0 1.0
CC A:CGS998 4.8 32.8 1.0
N1 A:CGS998 4.9 33.0 1.0
CE A:MET137 4.9 24.4 1.0

Zinc binding site 2 out of 4 in 1jiz

Go back to Zinc Binding Sites List in 1jiz
Zinc binding site 2 out of 4 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn258

b:19.9
occ:1.00
OD1 A:ASP71 1.9 20.7 1.0
NE2 A:HIS69 1.9 17.3 1.0
ND1 A:HIS97 2.0 18.1 1.0
NE2 A:HIS84 2.1 20.6 1.0
CD2 A:HIS69 2.8 17.3 1.0
CG A:ASP71 2.9 21.1 1.0
CE1 A:HIS97 2.9 18.5 1.0
CE1 A:HIS84 2.9 20.2 1.0
CE1 A:HIS69 3.0 16.8 1.0
CG A:HIS97 3.1 18.8 1.0
CD2 A:HIS84 3.3 20.1 1.0
OD2 A:ASP71 3.3 21.6 1.0
CB A:HIS97 3.5 18.8 1.0
O A:HIS73 4.0 19.0 1.0
CG A:HIS69 4.0 17.8 1.0
NE2 A:HIS97 4.0 18.2 1.0
ND1 A:HIS69 4.1 16.9 1.0
ND1 A:HIS84 4.1 20.4 1.0
CD2 A:HIS97 4.1 18.1 1.0
CB A:ASP71 4.1 20.3 1.0
CG A:HIS84 4.3 19.9 1.0
CE1 A:PHE86 4.4 20.3 1.0
CZ A:PHE86 4.4 20.9 1.0
CB A:HIS73 4.5 18.2 1.0
CZ A:PHE75 4.6 16.1 1.0
CE1 A:PHE75 4.7 17.0 1.0
O A:HOH506 4.8 22.7 1.0
O A:HOH535 4.9 11.7 1.0
CA A:HIS97 5.0 18.7 1.0

Zinc binding site 3 out of 4 in 1jiz

Go back to Zinc Binding Sites List in 1jiz
Zinc binding site 3 out of 4 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn257

b:19.9
occ:1.00
O47 B:CGS999 2.1 29.2 1.0
NE2 B:HIS129 2.1 19.9 1.0
NE2 B:HIS123 2.2 20.3 1.0
NE2 B:HIS119 2.2 21.3 1.0
O48 B:CGS999 2.3 28.7 1.0
C34 B:CGS999 2.9 29.7 1.0
N35 B:CGS999 3.0 29.1 1.0
CD2 B:HIS119 3.1 21.5 1.0
CD2 B:HIS123 3.1 20.8 1.0
CE1 B:HIS129 3.1 19.5 1.0
CD2 B:HIS129 3.1 20.1 1.0
CE1 B:HIS123 3.2 20.8 1.0
CE1 B:HIS119 3.2 21.8 1.0
OE2 B:GLU120 4.2 22.7 1.0
ND1 B:HIS129 4.2 19.9 1.0
CG B:HIS119 4.3 21.3 1.0
CG B:HIS129 4.3 20.7 1.0
CG B:HIS123 4.3 20.5 1.0
ND1 B:HIS119 4.3 21.4 1.0
ND1 B:HIS123 4.3 21.1 1.0
CA B:CGS999 4.4 30.6 1.0
O B:HOH530 4.4 23.2 1.0
O B:HOH904 4.6 27.6 1.0
CC B:CGS999 4.8 32.2 1.0
N1 B:CGS999 4.8 32.1 1.0
CE B:MET137 4.9 24.6 1.0

Zinc binding site 4 out of 4 in 1jiz

Go back to Zinc Binding Sites List in 1jiz
Zinc binding site 4 out of 4 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn258

b:20.3
occ:1.00
OD1 B:ASP71 1.9 19.9 1.0
NE2 B:HIS69 2.0 16.5 1.0
ND1 B:HIS97 2.0 17.9 1.0
NE2 B:HIS84 2.1 19.0 1.0
CD2 B:HIS69 2.8 16.8 1.0
CE1 B:HIS84 2.9 19.5 1.0
CG B:ASP71 2.9 20.1 1.0
CE1 B:HIS97 3.0 17.9 1.0
CE1 B:HIS69 3.0 16.4 1.0
CG B:HIS97 3.1 17.6 1.0
CD2 B:HIS84 3.3 19.5 1.0
OD2 B:ASP71 3.3 20.3 1.0
CB B:HIS97 3.5 17.6 1.0
O B:HIS73 4.0 17.8 1.0
CG B:HIS69 4.0 17.5 1.0
ND1 B:HIS69 4.1 16.6 1.0
ND1 B:HIS84 4.1 19.3 1.0
NE2 B:HIS97 4.1 17.8 1.0
CD2 B:HIS97 4.2 17.4 1.0
CB B:ASP71 4.2 19.5 1.0
CG B:HIS84 4.3 18.9 1.0
CE1 B:PHE86 4.3 20.9 1.0
CZ B:PHE86 4.4 21.6 1.0
CB B:HIS73 4.4 17.8 1.0
CZ B:PHE75 4.6 16.4 1.0
CE1 B:PHE75 4.7 16.2 1.0
C B:HIS73 5.0 18.1 1.0
CA B:HIS97 5.0 18.2 1.0

Reference:

H.Nar, K.Werle, M.M.Bauer, H.Dollinger, B.Jung. Crystal Structure of Human Macrophage Elastase (Mmp-12) in Complex with A Hydroxamic Acid Inhibitor. J.Mol.Biol. V. 312 743 2001.
ISSN: ISSN 0022-2836
PubMed: 11575929
DOI: 10.1006/JMBI.2001.4953
Page generated: Wed Dec 16 02:53:54 2020

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