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Zinc in PDB 1jk3: Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution

Enzymatic activity of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution

All present enzymatic activity of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution, PDB code: 1jk3 was solved by R.Lang, A.Kocourek, M.Braun, H.Tschesche, R.Huber, W.Bode, K.Maskos, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.36 / 1.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 51.905, 60.263, 54.612, 90.00, 114.65, 90.00
R / Rfree (%) 16.7 / 19.6

Other elements in 1jk3:

The structure of Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution (pdb code 1jk3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution, PDB code: 1jk3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1jk3

Go back to Zinc Binding Sites List in 1jk3
Zinc binding site 1 out of 2 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


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 Mmp-12 (Macrophage Elastase) at True Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn400

b:11.0
occ:1.00
NE2 A:HIS228 2.1 10.3 1.0
NE2 A:HIS218 2.1 10.3 1.0
O2 A:BAT900 2.1 11.3 1.0
O1 A:BAT900 2.1 12.5 1.0
NE2 A:HIS222 2.1 10.4 1.0
C2 A:BAT900 2.8 10.5 1.0
N1 A:BAT900 2.8 10.0 1.0
CE1 A:HIS228 3.0 10.4 1.0
CD2 A:HIS218 3.0 9.7 1.0
CD2 A:HIS228 3.1 10.4 1.0
CE1 A:HIS218 3.1 11.4 1.0
CD2 A:HIS222 3.1 9.9 1.0
CE1 A:HIS222 3.1 11.1 1.0
O A:HOH1007 4.1 12.3 1.0
O A:HOH1066 4.2 24.2 1.0
ND1 A:HIS228 4.2 9.7 1.0
ND1 A:HIS218 4.2 10.6 1.0
CG A:HIS218 4.2 9.7 1.0
CG A:HIS228 4.2 10.4 1.0
C1 A:BAT900 4.2 11.2 1.0
ND1 A:HIS222 4.3 11.2 1.0
CG A:HIS222 4.3 9.6 1.0
S2 A:BAT900 4.4 18.6 0.5
C5 A:BAT900 4.7 14.9 0.5
C9 A:BAT900 4.7 11.1 1.0
C8 A:BAT900 4.7 10.9 1.0
O A:HOH1186 4.7 26.2 1.0
CE A:MET236 4.8 11.2 1.0
C6 A:BAT900 4.9 17.2 0.5
C3 A:BAT900 4.9 12.9 1.0
C4 A:BAT900 4.9 13.5 0.5
C4 A:BAT900 4.9 14.8 0.5
C7 A:BAT900 4.9 18.6 0.5

Zinc binding site 2 out of 2 in 1jk3

Go back to Zinc Binding Sites List in 1jk3
Zinc binding site 2 out of 2 in the Crystal Structure of Human Mmp-12 (Macrophage Elastase) at True Atomic Resolution


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 Mmp-12 (Macrophage Elastase) at True Atomic Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:17.4
occ:1.00
NE2 A:HIS183 1.8 8.8 0.5
OD1 A:ASP170 2.0 14.4 0.7
NE2 A:HIS168 2.0 15.0 1.0
ND1 A:HIS196 2.1 13.0 1.0
NE2 A:HIS183 2.2 9.5 0.5
CE1 A:HIS183 2.5 11.2 0.5
CD2 A:HIS168 2.8 15.1 1.0
CG A:ASP170 2.9 14.4 0.7
CD2 A:HIS183 3.0 12.0 0.5
CE1 A:HIS196 3.0 14.4 1.0
CE1 A:HIS183 3.0 9.8 0.5
CE1 A:HIS168 3.1 14.4 1.0
CG A:HIS196 3.1 12.3 1.0
OD2 A:ASP170 3.1 15.4 0.7
CD2 A:HIS183 3.3 8.9 0.5
CB A:HIS196 3.5 10.9 1.0
ND1 A:HIS183 3.7 13.4 0.5
CG A:HIS183 4.0 11.1 0.5
CG A:HIS168 4.0 15.7 1.0
ND1 A:HIS168 4.1 14.9 1.0
NE2 A:HIS196 4.1 13.1 1.0
ND1 A:HIS183 4.2 9.9 0.5
CD2 A:HIS196 4.2 11.8 1.0
CB A:ASP170 4.3 13.8 0.7
CG A:HIS183 4.3 9.6 0.5
CE1 A:PHE185 4.5 15.7 1.0
O A:HIS172 4.5 15.0 1.0
CZ A:PHE174 4.7 12.1 1.0
CB A:HIS172 4.8 15.3 1.0
CZ A:PHE185 4.8 17.6 1.0
CE2 A:PHE174 4.8 13.1 1.0
CA A:HIS196 5.0 10.0 1.0

Reference:

R.Lang, A.Kocourek, M.Braun, H.Tschesche, R.Huber, W.Bode, K.Maskos. Substrate Specificity Determinants of Human Macrophage Elastase (Mmp-12) Based on the 1.1 A Crystal Structure. J.Mol.Biol. V. 312 731 2001.
ISSN: ISSN 0022-2836
PubMed: 11575928
DOI: 10.1006/JMBI.2001.4954
Page generated: Wed Dec 16 02:53:55 2020

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