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Calcium 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:

Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12, PDB code: 1jiz:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1jiz

Go back to Calcium Binding Sites List in 1jiz
Calcium binding site 1 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca259

b:24.4
occ:1.00
 O A:GLY77 2.3 21.9 1.0
O A:GLY79 2.3 22.6 1.0
O A:ILE81 2.3 21.8 1.0
OD2 A:ASP99 2.3 22.1 1.0
OE2 A:GLU102 2.3 23.6 1.0
OD2 A:ASP76 2.4 21.3 1.0
CG A:ASP99 3.3 21.1 1.0
C A:GLY77 3.4 22.0 1.0
C A:ILE81 3.4 21.6 1.0
CG A:ASP76 3.5 21.6 1.0
C A:GLY79 3.5 21.9 1.0
CD A:GLU102 3.5 23.0 1.0
N A:ILE81 3.8 21.2 1.0
N A:GLY79 3.8 22.1 1.0
N A:GLY77 3.9 20.5 1.0
CB A:ASP99 4.0 20.9 1.0
CA A:ILE81 4.1 21.4 1.0
OD1 A:ASP76 4.1 22.2 1.0
C A:ASP76 4.1 19.9 1.0
C A:LYS78 4.2 22.4 1.0
N A:ASP76 4.2 18.9 1.0
C A:GLY80 4.2 21.8 1.0
OD1 A:ASP99 4.2 19.7 1.0
CA A:GLY79 4.3 21.8 1.0
CG A:GLU102 4.3 23.1 1.0
N A:LYS78 4.3 22.6 1.0
CA A:LYS78 4.3 22.6 1.0
CA A:GLY77 4.3 21.3 1.0
OE1 A:GLU102 4.4 23.0 1.0
CB A:ILE81 4.4 21.4 1.0
CA A:ASP76 4.5 19.7 1.0
O A:HOH619 4.5 26.0 1.0
N A:GLY80 4.5 22.0 1.0
N A:LEU82 4.5 20.7 1.0
CB A:ASP76 4.6 20.4 1.0
O A:ASP76 4.6 19.1 1.0
CA A:GLY80 4.6 21.9 1.0
O A:GLY80 4.7 22.0 1.0
O A:LYS78 4.8 22.0 1.0
CA A:LEU82 4.9 20.4 1.0

Calcium binding site 2 out of 6 in 1jiz

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Calcium binding site 2 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca260

b:54.6
occ:1.00
 O A:GLY93 2.4 20.1 1.0
O A:ASP59 2.4 22.9 1.0
O A:GLY91 2.5 19.1 1.0
O A:HOH857 2.5 32.2 1.0
OD1 A:ASP95 2.5 20.5 1.0
O A:HOH555 2.8 13.8 1.0
CG A:ASP95 3.4 20.1 1.0
C A:GLY93 3.5 19.4 1.0
C A:ASP59 3.5 22.8 1.0
C A:GLY91 3.6 19.8 1.0
C A:ILE92 3.7 18.7 1.0
O A:ILE92 3.8 18.8 1.0
OD2 A:ASP95 3.8 20.6 1.0
N A:GLY93 3.9 18.8 1.0
N A:ASP95 4.2 20.0 1.0
CA A:GLY93 4.2 19.1 1.0
CA A:ILE92 4.3 18.7 1.0
N A:ILE60 4.3 21.3 1.0
O A:ALA58 4.3 25.8 1.0
CA A:ILE60 4.3 19.4 1.0
O A:GLY89 4.4 20.1 1.0
N A:ILE92 4.4 19.5 1.0
N A:GLY94 4.4 19.4 1.0
N A:GLY91 4.5 20.5 1.0
CA A:ASP59 4.5 23.9 1.0
N A:LEU61 4.5 19.0 1.0
O A:HOH569 4.5 24.9 1.0
C A:GLY94 4.6 20.1 1.0
CB A:ASP95 4.6 20.0 1.0
CA A:GLY94 4.6 19.5 1.0
CA A:GLY91 4.6 19.9 1.0
CA A:ASP95 4.8 20.0 1.0
C A:ILE60 4.9 19.4 1.0
C A:SER90 4.9 21.0 1.0
O A:HOH720 4.9 33.6 1.0

