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Zinc in PDB 1rmz: Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution:
3.4.24.65;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution, PDB code: 1rmz was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, S.Mangani, B.Terni, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.34
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 69.194, 62.564, 37.262, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 1rmz:

The structure of Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution (pdb code 1rmz). 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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution, PDB code: 1rmz:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1rmz

Go back to Zinc Binding Sites List in 1rmz
Zinc binding site 1 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn264

b:14.4
occ:1.00
O5 A:NGH269 2.1 21.0 1.0
NE2 A:HIS218 2.1 13.1 1.0
NE2 A:HIS228 2.1 14.9 1.0
NE2 A:HIS222 2.1 13.5 1.0
O4 A:NGH269 2.2 14.5 1.0
N1 A:NGH269 2.9 15.5 1.0
C11 A:NGH269 2.9 21.7 1.0
CE1 A:HIS228 3.0 16.1 1.0
CD2 A:HIS218 3.0 13.4 1.0
CE1 A:HIS218 3.1 13.6 1.0
CE1 A:HIS222 3.1 13.3 1.0
CD2 A:HIS228 3.1 14.4 1.0
CD2 A:HIS222 3.1 12.6 1.0
O A:HOH270 4.0 15.1 1.0
ND1 A:HIS228 4.2 15.6 1.0
ND1 A:HIS218 4.2 14.1 1.0
ND1 A:HIS222 4.2 13.7 1.0
CG A:HIS218 4.2 12.2 1.0
CG A:HIS222 4.2 13.3 1.0
CG A:HIS228 4.2 14.5 1.0
OE1 A:GLU219 4.3 15.0 1.0
C10 A:NGH269 4.4 23.6 1.0
C5 A:NGH269 4.8 17.2 1.0
O A:HOH424 4.8 30.6 1.0
N A:NGH269 4.9 24.3 1.0
O A:HOH388 4.9 36.7 1.0
CE A:MET236 4.9 15.2 1.0
C4 A:NGH269 4.9 17.9 1.0
C6 A:NGH269 5.0 19.8 1.0
C9 A:NGH269 5.0 26.6 1.0
OE2 A:GLU219 5.0 15.0 1.0
CD A:GLU219 5.0 15.0 1.0
O A:HOH375 5.0 34.3 1.0

Zinc binding site 2 out of 2 in 1rmz

Go back to Zinc Binding Sites List in 1rmz
Zinc binding site 2 out of 2 in the Crystal Structure of the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A 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 the Catalytic Domain of Human MMP12 Complexed with the Inhibitor Nngh at 1.3 A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn265

b:15.2
occ:1.00
OD1 A:ASP170 1.8 12.3 0.7
NE2 A:HIS168 2.0 14.8 1.0
NE2 A:HIS183 2.1 14.9 1.0
ND1 A:HIS196 2.1 15.1 1.0
CG A:ASP170 2.8 15.7 0.7
CD2 A:HIS168 2.9 14.3 1.0
CE1 A:HIS196 2.9 16.8 1.0
CE1 A:HIS183 3.0 17.1 1.0
CE1 A:HIS168 3.1 15.8 1.0
CD2 A:HIS183 3.1 18.0 1.0
CG A:HIS196 3.2 14.2 1.0
OD2 A:ASP170 3.2 15.3 0.7
CB A:HIS196 3.5 14.0 1.0
NE2 A:HIS196 4.1 15.1 1.0
CG A:HIS168 4.1 15.3 1.0
ND1 A:HIS183 4.1 17.1 1.0
ND1 A:HIS168 4.1 15.0 1.0
CB A:ASP170 4.2 17.3 0.7
CG A:HIS183 4.2 15.6 1.0
CD2 A:HIS196 4.2 13.6 1.0
O A:HIS172 4.2 20.3 1.0
CE2 A:PHE185 4.3 19.1 1.0
CZ A:PHE185 4.6 18.7 1.0
CZ A:PHE174 4.6 16.3 1.0
CE1 A:PHE174 4.8 17.2 1.0
O A:HOH272 4.9 17.7 1.0
CB A:HIS172 4.9 23.2 1.0

Reference:

I.Bertini, V.Calderone, M.Cosenza, M.Fragai, Y.M.Lee, C.Luchinat, S.Mangani, B.Terni, P.Turano. Conformational Variability of Matrix Metalloproteinases: Beyond A Single 3D Structure. Proc.Natl.Acad.Sci.Usa V. 102 5334 2005.
ISSN: ISSN 0027-8424
PubMed: 15809432
DOI: 10.1073/PNAS.0407106102
Page generated: Mon Jan 25 16:12:43 2021

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