Calcium binding site 3 out of 6 in 1jiz

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Calcium binding site 3 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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
A:Ca261

b:74.1
occ:1.00
 OD2 A:ASP25 2.3 30.0 1.0
O A:GLU100 2.3 21.5 1.0
OE1 A:GLU100 2.5 24.4 1.0
O A:HOH722 2.5 36.1 1.0
O A:GLU102 2.5 21.7 1.0
CG A:ASP25 3.2 28.5 1.0
OD1 A:ASP25 3.3 28.6 1.0
O A:HOH855 3.3 29.4 1.0
C A:GLU100 3.4 21.7 1.0
CD A:GLU100 3.5 24.2 1.0
C A:GLU102 3.8 21.9 1.0
CG A:GLU100 3.9 23.6 1.0
OG1 A:THR23 3.9 22.2 1.0
CA A:GLU100 4.0 22.0 1.0
CD1 A:TRP104 4.1 17.7 1.0
N A:GLU102 4.3 22.0 1.0
O A:HOH896 4.3 49.7 1.0
CA A:PHE103 4.3 22.4 1.0
N A:ASP101 4.4 21.4 1.0
C A:ASP101 4.5 21.8 1.0
OE2 A:GLU100 4.5 25.3 1.0
N A:PHE103 4.5 22.2 1.0
CB A:ASP25 4.6 27.6 1.0
CB A:GLU100 4.6 23.2 1.0
NE1 A:TRP104 4.6 16.9 1.0
CA A:ASP101 4.6 21.2 1.0
N A:TRP104 4.7 21.9 1.0
CA A:GLU102 4.8 21.9 1.0
NH1 A:ARG66 5.0 25.4 1.0

Calcium binding site 4 out of 6 in 1jiz

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Calcium binding site 4 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca259

b:22.9
occ:1.00
 O B:GLY77 2.1 21.3 1.0
O B:GLY79 2.2 22.3 1.0
OE2 B:GLU102 2.2 24.2 1.0
OD2 B:ASP76 2.4 22.2 1.0
OD2 B:ASP99 2.4 20.5 1.0
O B:ILE81 2.5 21.4 1.0
C B:GLY77 3.3 21.8 1.0
C B:GLY79 3.4 21.9 1.0
CD B:GLU102 3.4 23.6 1.0
CG B:ASP99 3.5 19.8 1.0
CG B:ASP76 3.5 22.0 1.0
C B:ILE81 3.5 21.5 1.0
N B:GLY79 3.6 22.3 1.0
N B:ILE81 3.8 21.6 1.0
N B:GLY77 3.9 20.9 1.0
O B:HOH570 4.0 16.9 1.0
C B:LYS78 4.0 22.4 1.0
OD1 B:ASP76 4.1 22.4 1.0
C B:ASP76 4.1 20.3 1.0
CB B:ASP99 4.1 19.5 1.0
CA B:ILE81 4.1 21.5 1.0
CA B:GLY79 4.2 21.9 1.0
C B:GLY80 4.2 21.8 1.0
CA B:LYS78 4.2 22.5 1.0
N B:LYS78 4.2 21.9 1.0
N B:ASP76 4.2 19.7 1.0
CG B:GLU102 4.2 23.1 1.0
CA B:GLY77 4.3 21.4 1.0
OE1 B:GLU102 4.3 24.2 1.0
OD1 B:ASP99 4.4 19.8 1.0
N B:GLY80 4.4 21.9 1.0
CA B:ASP76 4.5 20.2 1.0
CB B:ILE81 4.5 21.0 1.0
O B:ASP76 4.6 20.3 1.0
CB B:ASP76 4.6 21.2 1.0
CA B:GLY80 4.6 21.7 1.0
N B:LEU82 4.6 20.8 1.0
O B:GLY80 4.7 21.5 1.0
O B:LYS78 4.7 22.1 1.0
CA B:LEU82 4.9 20.2 1.0
O B:HOH561 5.0 13.0 1.0

Calcium binding site 5 out of 6 in 1jiz

Go back to Calcium Binding Sites List in 1jiz
Calcium binding site 5 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca260

b:55.1
occ:1.00
 O B:GLY93 2.3 19.6 1.0
O B:GLY91 2.4 18.5 1.0
O B:ASP59 2.5 22.1 1.0
O B:HOH863 2.6 29.0 1.0
OD1 B:ASP95 2.6 21.1 1.0
O B:HOH572 3.0 6.1 1.0
CG B:ASP95 3.4 21.4 1.0
C B:GLY93 3.4 19.5 1.0
C B:GLY91 3.6 18.9 1.0
C B:ASP59 3.6 22.3 1.0
C B:ILE92 3.7 18.3 1.0
OD2 B:ASP95 3.8 21.3 1.0
O B:HOH759 3.8 30.4 1.0
N B:GLY93 3.8 18.5 1.0
O B:ILE92 3.9 17.9 1.0
CA B:GLY93 4.2 19.0 1.0
N B:ASP95 4.2 19.9 1.0
CA B:ILE92 4.2 18.2 1.0
O B:HOH577 4.2 38.0 1.0
O B:GLY89 4.3 20.9 1.0
O B:ALA58 4.3 25.6 1.0
N B:ILE92 4.4 19.0 1.0
CA B:ILE60 4.4 19.2 1.0
N B:ILE60 4.4 21.2 1.0
N B:GLY91 4.4 19.7 1.0
N B:GLY94 4.4 19.8 1.0
CA B:ASP59 4.5 23.5 1.0
CB B:ASP95 4.6 20.7 1.0
CA B:GLY91 4.6 18.7 1.0
N B:LEU61 4.6 19.1 1.0
C B:GLY94 4.6 20.3 1.0
CA B:GLY94 4.6 20.0 1.0
CA B:ASP95 4.8 19.7 1.0
C B:SER90 4.8 20.5 1.0
C B:ILE60 4.9 19.4 1.0

Calcium binding site 6 out of 6 in 1jiz

Go back to Calcium Binding Sites List in 1jiz
Calcium binding site 6 out of 6 in the Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure Analysis of Human Macrophage Elastase Mmp- 12 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca261

b:70.9
occ:1.00
 OD2 B:ASP25 2.3 29.6 1.0
O B:GLU100 2.4 22.2 1.0
O B:GLU102 2.6 20.9 1.0
OE1 B:GLU100 2.6 25.8 1.0
O B:HOH851 2.6 38.2 1.0
CG B:ASP25 3.1 28.4 1.0
OD1 B:ASP25 3.1 28.3 1.0
C B:GLU100 3.5 21.6 1.0
O B:HOH723 3.6 26.0 1.0
CD B:GLU100 3.6 24.6 1.0
C B:GLU102 3.7 21.7 1.0
CG B:GLU100 4.0 23.1 1.0
OG1 B:THR23 4.0 20.1 1.0
CA B:GLU100 4.1 21.7 1.0
CD1 B:TRP104 4.2 17.8 1.0
CA B:PHE103 4.3 22.9 1.0
N B:GLU102 4.4 21.3 1.0
N B:ASP101 4.5 21.3 1.0
N B:PHE103 4.5 22.1 1.0
C B:ASP101 4.5 21.4 1.0
CB B:ASP25 4.5 27.9 1.0
CA B:ASP101 4.7 21.2 1.0
OE2 B:GLU100 4.7 25.7 1.0
NE1 B:TRP104 4.7 16.7 1.0
N B:TRP104 4.7 22.2 1.0
CB B:GLU100 4.7 22.5 1.0
CA B:GLU102 4.8 21.9 1.0
CD1 B:PHE103 4.9 25.0 1.0
O B:ASP101 5.0 21.3 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: Sat Dec 12 03:02:21 2020

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